Haplotypes associated with improved dicamba tolerance and glyphosate tolerance in transgenic soybean plants

Information

  • Patent Grant
  • 10604767
  • Patent Number
    10,604,767
  • Date Filed
    Thursday, May 23, 2013
    11 years ago
  • Date Issued
    Tuesday, March 31, 2020
    4 years ago
Abstract
Methods and compositions for the identification and selection of loci modulating phenotypic expression of transgenic dicamba and glyphosate resistance traits in plant breeding are disclosed. In addition, methods are provided for screening germplasm entries for the performance and expression of the improved dicamba and glyphosate tolerance conferred by the loci.
Description
INCORPORATION OF SEQUENCE LISTING

A sequence listing containing the file named “46_21_59246_A_PCT.txt” which is 33,292 bytes (measured in MS-Windows) and created on May 20, 2013, comprises 56 nucleotide sequences, is provided herewith via the USPTO's EFS system and is herein incorporated by reference in its entirety.


INCORPORATION OF TABLE 2

A listing of various soybean linkage group L (chromosome 19) markers is provided herewith in the Specification as Table 2.


BACKGROUND

International Patent Application Publication WO 2012/031097 describes genetic regions of soybean linkage group L that contain polymorphic loci that are associated with an undesirable “yellow flash” phenotype that is observed in the foliage of certain soybean varieties that comprise a transgene that confers resistance to glyphosate that are exposed to glyphosate.


SUMMARY

“Dicamba intolerance” is an undesirable phenotype observed in certain soybean varieties that comprise a transgene that can confer resistance to the broad-spectrum herbicide dicamba. After application of dicamba, it has been discovered that the leaves of certain soybean plant varieties comprising the transgene that confers resistance to dicamba can exhibit a “dicamba intolerance phenotype” comprising malformation (epinasty) of the main stem and petioles upon exposure to dicamba. The epinastic growth habit of such “dicamba intolerant” transgenic plants is manifest in pronounced bending/twisting of the main stem and petioles. In dicamba intolerant transgenic soybean plants exposed to dicamba, the upper nodes and petioles may die, but lower portion of the plant may remain vegetative and new growth can be limited. However, other soybean plant varieties containing the same transgene that confers resistance to dicamba do not exhibit the dicamba intolerance phenotype when co-exposed to the same dosage of dicamba. The dicamba intolerance phenotype can be observed within approximately 2 to 10 days after herbicide application in certain soybean varieties comprising the transgene that confers resistance to dicamba. The dicamba intolerance phenotype is undesirable as it can lead to reduced yield in certain transgenic soybean plant varieties exposed to dicamba.


Although the dicamba intolerance phenotype can be observed within approximately 2 to 10 days after dicamba application in certain soybean varieties comprising the transgene that confers dicamba resistance, distinct soybean varieties that comprise the same dicamba resistance transgene integrated at the same chromosomal locus (i.e. the same transgenic event) can show various degrees of dicamba intolerance upon exposure to high doses of dicamba. Some varieties comprising the dicamba resistance transgene insertion are highly tolerant to high dosages of dicamba, showing no dicamba intolerance phenotype (i.e. a “dicamba tolerance phenotype”), while other varieties comprising the same dicamba resistance transgene insertion are highly susceptible to high dosages of dicamba, showing a severe dicamba intolerance phenotype. Provided herein are soybean plants comprising an introgressed genomic region associated with a dicamba tolerance phenotype. Also provided herein are markers that reside outside of a genomic region associated with a dicamba tolerance phenotype and that facilitate breeding activities that include, but are not limited to, introgression of this genomic region. Markers and specific alleles thereof that are associated with a dicamba tolerance phenotype are also provided. Methods of obtaining a soybean plant that exhibits a dicamba tolerance phenotype and methods of obtaining a soybean plant comprising in its genome at least one dicamba tolerance locus are also provided. Methods that provide for the introgression of a genomic region associated with a dicamba tolerance phenotype into soybean germplasm that has a genomic region associated with a dicamba intolerance phenotype are also provided. Identification of molecular markers associated with loci that confer the dicamba tolerance phenotype has significant economic value. By using markers associated with the dicamba tolerance trait, breeders can select soybean varieties with the favorable alleles (i.e. alleles that are not associated with the dicamba intolerance trait) for use in trait integration. They can also use the markers to help them eliminate unfavorable alleles (i.e. alleles that are associated with the dicamba intolerance trait) in soybeans. In certain embodiments, commercially desirable transgenic soybean lines that carry a genomic region that is associated with a “dicamba tolerance” phenotype and tolerate high dosages of dicamba are thus provided.


It has also been surprisingly observed that soybean plants comprising the dicamba tolerance loci, a transgene conferring resistance to dicamba, and a transgene conferring resistance to glyphosate also exhibit improved reproductive tolerance to glyphosate application relative to plants with the same two transgenes that lack the dicamba tolerance loci. Although the glyphosate reproductive intolerance phenotype can be observed after late stage (i.e. V6/R1) glyphosate application in certain soybean varieties comprising the transgenes that confer dicamba and glyphosate resistance, distinct soybean varieties that comprise the same dicamba and glyphosate resistance transgene integrated at the same chromosomal loci (i.e. the same transgenic events) can show various degrees of glyphosate reproductive intolerance (i.e. varying degrees of sterility) upon such exposure to glyphosate. Some varieties comprising the dicamba and glyphosate resistance transgene insertions are highly tolerant to late stage glyphosate application, showing no sterility phenotype (i.e. a “glyphosate reproductive intolerance phenotype”), while other varieties comprising the same dicamba and glyphosate resistance transgene insertions are highly susceptible to late stage glyphosate application, showing varying levels of sterility. Provided herein are soybean plants comprising an introgressed genomic region associated with a dicamba tolerance phenotype that also provide for reproductive tolerance to glyphosate. Also provided herein are markers that reside outside of a genomic region associated with a dicamba tolerance/reproductive tolerance to glyphosate phenotype and that facilitate breeding activities that include, but are not limited to, introgression of this genomic region. Markers and specific alleles thereof that are associated with a dicamba tolerance/reproductive tolerance to glyphosate are also provided. Methods of obtaining a soybean plant that exhibits reproductive tolerance to glyphosate and methods of obtaining a soybean plant comprising in its genome at least one dicamba tolerance/reproductive tolerance to glyphosate locus are also provided. Methods that provide for the introgression of a genomic region associated with reproductive tolerance to glyphosate into soybean germplasm that has a genomic region associated with a reproductive tolerance to glyphosate are also provided. Identification of molecular markers associated with loci that confer reproductive tolerance to glyphosate has significant economic value. By using markers associated with the reproductive tolerance to glyphosate trait, breeders can select soybean varieties with the favorable alleles (i.e. alleles that are not associated with the glyphosate reproductive intolerance trait) for use in trait integration. They can also use the markers to help them eliminate unfavorable alleles (i.e. alleles that are associated with the glyphosate reproductive intolerance trait) in soybeans. In certain embodiments, commercially desirable transgenic soybean lines that carry a genomic region that is associated with a “glyphosate reproductive tolerance” phenotype and tolerate late stage (i.e. V6/R1) application of glyphosate are thus provided.


Methods of identifying a soybean plant that comprises a genotype associated with a dicamba tolerance phenotype and/or a glyphosate reproductive tolerance phenotype are thus provided.


In certain embodiments, the plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one dicamba tolerance locus with a parent plant comprising at least one dicamba intolerance locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one dicamba tolerance locus. In certain embodiments, the population contains plants that comprise a transgene that confers resistance to dicamba. In certain embodiments, the aforementioned methods can further comprise the step of assaying for the presence of at least one additional marker, where the additional marker is either linked or unlinked to the linkage group L genomic region. In certain embodiments of the aforementioned methods, the plurality of soybean plants, the soybean plant, and/or progeny thereof are exposed to a dosage of dicamba sufficient to cause dicamba intolerance in a susceptible variety. In certain embodiments of the aforementioned methods, a plant that exhibits a dicamba tolerance phenotype is selected.


Also provided herewith are methods for producing a soybean plant comprising in its genome at least one introgressed dicamba tolerance locus. Also provided herewith are soybean plants comprising an introgressed dicamba tolerance locus made by the aforementioned methods. In certain embodiments, a soybean plant comprising an introgressed dicamba tolerance locus and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a dicamba tolerant soybean variety and that are linked to the introgressed dicamba tolerance locus, where the plant is produced by the aforementioned methods are provided.


Also provided are soybean plants comprising an introgressed dicamba tolerance locus and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a dicamba tolerant soybean variety and that are linked to the introgressed dicamba tolerance locus.


Methods of identifying a soybean plant that comprises a genotype associated with dicamba tolerance and/or reproductive tolerance to glyphosate are thus provided. In certain embodiments, the methods can comprise detecting in a soybean plant an allele in at least one genetic locus associated with dicamba tolerance and/or reproductive tolerance to glyphosate, where the genetic locus is in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12), and denoting that the plant comprises a genotype associated with dicamba tolerance. In certain embodiments, the methods can further comprise the step of selecting the denoted plant from a population of plants. In certain embodiments, the plant comprises a transgene that confers resistance to dicamba and/or a transgene that confers resistance to glyphosate. In certain embodiments, the soybean plant or progeny thereof is exposed to a dosage of dicamba sufficient to cause a deleterious effect in a susceptible variety comprising the transgene and/or is exposed to a dosage of glyphosate sufficient to cause sterility in a susceptible variety comprising the transgene(s). In certain embodiments of any of the aforementioned methods, a plant that exhibits dicamba tolerance and/or reproductive tolerance to glyphosate is selected. In certain embodiments of any of the aforementioned methods, a genotype associated with a dicamba tolerance comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8) is provided. In certain embodiments of any of the aforementioned methods, the genotype associated with dicamba tolerance comprises at least one polymorphic allele of at least one marker in the linkage group L region selected from the group consisting of a TT allele M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52).


Methods for obtaining a soybean plant comprising in its genome at least one dicamba tolerance locus are also provided. In certain embodiments, these methods can compromise the steps of: (a) genotyping a plurality of soybean plants with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12); and, (b) selecting a soybean plant comprising in its genome at least one genetic locus comprising a genotype associated with dicamba tolerance. In certain embodiments of these methods, the genotype associated with dicamba tolerance comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8). In certain embodiments of any of these aforementioned methods, the genotype associated with dicamba tolerance comprises at least one polymorphic allele of at least one marker in the first linkage group L region, the first sub-region, the second sub-region, or the third sub-region, where the marker is selected from the group consisting of a TT allele M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments of these methods, the plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one dicamba tolerance locus with a parent plant comprising at least one dicamba sensitivity locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one dicamba tolerance locus. In certain embodiments of these methods, the population contains plants that comprise at least one transgene that confers resistance to dicamba and/or a transgene that confers resistance to glyphosate. In certain embodiments of any of the aforementioned methods, the methods can further comprise the step of assaying for the presence of at least one additional marker, where the additional marker is either linked or unlinked to the linkage group L genomic region. In certain embodiments of any of the aforementioned methods, the plurality of soybean plants, the soybean plant, and/or progeny thereof are exposed to a dosage of dicamba sufficient to cause a deleterious effect in a susceptible variety comprising the transgene and/or is exposed to a dosage of glyphosate sufficient to cause sterility in a susceptible variety comprising the transgene. In certain embodiments of any of the aforementioned methods, a plant that exhibits dicamba tolerance and/or reproductive tolerance to glyphosate is selected.


Methods for producing a soybean plant comprising in its genome at least one introgressed dicamba tolerance locus are also provided. In certain embodiments, these methods comprise the steps of: (a) crossing a first soybean plant with a dicamba tolerance locus with a second soybean plant comprising: a dicamba sensitivity locus in a first linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8) and at least one linked polymorphic locus not present in the first soybean plant to obtain a population segregating for the dicamba tolerance loci and the linked polymorphic locus; (b) detecting at least two polymorphic nucleic acids in at least one soybean plant from the population, where at least one of the polymorphic nucleic acids is located in the first linkage group L region and/or the second linkage group L region and where at least one of the polymorphic amino acids is a linked polymorphic locus not present in the first soybean plant; and (c) selecting a soybean plant comprising a genotype associated with dicamba tolerance and at least one linked marker found in the second soybean plant comprising a dicamba sensitivity locus but not in the first soybean plant, thereby obtaining a soybean plant comprising in its genome at least one introgressed dicamba tolerance locus. In certain embodiments of these methods, at least one of the first or the second soybean plants comprises a transgene that confers resistance to dicamba and/or a transgene that confers resistance to glyphosate. In certain embodiments of these methods, the population, the selected soybean plant, and/or progeny of selected soybean plant is exposed to a dosage of dicamba sufficient to cause a deleterious effect in a susceptible variety comprising the transgene and/or is exposed to a dosage of glyphosate sufficient to cause sterility in a susceptible variety comprising the transgene. In certain embodiments of these methods, the polymorphic nucleic acid detected in step (b) is detected with at least one marker selected from the group consisting of M0205350 (SEQ ID NO: 10), M0101742 (SEQ ID NO: 5), M0102027 (SEQ ID NO: 11), and NGMAX008197032 (SEQ ID NO:52). In certain embodiments of these methods, the polymorphic nucleic acid detected in step (b) comprises a TT allele of M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments of these methods, the polymorphic nucleic acid detected in step (b) is detected with marker M0205350 (SEQ ID NO: 10) or M0102027 (SEQ ID NO: 11). In certain embodiments of these methods, the polymorphic nucleic acids are detected with marker M0101742 (SEQ ID NO: 5). In certain embodiments of these methods, the polymorphic nucleic acids are detected with marker NGMAX008197032 (SEQ ID NO:52). In certain embodiments of any of the aforementioned methods, the linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both. In certain embodiments of these methods, the linked polymorphic locus is detected with a marker that is located within about 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of the dicamba tolerance locus. In certain embodiments of these methods, the linked polymorphic locus is detected with at least one marker selected from the group consisting of asmbl_11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO: 2), BI967232 (SEQ ID NO: 3), M0205537 (SEQ ID NO: 15), M0202715 (SEQ ID NO: 16), M0206286 (SEQ ID NO: 17), M0206054 (SEQ ID NO: 18), and M0205375 (SEQ ID NO: 19).


Transgenic soybean plants comprising introgressed linkage group L regions comprising at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8), where the polymorphic alleles are associated with dicamba tolerance and/or reproductive tolerance to glyphosate, and where the plant comprises a transgene that confers resistance to dicamba are also provided. In certain embodiments, the polymorphic alleles comprise a TT allele of M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments, the transgenic plant exhibits dicamba tolerance. In certain embodiments, the transgenic plant further comprises a transgene that confers resistance to glyphosate and exhibits reproductive tolerance to glyphosate. In certain embodiments of any one of the aforementioned methods, the plant further comprises at least one of a 2,4-D, glufosinate, bromoxynil, acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase), hydroxyphenyl pyruvate dioxygenase (HPPD), or sulfonylurea herbicide resistance transgenes and/or at least one transgene selected from the group of transgenes conferring insect resistance, nematode resistance, fungal resistance, an improvement in seed oil quantity, an improvement in seed oil quality, abiotic stress resistance, and intrinsic yield increases. In certain embodiments, the insect resistance conferring transgene is a transgene that expresses an insecticidal Bacillus thuringiensis protein.


Also provided herein are soybean plants comprising a dicamba tolerance locus, a transgene conferring resistance to glyphosate, a transgene conferring resistance to dicamba, where the plants exhibit both improved dicamba tolerance and improved reproductive tolerance to glyphosate relative to soybean plants comprising the same two transgenes but lacking the dicamba tolerance locus. Such improved reproductive tolerance to glyphosate is reflected in reduced sterility when the plants are exposed to glyphosate.


In certain embodiments, the dicamba tolerance locus provided herein can provide for improved performance of additional combinations of transgenic traits (i.e. “stacked transgenic traits”) in soybean plants. In such embodiments, the dicamba tolerance locus provided herein can be alternatively referred to and considered a “stacked transgenic trait improvement” locus. Allele(s) of the dicamba tolerance locus or “stacked transgenic trait improvement” locus that do not confer such dicamba tolerance or such stacked transgenic trait improvements are referred to herein as dicamba sensitivity or “stacked transgenic trait sensitivity” loci. Transgenic plants comprising the stacked transgenic trait improvement locus provided herein exhibit improved performance of both transgenes present in the transgenic plant relative to plants comprising the same two transgenes that lack the stacked transgenic trait improvement locus. Such improved performance can manifest in any of enhanced transgenic trait performance, increased transgene efficacy, and/or increased transgene expression. Transgenic plants comprising the stacked trait improvement locus and two transgenes are thus provided herein. Thus, in certain embodiments the two independent and distinct transgenes that exhibit improved performance in the presence of the stacked transgenic trait improvement locus both contribute to the same trait. In certain embodiments, this same trait is selected from the group consisting of resistance to a single herbicide, resistance to an insect, resistance to a nematode, resistance to a fungal disease, resistance to an abiotic stress, an improvement in seed oil quantity, an improvement in seed oil quality, and intrinsic yield increases. In certain embodiments, the two transgenes can contribute to the same herbicide resistance trait where the herbicide resistance is selected from the group consisting of glyphosate, dicamba, 2,4-D, glufosinate, bromoxynil, synthetic auxins, and inhibitors of acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase) and hydroxyphenyl pyruvate dioxygenase (HPPD) resistance. In certain embodiments, the two transgenes can contribute to the same insect, fungal, or nematode resistance trait where the resistance to the same insect, fungal, or nematode pest is by a different mode of action to provide for improved pest resistance management. In other embodiments, the two transgenes can be two independent and distinct transgenes that encode different genes but contribute to a different trait. In certain embodiments, this different trait is independently selected from the group consisting of resistance to one or more herbicide(s), resistance to one or more insect(s), resistance to one or more nematode(s), resistance to one or more fungal disease(s), resistance to one or more abiotic stress(es), one or more improvement(s) in seed oil quantity or quantities, one or more improvement(s) in seed oil quality or qualities, intrinsic yield increases, and combinations thereof. In certain embodiments the stacked trait improvement locus is an herbicide tolerance locus that provides for improved tolerance to at least two distinct herbicides in plants comprising at least two transgenes that respectively confer resistance to those two herbicides. In certain embodiments, the herbicide tolerance locus provides for improved tolerance to at least two herbicides selected from the group consisting of glyphosate, dicamba, 2,4-D, glufosinate, bromoxynil, synthetic auxins, and inhibitors of acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase) and hydroxyphenyl pyruvate dioxygenase (HPPD) resistance in plants comprising at least two transgenes that confer resistance to those two herbicides. In certain embodiments, the herbicide tolerance locus confers improved tolerance to dicamba, improved reproductive tolerance to glyphosate, and improved tolerance to a synthetic auxin that includes, but is not limited to 2,4-D, in a plant comprising transgenes that confer resistance to dicamba, glyphosate, and the synthetic auxin that includes, but is not limited to 2,4-D. In certain embodiments, the two transgenes can confer a distinct herbicide resistance trait where the herbicide resistance is selected from the group consisting of glyphosate, dicamba, 2,4-D, glufosinate, bromoxynil, synthetic auxins other than 2,4-D, acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase) and hydroxyphenyl pyruvate dioxygenase (HPPD) resistance. Provided herein are soybean plants comprising any combination of a stacked trait improvement locus and at least two transgenes conferring herbicide tolerance selected from the group consisting of glyphosate, dicamba, 2,4-D, glufosinate, bromoxynil, synthetic auxins, and inhibitors of acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase) and hydroxyphenyl pyruvate dioxygenase (HPPD). In certain embodiments, soybean plants comprising an introgressed stacked trait improvement locus, at least one transgene selected from the group consisting of glyphosate, dicamba, 2,4-D, glufosinate, bromoxynil, synthetic auxins other than 2,4-D, acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase), hydroxyphenyl pyruvate dioxygenase (HPPD), and sulfonylurea herbicide resistance transgenes, and at least one transgene selected from the group of transgenes conferring insect resistance, nematode resistance, fungal resistance, an improvement in seed oil quantity, an improvement in seed oil quality, abiotic stress resistance, and intrinsic yield increases are provided. In still other embodiments, soybean plants comprising an introgressed stacked trait improvement locus, at least one transgene selected from the group consisting of glyphosate, dicamba, 2,4-D, and at least one transgene conferring resistance to an insect are provided. In still other embodiments, soybean plants comprising an introgressed stacked trait improvement locus, at least one transgene selected from the group consisting of glyphosate, dicamba, glufosinate, and 2,4-D resistance conferring transgenes, and at least one transgene conferring resistance to an insect that encodes a Bacillus thuringiensis toxin are provided. In certain embodiments, soybean plants comprising an introgressed stacked trait improvement locus, a glyphosate and a dicamba resistance conferring transgene, and a cry1Ac insect resistance transgene are provided. In still other embodiments, soybean plants comprising at least one herbicide resistance transgene selected from the group consisting of a dicamba resistance conferring transgene. a glyphosate resistance conferring transgene, a 2,4-D resistance conferring transgene, and a glufosinate resistance conferring transgene and/or at least one transgene encoding a product that confers insect resistance selected from the group consisting of a dsRNA that inhibits a target gene of an insect pest, a patatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Bacillus laterosporous insecticidal protein, a Bacillus sphaericus insecticidal protein, and a lignin are provided.


Methods of identifying a soybean plant that comprises a genotype associated with stacked transgenic trait improvement are thus provided. In certain embodiments, the methods can comprise detecting in a soybean plant an allele in at least one genetic locus associated with stacked transgenic trait improvement, where the genetic locus is in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12), and denoting that the plant comprises a genotype associated with stacked transgenic trait improvement. In certain embodiments, the methods can further comprise the step of selecting the denoted plant from a population of plants. In certain embodiments, the plant comprises at least two transgenes that contribute to the same trait. In certain embodiments, this same trait is selected from the group consisting of resistance to a single herbicide, resistance to an insect, resistance to a nematode, resistance to a fungal disease, resistance to an abiotic stress, an improvement in seed oil quantity, an improvement in seed oil quality, and intrinsic yield increases. In certain embodiments, the plant comprises at least two transgenes that contribute to different traits. In certain embodiments, this different trait is independently selected from the group consisting of resistance to one or more herbicide(s), resistance to one or more insect(s), resistance to one or more nematode(s), resistance to one or more fungal disease(s), resistance to one or more abiotic stress(es), one or more improvement(s) in seed oil quantity or quantities, one or more improvement(s) in seed oil quality or qualities, intrinsic yield increases, and combinations thereof. In certain embodiments, the soybean plant or progeny thereof is exposed to a dosage of an herbicide sufficient to cause a deleterious effect in a susceptible variety comprising the transgene conferring resistance to that herbicide but lacking the stacked transgenic trait improvement locus. In certain embodiments of any of the aforementioned methods, a plant that exhibits stacked transgenic trait improvement is selected. In certain embodiments of any of the aforementioned methods, a genotype associated with stacked transgenic trait improvement comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8) is provided. In certain embodiments of any of the aforementioned methods, the genotype associated with stacked transgenic trait improvement comprises at least one polymorphic allele of at least one marker in the linkage group L region selected from the group consisting of a TT allele M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52).


Methods for obtaining a soybean plant comprising in its genome at least one stacked transgenic trait improvement locus are also provided. In certain embodiments, these methods can compromise the steps of: (a) genotyping a plurality of soybean plants with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12); and, (b) selecting a soybean plant comprising in its genome at least one genetic locus comprising a genotype associated with stacked transgenic trait improvement. In certain embodiments, the plant comprises at least two transgenes that contribute to the same trait. In certain embodiments, this same trait is selected from the group consisting of resistance to a single herbicide, resistance to an insect, resistance to a nematode, resistance to a fungal disease, resistance to an abiotic stress, an improvement in seed oil quantity, an improvement in seed oil quality, and intrinsic yield increases. In certain embodiments, the plant comprises at least two transgenes that contribute to different traits. In certain embodiments, this different trait is independently selected from the group consisting of resistance to one or more herbicide(s), resistance to one or more insect(s), resistance to one or more nematode(s), resistance to one or more fungal disease(s), resistance to one or more abiotic stress(es), one or more improvement(s) in seed oil quantity or quantities, one or more improvement(s) in seed oil quality or qualities, intrinsic yield increases, and combinations thereof. In certain embodiments of these methods, the genotype associated with stacked transgenic trait improvement comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8). In certain embodiments of any of these aforementioned methods, the genotype associated with stacked transgenic trait improvement comprises at least one polymorphic allele of at least one marker in the first linkage group L region, the first sub-region, the second sub-region, the third sub-region, where the marker is selected from the group consisting of a TT allele M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments of these methods, the plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one stacked transgenic trait improvement locus with a parent plant lacking a stacked transgenic trait improvement locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one stacked transgenic trait improvement locus. In certain embodiments of any of the aforementioned methods, the methods can further comprise the step of assaying for the presence of at least one additional marker, where the additional marker is either linked or unlinked to the linkage group L genomic region. In certain embodiments of any of the aforementioned methods, the plurality of soybean plants, the soybean plant, and/or progeny thereof are exposed to a dosage of an herbicide sufficient to cause a deleterious effect in a susceptible variety comprising the transgene conferring resistance to that herbicide but lacking the stacked transgenic trait improvement locus. In certain embodiments of any of the aforementioned methods, a plant that exhibits stacked transgenic trait improvement is selected.


Methods for producing a soybean plant comprising in its genome at least one introgressed stacked transgenic trait improvement locus are also provided. In certain embodiments, these methods comprise the steps of (a) crossing a first soybean plant with a stacked transgenic trait improvement locus with a second soybean plant lacking a stacked transgenic trait improvement locus in a first linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8) and at least one linked polymorphic locus not present in the first soybean plant to obtain a population segregating for the stacked transgenic trait improvement loci and the linked polymorphic locus; (b) detecting at least two polymorphic nucleic acids in at least one soybean plant from the population, where at least one of the polymorphic nucleic acids is located in the first linkage group L region and/or the second linkage group L region and where at least one of the polymorphic amino acids is a linked polymorphic locus not present in the first soybean plant; and (c) selecting a soybean plant comprising a genotype associated with stacked transgenic trait improvement and at least one linked marker found in the second soybean plant lacking the stacked transgenic trait improvement locus but not found in the first soybean plant, thereby obtaining a soybean plant comprising in its genome at least one introgressed stacked transgenic trait improvement locus. In certain embodiments, the first and/or second plant comprises at least two transgenes that contribute to the same trait. In certain embodiments, this same trait is selected from the group consisting of resistance to a single herbicide, resistance to an insect, resistance to a nematode, resistance to a fungal disease, resistance to an abiotic stress, an improvement in seed oil quantity, an improvement in seed oil quality, and intrinsic yield increases. In certain embodiments, the plant comprises at least two transgenes that contribute to different traits. In certain embodiments, this different trait is independently selected from the group consisting of resistance to one or more herbicide(s), resistance to one or more insect(s), resistance to one or more nematode(s), resistance to one or more fungal disease(s), resistance to one or more abiotic stress(es), one or more improvement(s) in seed oil quantity or quantities, one or more improvement(s) in seed oil quality or qualities, intrinsic yield increases, and combinations thereof. In certain embodiments of these methods, the population, the selected soybean plant, and/or progeny of selected soybean plant is exposed to a dosage of an herbicide sufficient to cause a deleterious effect in a susceptible variety comprising the transgene that confers resistance to the herbicide but lacking the stacked transgenic trait improvement locus. In certain embodiments of these methods, the polymorphic nucleic acid detected in step (b) is detected with at least one marker selected from the group consisting of M0205350 (SEQ ID NO: 10), M0101742 (SEQ ID NO: 5), M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments of these methods, the polymorphic nucleic acid detected in step (b) comprises a TT allele of M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11) and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments of these methods, the polymorphic nucleic acid detected in step (b) is detected with marker M0205350 (SEQ ID NO: 10), M0102027 (SEQ ID NO: 11) or NGMAX008197032 (SEQ ID NO: 52). In certain embodiments of these methods, the polymorphic nucleic acids are detected with marker M0101742 (SEQ ID NO: 5). In certain embodiments of these methods, the polymorphic nucleic acids are detected with marker NGMAX008197032 (SEQ ID NO:52). In certain embodiments of any of the aforementioned methods, the linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both. In certain embodiments of these methods, the linked polymorphic locus is detected with a marker that is located within about 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of the stacked transgenic trait improvement locus. In certain embodiments of these methods, the linked polymorphic locus is detected with at least one marker selected from the group consisting of asmbl_11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO: 2), BI967232 (SEQ ID NO: 3), M0205537 (SEQ ID NO: 15), M0202715 (SEQ ID NO: 16), M0206286 (SEQ ID NO: 17), M0206054 (SEQ ID NO: 18), and M0205375 (SEQ ID NO: 19).


Transgenic soybean plants comprising introgressed linkage group L regions comprising at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8), where the polymorphic alleles are associated with a stacked transgenic trait improvement locus, and where the plant comprises: (a) at least two transgenes that contribute to the same trait; or, (b) at least two transgenes that contribute different traits. In certain embodiments, this same trait is selected from the group consisting of resistance to a single herbicide, resistance to an insect, resistance to a nematode, resistance to a fungal disease, resistance to an abiotic stress, an improvement in seed oil quantity, an improvement in seed oil quality, and intrinsic yield increases. In certain embodiments, this different trait is independently selected from the group consisting of resistance to one or more herbicide(s), resistance to one or more insect(s), resistance to one or more nematode(s), resistance to one or more fungal disease(s), resistance to one or more abiotic stress(es), one or more improvement(s) in seed oil quantity or quantities, one or more improvement(s) in seed oil quality or qualities, intrinsic yield increases, and combinations thereof. In certain embodiments, the polymorphic alleles comprise a TT allele of M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments, the transgenic plant exhibits a stacked transgenic trait improvement. In certain embodiments, the transgenic plant further comprises a transgene that confers resistance to glyphosate and exhibits reproductive tolerance to glyphosate. In certain embodiments of any one of the aforementioned methods, the plant further comprises at least one of a 2,4-D, glufosinate, bromoxynil, synthetic auxins other than 2,4-D, acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase), hydroxyphenyl pyruvate dioxygenase (HPPD), or sulfonylurea herbicide resistance transgenes and/or at least one transgene selected from the group of transgenes conferring insect resistance, nematode resistance, fungal resistance, an improvement in seed oil quantity, an improvement in seed oil quality, abiotic stress resistance, and intrinsic yield increases.


Also provided herein are methods of identifying a soybean plant that comprises a genotype associated with stacked transgenic trait improvement, comprising: detecting in a soybean plant an allele in at least one genetic locus associated with stacked transgenic trait improvement, wherein the genetic locus is in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12), and denoting that the plant comprises a genotype associated with stacked transgenic trait improvement. In certain embodiments, the method further comprises the step of selecting the denoted plant from a population of plants and wherein the detection is performed either before or after the selection. In certain embodiments, the denoted plant comprises at least one transgene that confer resistance to an herbicide and is selected for improved tolerance to that herbicide. In certain embodiments, the selection comprises exposing the population of plants to a dosage of herbicide sufficient to cause a deleterious effect in a susceptible variety comprising the transgene that confers resistance to the herbicide. In certain embodiments: (i) the plants comprise an herbicide resistance transgene selected from the group consisting of a dicamba resistance conferring transgene, a glyphosate resistance conferring transgene, a 2,4-D resistance conferring transgene, and a glufosinate resistance conferring transgene; and (ii) the plants comprising the herbicide resistance transgene are exposed to a dosage of a corresponding herbicide selected from the group consisting of dicamba, glyphosate, glufosinate, and 2,4-D that is sufficient to cause a deleterious effect in a susceptible variety comprising the herbicide resistant transgene that confers resistance to the corresponding herbicide. In certain embodiments, the stacked transgenic trait improvement is independently selected from the group consisting of an improvement in transgene-mediated resistance to one or more herbicide(s), an improvement in transgene-mediated resistance to one or more insect(s), an improvement in transgene-mediated resistance to one or more nematode(s), an improvement in transgene-mediated resistance to one or more fungal disease(s), an improvement in transgene-mediated resistance to one or more abiotic stress(es), in one or more improvement(s) in transgene-mediated seed oil quantity trait(s), one or more improvement(s) in seed oil quality trait(s), an improvement in transgene-mediated intrinsic yield increases, and combinations thereof. In certain embodiments, the denoted plant comprises at least one herbicide resistance transgene and/or at least one insect resistance conferring transgene that encodes a Bacillus thuringiensis toxin. In certain embodiments, the denoted plant comprises at least one herbicide resistance transgene selected from the group consisting of a dicamba resistance conferring transgene. a glyphosate resistance conferring transgene, a 2,4-D resistance conferring transgene, and a glufosinate resistance conferring transgene and/or at least one transgene encoding a product that confers insect resistance selected from the group consisting of a dsRNA that inhibits a target gene of an insect pest, a patatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Bacillus laterosporous insecticidal protein, a Bacillus sphaericus insecticidal protein, and a lignin. In certain embodiments of any of the preceding methods, the genotype associated with stacked transgenic trait improvement comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8). In certain embodiments of any of the preceding methods, the genotype associated with stacked transgenic trait improvement comprises at least one polymorphic allele of at least one marker in the linkage group L region selected from the group consisting of a TT allele M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52).


Also provided are methods for obtaining a soybean plant comprising in its genome at least one stacked transgenic trait improvement locus, compromising the steps of genotyping a plurality of soybean plants with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12); and selecting a soybean plant comprising in its genome at least one genetic locus comprising a genotype associated with stacked transgenic trait improvement. In certain embodiments of the methods, the genotype associated with stacked transgenic trait improvement comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8). In certain embodiments of any of the preceding methods, the genotype associated with stacked transgenic trait improvement comprises at least one polymorphic allele of at least one marker in the first linkage group L region, the first sub-region, or the second sub-region, wherein the marker is selected from the group consisting of a TT allele M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments of the methods, the plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one stacked transgenic trait improvement locus with a parent plant comprising at least one stacked transgenic trait sensitivity locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one stacked transgenic trait improvement locus. In certain embodiments of the methods, the population contains plants that comprise at least one transgene that confers resistance to an herbicide and the stacked transgenic trait improvement comprises improved tolerance to a corresponding herbicide. In certain embodiments of any of the preceding methods, the methods further comprise the step of assaying for the presence of at least one additional marker, wherein the additional marker is either linked or unlinked to the linkage group L genomic region. In certain embodiments of any of the preceding methods, the plurality of soybean plants, the soybean plant, and/or progeny thereof are exposed to a dosage of herbicide sufficient to cause a deleterious effect in a susceptible variety comprising the transgene that confers resistance to the herbicide. In certain embodiments of any of the preceding methods, a plant that exhibits dicamba tolerance and/or reproductive tolerance to glyphosate and/or glufosinate tolerance and/or 2,4-D tolerance is selected. In certain embodiments of any of the preceding methods, the stacked transgenic trait improvement is selected from the group consisting of an improvement in transgene-mediated resistance to one or more herbicide(s), an improvement in transgene-mediated resistance to one or more insect(s), an improvement in transgene-mediated resistance to one or more nematode(s), an improvement in transgene-mediated resistance to one or more fungal disease(s), an improvement in transgene-mediated resistance to one or more abiotic stress(es), in one or more improvement(s) in transgene-mediated seed oil quantity trait(s), one or more improvement(s) in seed oil quality trait(s), an improvement in transgene-mediated intrinsic yield increases, and combinations thereof.


Also provided herein are methods for producing a soybean plant comprising in its genome at least one introgressed stacked transgenic trait improvement locus comprising the steps of: crossing a first soybean plant with a stacked transgenic trait improvement locus with a second soybean plant comprising: a stacked transgenic trait sensitivity locus in a first linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8) and at least one linked polymorphic locus not present in the first soybean plant to obtain a population segregating for the stacked transgenic trait improvement loci and the linked polymorphic locus; detecting at least two polymorphic nucleic acids in at least one soybean plant from the population, wherein at least one of the polymorphic nucleic acids is located in the first linkage group L region and/or the second linkage group L region and at least one of the polymorphic amino acids is a linked polymorphic locus not present in the first soybean plant; and selecting a soybean plant comprising a genotype associated with stacked transgenic trait improvement and at least one linked marker found in the second soybean plant comprising a stacked transgenic trait sensitivity locus but not in the first soybean plant, thereby obtaining a soybean plant comprising in its genome at least one introgressed stacked transgenic trait improvement locus. In certain embodiments of the methods, at least one of the first or the second soybean plants comprises a transgene that confers resistance to an herbicide. In certain embodiments of the methods, the population, the selected soybean plant, and/or progeny of selected soybean plant is exposed to a dosage of herbicide sufficient to cause a deleterious effect in a susceptible variety comprising the transgene that confers resistance to a corresponding herbicide. In certain embodiments of the methods, the polymorphic nucleic acid detected in step (b) is detected with at least one marker selected from the group consisting of M0205350 (SEQ ID NO: 10), M0101742 (SEQ ID NO: 5), M0102027 (SEQ ID NO: 11), and NGMAX008197032 (SEQ ID NO:52). In certain embodiments of the methods, the polymorphic nucleic acid detected in step (b) comprises a TT allele of M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments of the methods, the polymorphic nucleic acid detected in step (b) is detected with marker M0205350 (SEQ ID NO: 10), M0102027 (SEQ ID NO: 11), or marker NGMAX008197032 (SEQ ID NO:52). In certain embodiments of the methods, the polymorphic nucleic acids are detected with marker M0101742 (SEQ ID NO: 5). In certain embodiments of any of the preceding methods, the linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both. In certain embodiments, the linked polymorphic locus is detected with a marker that is located within about 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of the stacked transgenic trait improvement locus. In certain embodiments, the linked polymorphic locus is detected with at least one marker selected from the group consisting of asmbl_11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO: 2), BI967232 (SEQ ID NO: 3), M0205537 (SEQ ID NO: 15), M0202715 (SEQ ID NO: 16), M0206286 (SEQ ID NO: 17), M0206054 (SEQ ID NO:18), and M0205375 (SEQ ID NO: 19).


Also provided are transgenic soybean plants comprising introgressed linkage group L regions comprising at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of at least one marker in a third sub-region of the linkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8), wherein the polymorphic alleles are associated with stacked transgenic trait improvement and wherein the plant comprises at least one transgene. In certain embodiments, the transgene confers resistance to an herbicide. In certain embodiments, the polymorphic alleles comprise a TT allele of M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments of any of the preceding methods, the plant exhibits tolerance to at least one herbicide. In certain embodiments, the plant comprises: i) a transgene that confers resistance to glyphosate and exhibits reproductive tolerance to glyphosate; and/or (ii) a dicamba resistance conferring transgene and exhibits dicamba tolerance; and/or (iii) a glufosinate resistance conferring transgene and exhibits glufosinate tolerance; and/or (iv) a 2,4-D resistance conferring transgene and exhibits 2,4-D tolerance. In certain embodiments, the plant comprises at least one transgene conferring resistance to a herbicide selected from the group consisting of dicamba, 2,4-D, glufosinate, bromoxynil, synthetic auxins other than 2,4-D, acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase), hydroxyphenyl pyruvate dioxygenase (HPPD), and a sulfonylurea herbicide and/or at least one transgene selected from the group of transgenes conferring insect resistance, nematode resistance, fungal resistance, an improvement in seed oil quantity, an improvement in seed oil quality, abiotic stress resistance, and intrinsic yield increases. In certain embodiments, the plant comprises at least one herbicide resistance transgene and/or at least one insect resistance conferring transgene that encodes a Bacillus thuringiensis toxin. In certain embodiments, the plant comprises at least one herbicide resistance transgene selected from the group consisting of a dicamba resistance conferring transgene a glyphosate resistance conferring transgene, a 2,4-D resistance conferring transgene, and a glufosinate resistance conferring transgene and/or at least one transgene encoding a product that confers insect resistance selected from the group consisting of a dsRNA that inhibits a target gene of an insect pest, a patatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Bacillus laterosporous insecticidal protein, a Bacillus sphaericus insecticidal protein, and a lignin.


Also provided herein are methods of identifying a transgenic soybean plant that comprises a genotype associated with stacked transgenic trait improvement, the method comprising: (a) scoring at least one transgenic plant in a population of transgenic soybean plants that had been exposed to dicamba for dicamba tolerance, the plants having a transgene that confers resistance to dicamba; and, (b) selecting a transgenic plant that exhibits dicamba tolerance, thereby identifying a transgenic soybean plant that comprises a genotype associated with stacked transgenic trait improvement. In certain embodiments, the population is segregating for to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12) that is associated with stacked transgenic trait improvement. In certain embodiments, the method further comprises genotyping the selected soybean plant with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12). In certain embodiments, the selected transgenic plant further comprises a transgene that confers resistance to glyphosate and the selected transgenic plant or progeny thereof is scored for reproductive tolerance to glyphosate following exposure to glyphosate. In certain embodiments of any of the preceding methods, the methods further comprise exposing the population of transgenic soybean plants to dicamba. In certain embodiments of any of the preceding methods, dicamba tolerance is scored by determining a reduction in malformation when compared to a dicamba sensitive transgenic plant that comprises the transgene that confers resistance to dicamba. In certain embodiments of any of the preceding methods, the stacked transgenic trait improvement is selected from the group consisting of an improvement in transgene-mediated resistance to one or more herbicide(s), an improvement in transgene-mediated resistance to one or more insect(s), an improvement in transgene-mediated resistance to one or more nematode(s), an improvement in transgene-mediated resistance to one or more fungal disease(s), an improvement in transgene-mediated resistance to one or more abiotic stress(es), in one or more improvement(s) in transgene-mediated seed oil quantity trait(s), one or more improvement(s) in seed oil quality trait(s), an improvement in transgene-mediated intrinsic yield increases, and combinations thereof. In certain embodiments of any of the preceding methods, the selected plant comprises at least one additional herbicide resistance transgene selected from the group consisting of a glyphosate resistance conferring transgene, a 2,4-D resistance conferring transgene, and a glufosinate resistance conferring transgene and/or at least transgene encoding a product that confers insect resistance selected from the group consisting of a dsRNA that inhibits a target gene of an insect pest, a patatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Bacillus laterosporous insecticidal protein, a Bacillus sphaericus insecticidal protein, and a lignin.


Also provided herein are methods of identifying a transgenic soybean plant that comprises a genotype associated with stacked transgenic trait improvement, comprising: (a) scoring at least one plant in a population of transgenic soybean plants that had been exposed to glyphosate for reproductive tolerance to glyphosate, wherein the plants comprise a transgene that confers resistance to glyphosate; and, (b) selecting a transgenic plant that exhibits reproductive tolerance to glyphosate, thereby identifying a transgenic soybean plant that comprises a genotype associated with stacked transgenic trait improvement. In certain embodiments, the population is segregating for to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12) that is associated with stacked transgenic trait improvement. In certain embodiments, the method further comprises genotyping the selected soybean plant with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12). In certain embodiments of any of the preceding methods, the selected transgenic plant further comprises a transgene that confers resistance to dicamba and the selected transgenic plant or progeny thereof is scored for tolerance to dicamba following exposure to dicamba. In certain embodiments of any of the preceding methods, the methods further comprise exposing the population of transgenic soybean plants to glyphosate. In certain embodiments of any of the preceding methods, glyphosate reproductive tolerance is scored by determining a reduction in sterility when compared to a transgenic plant that exhibits glyphosate reproductive sensitivity and comprises the transgene that confers resistance to glyphosate. In certain embodiments of any of the preceding methods, the stacked transgenic trait improvement is selected from the group consisting of an improvement in transgene-mediated resistance to one or more herbicide(s), an improvement in transgene-mediated resistance to one or more insect(s), an improvement in transgene-mediated resistance to one or more nematode(s), an improvement in transgene-mediated resistance to one or more fungal disease(s), an improvement in transgene-mediated resistance to one or more abiotic stress(es), in one or more improvement(s) in transgene-mediated seed oil quantity trait(s), one or more improvement(s) in seed oil quality trait(s), an improvement in transgene-mediated intrinsic yield increases, and combinations thereof. In certain embodiments of any of the preceding methods, the selected plant comprises at least one additional herbicide resistance transgene selected from the group consisting of a dicamba resistance conferring transgene, a 2,4-D resistance conferring transgene, and a glufosinate resistance conferring transgene and/or at least one transgene encoding a product that confers insect resistance selected from the group consisting of a dsRNA that inhibits a target gene of an insect pest, a patatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Bacillus laterosporous insecticidal protein, a Bacillus sphaericus insecticidal protein, and a lignin.


Also provided are methods of obtaining a transgenic soybean plant that comprises a genotype associated with stacked transgenic trait improvement, the methods comprising: exposing a population of transgenic soybean plants to an herbicide, wherein the plants have a transgene that confers resistance to the herbicide; observing herbicide tolerance exhibited by one or more soybean plants following exposure to the herbicide; and, (c) selecting a transgenic plant that exhibits herbicidetolerance, thereby obtaining a transgenic soybean plant that comprises a genotype associated with stacked transgenic trait improvement. In certain embodiments, the population is segregating for to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12) that is associated with stacked transgenic trait improvement. In certain embodiments, the method further comprises genotyping the selected soybean plant with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12). In certain embodiments of any of the preceding methods, the transgene that confers resistance to the herbicide is selected from the group consisting of a dicamba resistance conferring transgene, a glyphosate resistance conferring transgene, a 2,4-D resistance conferring transgene, and a glufosinate resistance conferring transgene and the plants are exposed to the corresponding herbicide. In certain embodiments of any of the preceding methods, the transgene confers resistance to glyphosate and the selected transgenic plant or progeny thereof is scored for reproductive tolerance to glyphosate following exposure to glyphosate. In certain embodiments of any of the preceeding methods, the transgene confers resistance to dicamba and the selected transgenic plant or progeny thereof are scored for dicamba tolerance.


Also provided herein are methods of identifying a transgenic soybean plant that comprises a genotype associated with reproductive tolerance to glyphosate, the method comprising: (a) scoring at least one transgenic plant in a population of transgenic soybean plants that had been exposed to dicamba for dicamba tolerance, the plants having a transgene that confers resistance to dicamba; and, (b) selecting a transgenic plant that exhibits dicamba tolerance, thereby identifying a transgenic soybean plant that comprises a genotype associated with reproductive tolerance to glyphosate. In certain embodiments of the methods, the population is segregating for to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12) that is associated with dicamba tolerance. In certain embodiments of the methods, the methods further comprise genotyping the selected soybean plant with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12). In certain embodiments of any of the aforementioned methods, the selected transgenic plant further comprises a transgene that confers resistance to glyphosate and wherein the selected transgenic plant or progeny thereof is scored for reproductive tolerance to glyphosate following exposure to glyphosate. In certain embodiments of any of the aforementioned methods, the methods further comprise exposing the population of transgenic soybean plants to dicamba. In certain embodiments of any of the aforementioned methods, the dicamba tolerance is scored by determining a reduction in malformation when compared to a dicamba sensitive transgenic plant that comprises the transgene that confers resistance to dicamba.


Also provided herein are methods of identifying a transgenic soybean plant that comprises a genotype associated with tolerance to dicamba, comprising: (a) scoring at least one plant in a population of transgenic soybean plants that had been exposed to glyphosate for reproductive tolerance to glyphosate, wherein the plants comprise a transgene that confers resistance to glyphosate; and, (b) selecting a transgenic plant that exhibits reproductive tolerance to glyphosate, thereby identifying a transgenic soybean plant that comprises a genotype associated with dicamba tolerance. In certain embodiments of the methods, the population is segregating for to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12) that is associated with dicamba tolerance. In certain embodiments of the methods, the method further comprises genotyping the selected soybean plant with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12). In certain embodiments of any of the aforementioned methods, the selected transgenic plant further comprises a transgene that confers resistance to dicamba and wherein the selected transgenic plant or progeny thereof is scored for tolerance to dicamba following exposure to dicamba. In certain embodiments of any of the aforementioned methods, the methods further comprise exposing the population of transgenic soybean plants to glyphosate. In certain embodiments of any of the aforementioned methods, the glyphosate reproductive tolerance is scored by determining a reduction in sterility when compared to a transgenic plant that exhibits glyphosate reproductive sensitivity and comprises the transgene that confers resistance to glyphosate.


Also provided herein are methods of obtaining a transgenic soybean plant that comprises a genotype associated with reproductive tolerance to glyphosate, the methods comprising: (a) exposing a population of transgenic soybean plants to dicamba, wherein the plants have a transgene that confers resistance to dicamba; (b) observing dicamba tolerance exhibited by one or more soybean plants following exposure to dicamba; and, (c) selecting a transgenic plant that exhibits dicamba tolerance, thereby obtaining a transgenic soybean plant that comprises a genotype associated with reproductive tolerance to glyphosate. In certain embodiments of the methods, the population is segregating for to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12) that is associated with dicamba tolerance. In certain embodiments of the methods, the methods further comprise genotyping the selected soybean plant with respect to at least one genetic locus in a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12). In certain embodiments of any of the aforementioned methods, the selected transgenic plant further comprises a transgene that confers resistance to glyphosate and the selected transgenic plant or progeny thereof is scored for reproductive tolerance to glyphosate following exposure to glyphosate. In certain embodiments of any of the aforementioned methods, the dicamba tolerance is scored by determining a reduction in malformation when compared to a dicamba sensitive transgenic plant that comprises the transgene that confers resistance to dicamba. Further areas of applicability will become apparent from the description provided herein. It should be understood that the description and specific examples are intended for purposes of illustration only and are not intended to limit the scope of the present disclosure.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 shows a bar graph of the percent injury at 7 days after treatment with Dicamba (y-axis) for various favorable and unfavorable soybean plant haplotypes containing a dicamba resistance conferring transgene (x-axis). The favorable haplotypes are haplotypes that are not associated with the dicamba intolerance trait and the unfavorable haplotypes are associated with the dicamba intolerance trait. In the graph, “Fav Hap is “Favorable Haplotype” and “Unf Hap” is “Unfavorable Haplotype”. The data show that presence of the favorable haplotype is associated with improved tolerance to dicamba.



FIG. 2 shows a bar graph of the percent injury at 7 days after treatment with either a single treatment (V6 stage, solid bars) or two treatments (V3+V6 stages, open bars) of Dicamba (y-axis) for various favorable and unfavorable soybean plant haplotypes (x-axis) containing a dicamba resistance conferring transgene (x-axis). In the graph, “Fav Hap is “Favorable Haplotype” and “Unf Hap” is “Unfavorable Haplotype”. The data show that favorable haplotypes can be selected with either a single treatment at the V6 stageor two treatments at the V3 and V6 stages.





DETAILED DESCRIPTION
Definitions

As used herein, an “allele” refers to one of two or more alternative forms of a genomic sequence at a given locus on a chromosome. When all the alleles present at a given locus on a chromosome are the same, that plant is homozygous at that locus. If the alleles present at a given locus on a chromosome differ, that plant is heterozygous at that locus.


As used herein, the term “denoting” when used in reference to a plant genotype refers to any method whereby a plant is indicated to have a certain genotype. Such indications of a certain genotype include, but are not limited to, any method where a plant is physically marked or tagged. Physical markings or tags that can be used include, but not limited to, a barcode, a radio-frequency identification (RFID), a label or the like. Indications of a certain genotype also include, but are not limited to, any entry into any type of written or electronic database whereby the plant's genotype is provided.


A “locus” is a position on a genomic sequence that is usually found by a point of reference; e.g., a short DNA sequence that is a gene, or part of a gene or intergenic region. A locus may refer to a nucleotide position at a reference point on a chromosome, such as a position from the end of the chromosome.


As used herein, “linkage group L” corresponds to the soybean linkage group L described in Choi, et al., Genetics. 2007 May; 176(1): 685-696. Linkage group L, as used herein, also corresponds to soybean chromosome 19 (as described on the World Wide Web at soybase.org/LG2Xsome.php). As used herein, “polymorphism” means the presence of one or more variations of a nucleic acid sequence at one or more loci in a population of at least two members. The variation can comprise but is not limited to one or more nucleotide base substitutions, the insertion of one or more nucleotides, a nucleotide sequence inversion, and/or the deletion of one or more nucleotides.


As used herein, the term “single nucleotide polymorphism,” also referred to by the abbreviation “SNP,” means a polymorphism at a single site wherein the polymorphism constitutes any or all of a single base pair change, an insertion of one or more base pairs, and/or a deletion of one or more base pairs.


As used herein, “marker” means a detectable characteristic that can be used to discriminate between organisms. Examples of such characteristics include, but are not limited to, genetic markers, biochemical markers, fermentation yield, fermentation efficiency, energy yield, secondary compounds, metabolites, morphological characteristics, and agronomic characteristics.


As used herein, “marker assay” means a method for detecting a polymorphism at a particular locus using a particular method. Marker assays thus include, but are not limited to, measurement of at least one phenotype (such as seed color, flower color, or other visually detectable trait as well as any biochemical trait), restriction fragment length polymorphism (RFLP), single base extension, electrophoresis, sequence alignment, allelic specific oligonucleotide hybridization (ASO), random amplified polymorphic DNA (RAPD), microarray-based polymorphism detection technologies, and the like.


As used herein, “genotype” means the genetic component of the phenotype and it can be indirectly characterized using markers or directly characterized by nucleic acid sequencing.


As used herein, the term “introgressed”, when used in reference to a genetic locus, refers to a genetic locus that has been introduced into a new genetic background. Introgression of a genetic locus can thus be achieved through both plant breeding methods or by molecular genetic methods. Such molecular genetic methods include, but are not limited to, various plant transformation techniques and/or methods that provide for homologous recombination, non-homologous recombination, site-specific recombination, and/or genomic modifications that provide for locus substitution or locus conversion. In certain embodiments, introgression could thus be achieved by substitution of a dicamba intolerance locus with a corresponding dicamba tolerance locus or by conversion of a locus from a dicamba intolerance genotype to a dicamba tolerance genotype.


As used herein, “phenotype” means the detectable characteristics of a cell or organism which can be influenced by gene expression.


As used herein, “linkage” refers to relative frequency at which types of gametes are produced in a cross. For example, if locus A has genes “A” or “a” and locus B has genes “B” or “b” and a cross between parent I with AABB and parent B with aabb will produce four possible gametes where the genes are segregated into AB, Ab, aB and ab. The null expectation is that there will be independent equal segregation into each of the four possible genotypes, i.e. with no linkage ¼ of the gametes will of each genotype. Segregation of gametes into a genotypes differing from ¼ are attributed to linkage.


As used herein, the termed “linked”, when used in the context of markers and/or genomic regions, means that the markers and/or genomic regions are located on the same linkage group or chromosome.


As used herein, a “nucleic acid molecule,” be it a naturally occurring molecule or otherwise may be “substantially purified”, if desired, referring to a molecule separated from substantially all other molecules normally associated with it in its native state. More preferably, a substantially purified molecule is the predominant species present in a preparation. A substantially purified molecule may be at least about 60% free, preferably at least about 75% free, more preferably at least about 90% free, and most preferably at least about 95% free from the other molecules (exclusive of solvent) present in the natural mixture. The term “substantially purified” is not intended to encompass molecules present in their native state.


As used herein, “quantitative trait locus (QTL)” means a locus that controls to some degree numerically representable traits that are usually continuously distributed. As used herein, the term “transgene” means nucleic acid molecules in the form of DNA, such as cDNA or genomic DNA, and RNA, such as mRNA or microRNA, which may be single or double stranded.


As used herein, the term “event”, when used in the context of describing a transgenic plant, refers to a particular transformed plant line. In a typical transgenic breeding program, a transformation construct responsible for a trait is introduced into the genome via a transformation method. Numerous independent transformants (events) are usually generated for each construct. These events are evaluated to select those with superior performance.


As used herein, the term “soybean” means Glycine max and includes all plant varieties that can be bred with soybean, including wild soybean species. In certain embodiments, soybean plants from the species Glycine max and the subspecies Glycine max L. ssp. max or Glycine max ssp. formosana can be genotyped using the compositions and methods of the present invention. In an additional aspect, the soybean plant is from the species Glycine soja, otherwise known as wild soybean, can be genotyped using these compositions and methods. Alternatively, soybean germplasm derived from any of Glycine max, Glycine max L. ssp. max, Glycine max ssp. Formosana, and/or Glycine soja can be genotyped using compositions and methods provided herein.


As used herein, the term “bulk” refers to a method of managing a segregating population during inbreeding that involves growing the population in a bulk plot, harvesting the self-pollinated seed of plants in bulk, and using a sample of the bulk to plant the next generation.


As used herein, the phrase “transgene that confers tolerance to dicamba” refers to the ability of a transgene to provide a soybean plant capable of surviving exposure to dicamba at a rate of about 0.5 pounds of acid equivalent per acre of dicamba acid to about 1.5 pounds of acid equivalent per acre of dicamba acid applied at either pre-emergence and/or postemergence. Transgenic plants comprising a transgene that confers tolerance to dicamba can exhibit, either a “dicamba tolerant” phenotype in certain soybean germplasms or a “dicamba sensitive” phenotype in other distinct soybean germplasms when exposed to dicamba.


As used herein, the phrase “dicamba intolerant” refers to undesirable phenotypic traits observed in certain soybean germplasms that comprise a transgene that confers resistance to dicamba after exposure to dicamba at a rate of about 0.5 pounds of acid equivalent per acre of dicamba acid to about 1.5 pounds of acid equivalent per acre of dicamba acid. Such undesirable phenotypic traits include, but are not limited to, pronounced bending/twisting of the main stem and petioles, necrosis of the upper nodes and petioles, and/or limitation of new growth.


As used herein, the phrase “dicamba tolerant” refers to either the absence or reduction of undesirable phenotypic traits observed after exposure to dicamba in “dicamba intolerant” soybean germplasms that comprise a transgene that confers resistance to dicamba.


As used herein, the term “comprising” means “including but not limited to”.


As used herein, the terms “scoring” or “score”, refer to any qualitive, semi-quantitive, or quantitive method for determining the presence, absence, and/or the partial presence or absence, of a phenotypic trait.


As used herein, the phrase “susceptible variety”, when used in reference to herbicide tolerance in a soybean plant comprising a transgene that confers resistance to that herbicide, refers to a soybean variety that allele(s) of the stacked transgenic trait improvement locus that do not confer such stacked transgenic trait improvements. “Susceptible varieties’ are also referred to herein as “sensitive varieties” in the context of herbicide tolerance in a soybean plant comprising a transgene that confers resistance to that herbicide.


As used herein, the phrase “corresponding herbicide”, when used in reference to a transgene that confers herbicide resistance, refers to the herbicide that the transgene confers resistance to. Thus, a corresponding herbicide for a transgene that confers resistance to glyphosate, dicamba, 2,4-D, or glufosinate is respectively glyphosate, dicamba, 2,4-D, or glufosinate.


DESCRIPTION

In accordance with the present invention, Applicants have discovered genomic regions, associated markers, and associated methods for identifying and associating genotypes that effect the levels of dicamba tolerance observed in soybean plants comprising a transgene that confers resistance to dicamba. Dicamba (3,6-dichloro-o-anisic acid) is a useful broad spectrum herbicide for controlling weeds. For example, in one embodiment, a method of the invention comprises screening a plurality of transgenic germplasm entries displaying a heritable variation for at least one transgene mediated dicamba resistance trait wherein the heritable variation is linked to at least one genotype; and associating at least one genotype from the transgenic germplasm entries to at least one dicamba tolerance trait. In another embodiment, a method of the invention comprises crossing at least two germplasm entries with a test germplasm entry for the evaluation of performance of at least one dicamba tolerance trait in order to determine preferred crossing schemes. The methods of the present invention can be used with traditional breeding techniques as described below to more efficiently screen and identify genotypes affecting a dicamba tolerance trait.


The use of markers to infer a phenotype of interest results in the economization of a breeding program by substituting costly, time-intensive phenotyping assays with genotyping assays. Further, breeding programs can be designed to explicitly drive the frequency of specific, favorable phenotypes by targeting particular genotypes (U.S. Pat. No. 6,399,855). Fidelity of these associations may be monitored continuously to ensure maintained predictive ability and, thus, informed breeding decisions (US Patent Application 2005/0015827). In this case, costly, time-intensive phenotyping assays required for determining if a plant or plants contains a genomic region associated with a “dicamba tolerance” or “Dicamba intolerance” phenotype can be supplanted by genotypic assays that provide for identification of a plant or plants that contain the desired genomic region that confers dicamba tolerance.


A Genomic Region Associated with a Dicamba Tolerance Phenotype


Provided herewith is a soybean genomic region that is shown herein to be associated with a desirable dicamba tolerance phenotype when present in certain allelic forms and when combined with certain transgenic loci that confer dicamba tolerance.


A soybean genomic region provided that can be associated with a desirable dicamba tolerance phenotype when present in certain allelic forms is located on the telomere proximal end of the short arm of soybean linkage group L (chromosome 19). A series of markers useful in practicing the methods of this invention are provided herewith in Table 1. Additional markers useful in the practice of the invention are provided herewith in Table 2 of the Specification, which is incorporated herewith by reference in its entirety. Table 2 provides the Table 1 markers, additional nucleic acid markers or loci that have been disclosed in various databases, the relative positions of the markers on a physical map of linkage group L (soybean chromosome 19), and sources for the markers.









TABLE 1







Markers spanning a genomic region associated


with a desirable dicamba tolerance phenotype













Allelic form(s)


Marker or Locus
SEQ ID
Map
Associated with


Name
NO:
Position1
Dicamba Tolerance2













asmbl_11856
1
16506



TC122822
2
32108



BI967232
3
66686



M0205928
4
92526



M01017423
5
112836
TT6


M0129138
6
114013



BU551345
7
116147



M0114388
8
380897



BU551363
9
422447



M02053504
10
423935
TT7


M01020275
11
466558
CC8


BU765955
12
474316



M0093116
13
805580



M0129925
14
831128



M0205537
15
890254



M0202715
16
921431



M0206286
17
1209977



M0206054
18
1465354



M0205375
19
2009800



NGMAX0081970329
52
314997
AA10






1The relative positions of the approximate middle position of the listed markers or loci based on nucleotide positions on a physical map of soybean linkage group L (chromosome 19) of Table 2 are provided where nucleotide position 0 (zero) is telomere proximal and nucleotide position 2009800 is centromere proximal. Polymorphic nucleotide bases are designated in the sequence listing provided herewith according to the WIPO Standard ST.25 (1998), Table 1, as follows: r = g or a (purine); y = t/u or c (pyrimidine); m = a or c; (amino); k = g or t/u (keto); s = g or c (strong interactions 3 H-bonds); w = a or t/u (weak interactions 2H-bonds); b = g or c or t/u (not a); d = a or g or t/u (not c); h = a or c or t/u (not g); v = a or g or c (not t, not u); and n = a or g or c or t/u (unknown, or other; any.)




2Both the maternal and paternal alleles of the single nucleotide polymorphisms that can be associated with a dicamba tolerance phenotype are shown.




3The identified polymorphic allele of marker M0101742 is located at nucleotide 1206 of SEQ ID NO: 5.




4The identified polymorphic allele of marker M0205350 is located at nucleotide 148 of SEQ ID NO: 10.




5The identified polymorphic allele of marker M0102027is located at nucleotide 349 of SEQ ID NO: 11.




6The identified polymorphic allele of marker M0101742 “TT” can be associated with a dicamba tolerance phenotype when the identified polymorphic alleles of the other markers are: “TT” for M0205350 and, in certain embodiments, “CC” for M0102027.




7The identified polymorphic allele of marker M020350 “TT” can be associated with a dicamba tolerance phenotype when the identified polymorphic alleles of the other markers are: “TT” for M0101742 and, in certain embodiments, “CC” for M0102027.




8In certain embodiments, the identified polymorphic allele “CC” for marker M0102027 can be associated with a dicamba tolerance phenotype when the identified polymorphic alleles of the other markers are: “TT” for M0101742 and “TT” for M020350.




9The identified polymorphic allele of marker NGMAX008197032 is located at nucleotide 201 of SEQ ID NO: 52.




10In certain embodiments, the identified polymorphic allele of marker NGMAX008197032 “AA” can be associated with a dicamba tolerance phenotype when the identified polymorphic alleles of the other markers are: “TT” for M0205350 and, in certain embodiments, “CC” for M0102027, and “TT” for M0101742.







Also provided herein are sub-regions of the linkage group L region that is flanked by loci M0205928 (SEQ ID NO: 4) and BU765995 (SEQ ID NO: 12) that are associated with a dicamba tolerance phenotype. A first sub-region of the linkage group L region associated with a dicamba tolerance phenotype is flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6). These loci flank a first sub-region that spans telomere proximal nucleotide 92334 to centromere proximal nucleotide 113494 in the physical map of linkage group L provided in Table 2 of the specification. Polymorphisms located in this first sub-region that are associated with a dicamba tolerance phenotype can be detected with markers that include, but are not limited to, M0101742 (SEQ ID NO: 5). A second sub-region of the linkage group L region associated with a dicamba tolerance phenotype is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12). These loci flank the second sub-region that spans telomere proximal nucleotide 422447 to centromere proximal nucleotide 474316 in the physical map of linkage group L provided in Table 2 of the specification. Polymorphisms located in this second sub-region that are associated with a dicamba tolerance phenotype can be detected with markers that include, but are not limited to, M0205350 (SEQ ID NO: 10) or M0102027 (SEQ ID NO: 11). A third sub-region of the linkage group L region associated with a dicamba tolerance phenotype is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8). These loci flank the second sub-region that spans telomere proximal nucleotide 115,956 to centromere proximal nucleotide 380,486 in the physical map of linkage group L provided in Table 2 of the specification. Polymorphisms located in this third sub-region that are associated with a dicamba tolerance phenotype can be detected with markers that include, but are not limited to, NGMAX008197032 (SEQ ID NO:52). In certain embodiments of invention, a polymorphism associated with a dicamba tolerant phenotype is detected in only one of these sub-regions. In other embodiments of the invention, at least one polymorphism associated with a dicamba tolerant phenotype is detected in any two of these sub-regions. Thus, a marker including, but not limited to, M0101742 (SEQ ID NO: 5) can be used either independently of, or in combination with, one or more markers selected from the group consisting of M0205350 (SEQ ID NO: 10) and/or M0102027 (SEQ ID NO: 11) to detect polymorphisms associated with a dicamba tolerance phenotype. In certain embodiments, a marker including, but not limited to, M0101742 (SEQ ID NO: 5) can be used either independently of, or in combination with, marker NGMAX008197032 (SEQ ID NO:52) to detect polymorphisms associated with a dicamba tolerance phenotype. In certain embodiments, a marker including, but not limited to, marker NGMAX008197032 (SEQ ID NO:52) can be used either independently of, or in combination with, one or more markers selected from the group consisting of M0205350 (SEQ ID NO: 10) and/or M0102027 (SEQ ID NO: 11) to detect polymorphisms associated with a dicamba tolerance phenotype. In certain embodiments, a polymorphism in the first sub-region is detected with marker M0101742 (SEQ ID NO: 5) and a polymorphism in the second sub-region is detected with markers M0205350 (SEQ ID NO: 10) and/or M0102027 (SEQ ID NO: 11). In certain embodiments, a polymorphism in the first sub-region is detected with marker M0101742 (SEQ ID NO: 5) and a polymorphism in the third sub-region is detected with marker NGMAX008197032 (SEQ ID NO: 52). In certain embodiments, the alleles of these markers associated with dicamba tolerance are a TT allele M0101742 (SEQ ID NO: 5), a TT allele of M0205350 (SEQ ID NO: 10), and, in certain embodiments, a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52).


Additional genetic markers can be used either in conjunction with the markers provided in Table 1 and/or Table 2 or independently of the markers provided in Table 1 and/or Table 2 to practice the methods of the instant invention. Publicly available marker databases from which useful markers can be obtained include, but are not limited to, the soybase.org website on the internet (World Wide Web) that is administered by the United States Agricultural Research Service, the United States Department of Agriculture, and Iowa State University. Additional soybean markers that can be used and that have been described in the literature include, but are not limited to, Hyten et al., BMC Genomics. 11:38, 2010; Choi et al., Genetics. 176(1):685-96, 2007; Yoon et al., Theor Appl Genet. 2007 March; 114(5):885-99; and Hyten et al. Crop Sci. 2010 50: 960-968. Given the provision herein of a genomic region on linkage group L (chromosome 19) delimited or flanked by the telomere proximal locus M0205928 (SEQ ID NO: 4) of Table 2 and the centromere proximal locus BU765955 (SEQ ID NO: 12) of Table 2 as well as an assortment of soybean germplasms exhibiting either a “dicamba intolerant” or “dicamba tolerant” phenotype, additional markers located either within or near this genomic region that are associated with these phenotypes can be obtained by merely typing the new markers in the various germplasms provided herewith. The genomic region on linkage group L (chromosome 19) delimited or flanked by the telomere proximal locus M0205928 (SEQ ID NO: 5) of Table 2 and the centromere proximal locus BU765955 (SEQ ID NO: 12) of Table 2 can also be mapped relative to markers provided in any publicly available or other soybean physical or genetic map to place this genetic locus on that map.


Identification of Plants Exhibiting the “Dicamba Intolerance” or “Dicamba Tolerance” Phenotype


To observe the presence or absence of the “dicamba intolerance” or dicamba tolerance phenotypes, transgenic soybean plants comprising a transgene that confers resistance to dicamba are typically exposed in early to mid-vegetative growth stages to one or more high doses of dicamba. Typical doses of dicamba that can elicit a dicamba intolerance phenotype can range from about a 2-fold label application rate of a commercially available dicamba formulation to about a 3-fold label application rate of a commercially available dicamba formulation. In terms of acid equivalents of dicamba acid applied, typical doses of dicamba that can elicit a dicamba intolerance phenotype can range from an application rate of about 1.0 pounds of acid equivalent per acre of dicamba acid to about 1.5 pounds of acid equivalent per acre of dicamba acid when the indicated amounts of dicamba acid are provided in either a commercially available dicamba formulation or when the indicated amounts of dicamba acid is provided in a similar formulation suitable for application to dicamba-tolerant crops. Commercially available dicamba formulations that can be used include, but are not limited to, Clarity® (BASF, NC, USA); Banvel®, Banvel M®, Banvel II®, Banvel SGF®, or Vanquish® (Syngenta, Wilmington, Del., USA); or Rifle® (Loveland Products, Inc., Loveland, Colo., USA). In certain embodiments, the commercially available dicamba formulation used is Clarity®. In certain embodiments, doses of dicamba that can elicit a dicamba intolerance phenotype can range from about a 2 fold application rate of about 0.25 gallons per acre Clarity® to about a three fold application rate of about 0.375 gallons per acre per acre Clarity®.


The dicamba intolerance phenotype can be observed approximately a week after herbicide application in certain soybean varieties comprising the transgene that confers resistance to dicamba. Dicamba is typically applied during pre and post-emergent vegetative growth stages. In certain embodiments of these methods, dicamba can be applied in weekly intervals (i.e. once a week) for any of 2, 3, 4 or more successive weeks to score for the presence of the dicamba intolerance phenotype. In certain embodiments, soybean plants at about the V3 vegetative development stage are exposed to an initial dicamba spray followed by a subsequent spray at V6/R1. Genotypes provided herein are especially useful for providing dicamba tolerance to plants sprayed at the V6 stage. As discussed herein, the vegetative stages of soybean are as follows: VE (emergence), VC (cotyledon stage), V1 (first trifoliate leaf), V2 (second trifoliate leaf), V3 (third trifoliate leaf), V(n) (nth trifoliate leaf), and V6 (flowering will soon start). As discussed herein, the reproductive stages of soybean are as follows: R1 (beginning bloom), R2 (full bloom), R3 (beginning pod), R4 (full pod), R5 (beginning seed), R6 (full seed), R7 (beginning maturity) and R8 (full maturity). A description of the soybean vegetative and reproductive stages can be found on the world wide web (interne) at ag.ndsu.edu/pubs/plantsci/rowcrops/a1174/a1174w.htm (North Dakota State University publication A-1174, June 1999, Reviewed and Reprinted August 2004).


A rating scale that evaluates the degree of dicamba intolerance can also be employed to identify “dicamba intolerant” and “dicamba tolerant” plants. An exemplary and non-limiting scale for evaluating the Dicamba intolerance phenotype is as follows, where a low number corresponds to a “dicamba tolerance” phenotype and the a high number correlates to a “dicamba intolerance” phenotype:


A rating of 1: Less than 10% of plants show malformation


A rating of 2: 10-50% of plants show malformation


A rating of 3: Greater than 50% of plants show malformation


Identification of Plants Exhibiting Reproductive Tolerance to Glyphosate Phenotype


To observe the presence or absence of reproductive tolerance to glyphosate phenotypes, transgenic soybean plants comprising a transgene that confers glyphosate resistance are typically exposed in mid- to late-vegetative growth stages to one or more high doses of glyphosate. Doses of glyphosate that can elicit a reproductive sensitivity phenotype are usually at least about twice the typical application rates of commercial glyphosate formulations that are used to provide weed control in transgenic, glyphosate resistant soybean plants. In terms of acid equivalents of glyphosate acid applied, typical doses of glyphosate that can elicit a reproductive sensitivity phenotype can range from an application rate of about 1.0 pounds of acid equivalent per acre (about 1.12 kilograms per hectare) of glyphosate acid to about 2.25 pounds of acid equivalent per acre (i.e. about 2.52 kilograms per hectare) of glyphosate acid when the indicated amounts of glyphosate acid are provided in either a commercially available glyphosate formulation or when the indicated amounts of glyphosate acid is provided in a similar formulation suitable for application to glyphosate-tolerant crops. Commercially available glyphosate formulations that can be used include, but are not limited to, Roundup Original MAX®, Roundup PowerMAX®, Roundup UltraMax®, or RoundUp WeatherMAX® (Monsanto Co., St. Louis, Mo., USA); Touchdown IQ® or Touchdown Total® (Syngenta, Wilmington, Del., USA); Glyphomax®, Glyphomax Plus®, or Glyphomax XRT® (Dow Agrosciences LLC, Indianapolis, Ind., USA). In certain embodiments, the commercially available glyphosate formulation used is RoundUp WeatherMAX®. In certain embodiments, doses of glyphosate that can elicit a reproductive sensitivity phenotype can range from about a 2 fold application rate of about 42.6 ounces per acre RoundUp WeatherMax® (1.68 kilograms per hectare) to about a three fold application rate of about 63.9 ounces per acre RoundUp WeatherMax® (i.e. about 2.52 kilograms per hectare).


The reproductive sensitivity phenotype can be observed at an appropriate stage of reproductive development after herbicide application in certain soybean varieties comprising the transgene that confers glyphosate resistance. Glyphosate is typically applied during vegetative growth stages, where applications in later vegetative growth stages can typically elicit reproductive sensitivity at lower application rates. In certain embodiments of these methods, glyphosate can be applied in weekly intervals (i.e. once a week) for any of 2, 3, 4 or more successive weeks to score for the presence of the reproductive sensitivity phenotype. In certain embodiments, soybean plants at about the V3 vegetative development stage are exposed to an initial glyphosate spray followed by a subsequent spray at the V6 vegetative stage. In certain embodiments, soybean plants at about the V6 vegetative development stage are exposed to a glyphosate spray. As discussed herein, the vegetative stages of soybean are as follows: VE (emergence), VC (cotyledon stage), V1 (first trifoliolate leaf), V2 (second trifoliolate leaf), V3 (third trifoliolate leaf), V(n) (nth trifoliolate leaf), and V6 (flowering will soon start). As discussed herein, the reproductive stages of soybean are as follows R1 (beginning bloom, first flower); R2 (full bloom, flower in top 2 nodes); R3 (beginning pod, 3/16″ pod in top 4 nodes); R4 (full pod, ¾″ pod in top 4 nodes); R5 (⅛″ seed in top 4 nodes); R6 (full size seed in top 4 nodes); R7 (beginning maturity, one mature pod); and, R8 (full maturity, 95% of pods on the plant are mature). A description of the soybean vegetative and reproductive stages can be found on the world wide web (internet) at ag.ndsu.edu/pubs/plantsci/rowcrops/a1174/a1174w.htm (North Dakota State University publication A-1174, June 1999, Reviewed and Reprinted August 2004). Expression of the reproductive sensitivity trait can also be influenced by temperature, where the trait in varieties that display the reproductive sensitivity phenotype is more pronounced following treatment at temperatures of about 32 degrees Celsius or more.


A rating scale that evaluates the degree of reproductive sensitivity can also be employed to identify “tolerant” and “sensitive” plants. An exemplary and non limiting scale for evaluating the reproductive sensitivity phenotype is as follows, where the low numbers correspond to a “glyphosate reproductive tolerance” phenotype and the high numbers correlate to a “glyphosate reproductive sensitivity” phenotype where sterility is monitored as follows:

    • A rating scale of 1: Less than 10% of plants show sterility (glyphosate reproductive tolerance)
    • A rating scale of 2: Less than 10-50% of plants show sterility
    • A rating scale 3: Greater than 50% of plants show sterility (glyphosate reproductive sensitivity)


      Soybean plant sterility can be measured by a variety of methods that include, but are not limited to, determining pollen counts, seed yield per plant, seed yield per pod, and the like. Controls used to determine glyphosate reproductive sensitivity or tolerance of a given transgenic soybean test plant comprising a transgenic insertion event that confers glyphosate resistance in a certain genetic background (i.e. genotype) in comparison tests include, but are not limited to, (a) co-cultivated soybean plants comprising the same transgenic insertion event in a genetic background that provides for glyphosate reproductive sensitivity; and/or (b) co-cultivated soybean plants comprising the same transgenic insertion event in a genetic background that provides for glyphosate reproductive tolerance, where the test and control plants are sprayed with glyphosate. Additional controls used to determine glyphosate reproductive sensitivity or tolerance can also include, but are not limited to, co-cultivated soybean plants of the same genotypes (i.e soybean plants that are isogenic with respect to both the transgenic insertion event and genetic background as either the test or control soybean lines) that are not sprayed with glyphosate.


      Introgression of a Genomic Region Associated with a Dicamba Tolerance Phenotype


Also provided herewith is unique soybean germplasm comprising an introgressed genomic region that is associated with a dicamba tolerance phenotype and methods of obtaining the same. Marker-assisted introgression involves the transfer of a chromosomal region, defined by one or more markers, from one germplasm to a second germplasm. Offspring of a cross that contain the introgressed genomic region can be identified by the combination of markers characteristic of the desired introgressed genomic region from a first germplasm (i.e. such as a dicamba tolerance germplasm) and both linked and unlinked markers characteristic of the desired genetic background of a second germplasm (i.e. a dicamba intolerance germplasm). In addition to the markers provided herewith that identify alleles of genomic region that is associated with a dicamba tolerance phenotype, flanking markers that fall on both the telomere proximal end of the genomic region on linkage group L (chromosome 19) and the centromere proximal end of the linkage group L (chromosome 19) genomic region are also provided in Tables 1 and 2. Table 2 is provided at the end of the specification immediately before the claims. Such flanking markers are useful in a variety of breeding efforts that include, but are not limited to, introgression of the genomic region associated with a dicamba tolerance phenotype into a genetic background comprising markers associated with germplasm that ordinarily contains the allelic forms of the genomic region that is associated with a “Dicamba intolerance” phenotype. Telomere proximal flanking markers that can be used in these methods include, but are not limited to, asmbl_11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO: 2), BI967232 (SEQ ID NO: 3), and/or polymorphisms in any of the loci listed in Table 2 of the Specification located between starting base 16426 (the telomere proximal base) of locus asmbl_11856 and starting base 92334 of locus M0205928 (SEQ ID NO: 4). Centromere proximal flanking markers that can be used in these methods include, but are not limited to, M0205537 (SEQ ID NO: 15), M0202715 (SEQ ID NO: 16), M0206286 (SEQ ID NO: 17), M0206054 (SEQ ID NO: 18) and M0205375 (SEQ ID NO: 19) and/or polymorphisms in any of the other loci listed in Table 2 that are centromere proximal to BU765955 (SEQ ID NO: 12). Soybean plants wherein the two subregions that are respectively flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6 and by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) are selectively introgressed can be obtained by using the BU551345 (SEQ ID NO: 7), SATT723, and/or M0114388 (SEQ ID NO: 8) markers, or by using any of the markers located between these two subregions that are provided in Table 2. Any of the aforementioned polymorphisms can be identified by sequencing loci from dicamba intolerant and dicamba tolerance germplasms. Additional markers located on linkage group L (chromosome 19) and other chromosomes are disclosed in US Patent Application Publication 20090208964. Publicly available marker databases from which additional useful markers located on linkage group L (chromosome 19) and other chromosomes can be obtained include, but are not limited to, the soybase.org website on the internet that is administered by the United States Agricultural Research Service, the United States Department of Agriculture, and Iowa State University. Soybean plants or germplasm comprising an introgressed genomic region that is associated with a dicamba tolerance phenotype wherein at least 10%, 25%, 50%, 75%, 90%, or 99% of the remain genomic sequences carry markers characteristic of soybean plants or germplasm that are otherwise or ordinarily comprise a genomic region associated with the Dicamba intolerance phenotype are thus provided.


Soybean Plants Comprising Genomic Region Associated with the Dicamba Intolerance and Dicamba Tolerance Phenotypes and Transgenes that Confer Resistance to Dicamba


A non-limiting and exemplary list of soybean plants that comprise genomic regions associated with either a dicamba-intolerance or a dicamba tolerance phenotype are provided herewith in Table 3.









TABLE 3







Soybean varieties comprising a genomic region associated


with a dicamba tolerance or dicamba intolerant phenotype.
















ATCC






Variety
Depository
Date of


Branded
Dicamba
U.S. Pat.
Name in
Accession
Patent


Name 1
Phenotype
No.
Patent
Number 2
Issue





AG3102
Intolerant
7,964,777
7629164
PTA-10825
Jun. 21, 2011


AG3603
Intolerant
7,592,516
D4328762
PTA-9797
Sep. 22, 2009


AG4903







AG4907
Intolerant
7,687,685
D5703684
PTA-10153
Mar. 30, 2010


AG0803
Tolerant
7,498,489
4498438
PTA-9064



AG3102
Tolerant
7,964,777
7629164
PTA-10825
Jun. 21, 2011


AG3603
Tolerant
7,592,516
D4328762
PTA-9797
Sep. 22, 2009


BBL3606N0R







BL3307M2-







D0RL







AG4903







AG4907
Tolerant
7,687,685
D5703684
PTA-10153
Mar. 30, 2010


260744-14







AFL0506C0R
Tolerant
7,723,583
D5864369
PTA-10719
May 25, 2010


AG0808
Tolerant
7,732,672
D5142326
PTA-10168
Jun. 8, 2010


263619-24







4065735-51







5463213-25







AG1002
Tolerant
7,294,770
5826175
PTA-8148
Nov. 13, 2007


AG1403
Tolerant
7,557,273
6943322
PTA-9554
Jul. 7, 2009


AG1406
Tolerant
7,732,673
D5232589
PTA-10268
Jun. 8, 2010


CSR1920
Tolerant
7,728,199
7821295
PTA-10519
Jun. 1, 2010


15733-79-59







5081541-27







5464705-06







AG2110
Tolerant
7,678,965
D5624834
PTA-10134
Mar. 16, 2010


AG2606
Tolerant
7,622,644
D4201139
PTA-9749
Nov. 24, 2009


AG2909
Tolerant
7,999,153
D5502014
PTA-11081
Aug. 16, 2011


AG2921V
Tolerant
7,390,940
4858197
PTA-9072
Jun. 24, 2008


AG3021V
Tolerant
7,572,958
D4361423
PTA-9801
Aug. 11, 2009


BOX2906H0R







DFN3306B0R
Tolerant
7,626,089
D4311702
PTA-9781
Dec. 1, 2009


CSRS4782N
Tolerant
7,700,847
D5898941
PTA-10598
Apr. 20, 2010


GL4807A2-
Tolerant
7,868,230
D5523145
PTA-11362
Jan. 11, 2011


D0RN






1 Branded names of Asgrow ® (designated “AG”) and DEKALB ® soybean varieties from Monsanto Co. 800 N. Lindbergh Blvd., St. Louis, MO, USA.




2 Deposit numbers of seed available through the American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, Va., USA, 20110-2209.




3 Dicamba phenotype is the phenotype observed in the indicated germplasm containing a transgene that confers resistance to dicamba when exposed to dicamba.







Also provided herewith are additional soybean plants that comprising a genomic region associated with a dicamba intolerant or dicamba tolerance phenotype that are identified by use of the markers provided in Table 1 and/or Table 2 and/or methods provided herein. Any of the soybean plants identified in Table 3 or other soybean plants that are otherwise identified using the markers or methods provided herein can be used in methods that include, but are not limited to, methods of obtaining soybean plants with an introgressed dicamba tolerance locus, obtaining a soybean plant that exhibits a dicamba tolerance phenotype, or obtaining a soybean plant comprising in its genome a genetic region associated with a dicamba tolerance phenotype.


In certain embodiments, the soybean plants provided herein or used in the methods provided herein can comprise a transgene that confers resistance to dicamba. In certain embodiments, the dicamba tolerant soybean plants can comprise a transgene encoding a dicamba-degrading dicamba monoxygenase (DMO) enzyme that catalyzes the conversion of herbicidal dicamba (3,6-dichloro-o-anisic acid) to a non-toxic 3,6-dichlorosalicylic acid. In certain embodiments, the dicamba-degrading dicamba monoxygenase (DMOw) comprise a DMO enzyme disclosed in U.S. Pat. Nos. 7,022,896, 7,105,724, and 7,812,224, each incorporated herein by reference in their entireties. Exemplary and non-limiting DMOw dicamba monooxygenase encoding nucleic acid and protein sequences are provided herewith as SEQ ID NO: 20 and SEQ ID NO: 21. In certain embodiments, the dicamba tolerant soybean plants can comprise a dicamba monoxygenase variant which exhibits improved catalytic parameters such as increased turnover number and/or a lower km for the substrate, improved catalysis at lower pH values, and/or improved catalysis at higher temperatures relative to an unaltered dicamba monooxygenase. In certain embodiments, the dicamba monoxygenase variant comprises a DMOc variant enzyme disclosed in U.S. Pat. No. 7,884,262, incorporated herein by reference in its entirety. Exemplary and non-limiting DMOc dicamba monooxygenase variant encoding nucleic acid and protein sequences are provided herewith as SEQ ID NO: 22 and SEQ ID NO: 23. In certain embodiments, a dicamba monooxygenase is operably linked to a chloroplast transit peptide (CTP). Operable linkage of certain CTPs to DMO is disclosed in U.S. Pat. No. 8,084,666, which is incorporated herein by reference in its entirety. In certain embodiments, it is contemplated that the soybean plants used herein can comprise one or more specific genomic insertion(s) of a dicamba tolerant transgene including, but not limited to, as those found in MON87708 soybean (deposited under ATCC accession number PTA-9670 and described in US Patent Application Publication Number 20110067134).


In certain embodiments, the soybean plants provided herein or used in the methods provided herein can comprise a transgene that confers tolerance to glyphosate. Transgenes that can confer tolerance to glyphosate include, but are not limited to, transgenes that encode glyphosate tolerant Class I EPSPS (5-enolpyruvylshikimate-3-phosphate synthases) enzymes or glyphosate tolerant Class II EPSPS (5-enolpyruvylshikimate-3-phosphate synthases) enzymes. Useful glyphosate tolerant EPSPS enzymes provided herein are disclosed in U.S. Pat. Nos. 6,803,501, RE39,247, 6,225,114, 5,188,642, and 4,971,908. In certain embodiments, the glyphosate tolerant soybean plants can comprise a transgene encoding a glyphosate oxidoreductase or other enzyme which degrades glyphosate. Glyphosate oxidoreductase enzymes had been described in U.S. Pat. No. 5,776,760 and U.S. Reissue Pat. RE38,825. In certain embodiments the soybean plant can comprise a transgene encoding a glyphosate N-acetyltransferase gene that confers tolerance to glyphosate. In certain embodiments, the soybean plant can comprise a glyphosate n-acetyltransferase encoding transgene such as those described in U.S. Pat. No. 7,666,644. In still other embodiments, soybean plants comprising combinations of transgenes that confer glyphosate tolerance are provided. Soybean plants comprising both a glyphosate resistant EPSPS and a glyphosate N-acetyltransferase are also provided herewith. In certain embodiments, it is contemplated that the soybean plants used herein can comprise one or more specific genomic insertion(s) of a glyphosate tolerant transgene including, but not limited to, as those found in: i) MON89788 soybean (deposited under ATCC accession number PTA-6708 and described in US Patent Application Publication Number 20100099859), ii) GTS 40-3-2 soybean (Padgette et al., Crop Sci. 35: 1451-1461, 1995), iii) event 3560.4.3.5 soybean (seed deposited under ATCC accession number PTA-8287 and described in US Patent Publication 20090036308), or any combination of i (MON89788 soybean), ii (GTS 40-3-2 soybean), and iii (event 3560.4.3.5 soybean).


In certain embodiments, the gene that confers resistance to dicamba is a gene encoding a Dicamba monooxygenase (DMO). The DMO gene is a microbial gene that has been transformed into soybean and cotton to confer tolerance to the dicamba herbicide. The DMO protein expressed in the plants transformed with the DMO gene actively metabolizes dicamba to 3,6-dichloro salicylic acid (DCSA), which lacks herbicidal activity. In certain embodiments, Dicamba resistant (DR) soybeans can be crossed with “RoundUp Ready 2 Yield™” (RR2Y) soybeans to generate a stack (RR2YxDR) which can confer resistance to both dicamba and glyphosate. It has been observed in certain germplasms that a herbicide traits (i.e. transgene conferred glyphosate and dicamba resistance)×germplasm interaction can result in increased sensitivity to dicamba (i.e. “dicamba intolerance”) that may be commercially undesirable. In certain embodiments, favorable haplotypes are provided herein which are associated with robust tolerance to dicamba and glyphosate, and which are useful for selection of RR2YxDR soybeans that do not exhibit dicamba intolerance.


In certain embodiments, it is contemplated that genotypic assays that provide for non-destructive identification of the plant or plants can be performed either in seed, the emergence stage, the “VC” stage (i.e. cotyledons unfolded), the V1 stage (appearance of first node and unifoliate leaves), the V2 stage (appearance of the first trifoliate leaf), and thereafter. In certain embodiments, non-destructive genotypic assays are performed in seed using apparati and associated methods as described in U.S. Pat. Nos. 6,959,617; 7,134,351; 7,454,989; 7,502,113; 7,591,101; 7,611,842; and 7,685,768, which are incorporated herein by reference in their entireties. In certain embodiments, non-destructive genotypic assays are performed in seed using apparati and associated methods as described in US Patent Application Publications 20100086963, 20090215060, and 20090025288, which are incorporated herein by reference in their entireties. Published U.S. Patent Applications US 2006/0042527, US 2006/0046244, US 2006/0046264, US 2006/0048247, US 2006/0048248, US 2007/0204366, and US 2007/0207485, which are incorporated herein by reference in their entirety, also disclose apparatus and systems for the automated sampling of seeds as well as methods of sampling, testing and bulking seeds. Thus, in a certain embodiments, any of the methods provided herein can comprise screening for markers in individual seeds of a population wherein only seed with at least one genotype of interest is advanced.


Soybean Plants Comprising a Genomic Region Associated with Stacked Transgenic Trait Improvement and Transgenes that Confer Resistance to Other Herbicides and/or Insects


In certain embodiments, soybean plants comprising a genomic region associated with stacked transgenic trait improvement (or the dicamba tolerance phenotype) and at least one additional herbicide resistance transgene selected from the group consisting of a dicamba resistance conferring transgene, a 2,4-D resistance conferring transgene, and a glufosinate resistance conferring transgene and/or at least one transgene encoding a product that confers insect resistance selected from the group consisting of a dsRNA that inhibits a target gene of an insect pest, a patatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, a Bacillus laterosporous insecticidal protein, a Bacillus sphaericus insecticidal protein, and a lignin are provided herein. Such transgenic trait improvements that can occur in plants comprising the genomic regions provided herein can be ascertained by comparing transgenic trait performance in varieties containing the genomic regions to the transgenic trait performance in other varieties lacking the genomic region. Such transgenic herbicide resistance trait improvements that can occur in plants comprising the genomic regions provided herein can include, but are not limited to, decreased phytotoxicity upon herbicide exposure in varieties containing the genomic regions conferring the improved transgenic trait performance and the corresponding herbicide resistance conferring transgene in comparison to other varieties lacking the genomic region and the corresponding herbicide resistance conferring transgene upon herbicide exposure. Various dsRNAs that inhibit a target gene of an insect pest are described in US Patent Application Publication Number 20120137387, which is specifically incorporated herein by reference in its entirety. A Bacillus thuringiensis insecticidal protein can be any of a number of insecticidal proteins including but not limited to a Cry1, a Cry3, a TIC851, a CryET70, a Cry22, a TIC901, a TIC1201, a TIC407, a TIC417, a binary insecticidal protein CryET33 and CryET34, a binary insecticidal protein CryET80 and CryET76, a binary insecticidal protein TIC100 and TIC101, a binary insecticidal protein PS149B1, a VIP insecticidal protein, a TIC900 or related protein, or combinations of the insecticidal proteins ET29 or ET37 with insecticidal proteins TIC810 or TIC812, and insecticidal chimeras of any of the preceding insecticidal proteins. A Bacillus thuringiensis insecticidal protein can be any of a number of insecticidal proteins including but not limited to a Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ad, Cry1Ae, Cry1Ba, Cry1Bb, Cry1Ca, Cry1Cb, Cry1Da, Cry1Db, Cry1Ea, Cry1Eb, Cry1Fa, Cry1Fb, Cry1Ga, Cry1Ha, Cry2Aa, Cry2Ab, Cry1Ja, Cry1 Ka, Cry11 Aa, Cry11Ab, Cry12Aa, Cry3Ba, Cry3Bb, Cry3C, Cry4a, Cry4Ba, Cry5a, Cry5Ab, Cry6Aa, Cry6Ba, Cry7Aa, Cry7Ab, Cry8Aa, Cry8Ba, Cry8Ca, Cry9Aa, Cry9Ba, Cry9Ca, Cry10Aa, Cry11Aa, Cry12Aa, Cry13Aa, Cry14Aa, Cry15Aa, Cyt1Aa, and Cyt2Aa protein or an insecticidal chimeras thereof. Insecticidal chimeras of certain Bacillus thuringiensis insecticidal proteins include, but are not limited to, Cry1A/F and other chimeras disclosed in US Patent Application Publication No. 20090143298. Such transgenic insect resistance trait improvements that can occur in plants comprising the genomic regions provided herein can include, but are not limited to, decreased insect-mediated plant damage, or increased insect death, inhibition, stunting, or cessation of insect feeding in varieties containing the genomic regions that confer the transgenic trait performance in comparison to other varieties lacking the genomic region.


Molecular Assisted Breeding Techniques


Genetic markers that can be used in the practice of the instant invention include, but are not limited to, are Restriction Fragment Length Polymorphisms (RFLP), Amplified Fragment Length Polymorphisms (AFLP), Simple Sequence Repeats (SSR), Single Nucleotide Polymorphisms (SNP), Insertion or Deletion Polymorphisms (Indels), Variable Number Tandem Repeats (VNTR), and Random Amplified Polymorphic DNA (RAPD), and others known to those skilled in the art. Marker discovery and development in crops provides the initial framework for applications to marker-assisted breeding activities (US Patent Applications 2005/0204780, 2005/0216545, 2005/0218305, and 2006/00504538). The resulting “genetic map” is the representation of the relative position of characterized loci (DNA markers or any other locus for which alleles can be identified) along the chromosomes. The measure of distance on this map is relative to the frequency of crossover events between sister chromatids at meiosis.


As a set, polymorphic markers serve as a useful tool for fingerprinting plants to inform the degree of identity of lines or varieties (U.S. Pat. No. 6,207,367). These markers form the basis for determining associations with phenotype and can be used to drive genetic gain. The implementation of marker-assisted selection is dependent on the ability to detect underlying genetic differences between individuals.


Certain genetic markers for use in the present invention include “dominant” or “codominant” markers. “Codominant markers” reveal the presence of two or more alleles (two per diploid individual). “Dominant markers” reveal the presence of only a single allele. The presence of the dominant marker phenotype (e.g., a band of DNA) is an indication that one allele is present in either the homozygous or heterozygous condition. The absence of the dominant marker phenotype (e.g., absence of a DNA band) is merely evidence that “some other” undefined allele is present. In the case of populations where individuals are predominantly homozygous and loci are predominantly dimorphic, dominant and codominant markers can be equally valuable. As populations become more heterozygous and multiallelic, codominant markers often become more informative of the genotype than dominant markers.


In another embodiment, markers that include, but are not limited to, single sequence repeat markers (SSR), AFLP markers, RFLP markers, RAPD markers, phenotypic markers, isozyme markers, single nucleotide polymorphisms (SNPs), insertions or deletions (Indels), single feature polymorphisms (SFPs, for example, as described in Borevitz et al. 2003 Gen. Res. 13:513-523), microarray transcription profiles, DNA-derived sequences, and RNA-derived sequences that are genetically linked to or correlated with dicamba tolerance loci, regions flanking dicamba tolerance loci, regions linked to dicamba tolerance loci, and/or regions that are unlinked to dicamba tolerance loci can be used in certain embodiments of the instant invention.


In one embodiment, nucleic acid-based analyses for determining the presence or absence of the genetic polymorphism (i.e. for genotyping) can be used for the selection of seeds in a breeding population. A wide variety of genetic markers for the analysis of genetic polymorphisms are available and known to those of skill in the art. The analysis may be used to select for genes, portions of genes, QTL, alleles, or genomic regions (Genotypes) that comprise or are linked to a genetic marker that is linked to or correlated with dicamba tolerance loci, regions flanking dicamba tolerance loci, regions linked to dicamba tolerance loci, and/or regions that are unlinked to dicamba tolerance loci can be used in certain embodiments of the instant invention.


Nucleic acid analysis methods provided herein include, but are not limited to, PCR-based detection methods (for example, TaqMan™ assays), microarray methods, mass spectrometry-based methods and/or nucleic acid sequencing methods. In one embodiment, the detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods. Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it. Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means.


A method of achieving such amplification employs the polymerase chain reaction (PCR) (Mullis et al. 1986 Cold Spring Harbor Symp. Quant. Biol. 51:263-273; European Patent 50,424; European Patent 84,796; European Patent 258,017; European Patent 237,362; European Patent 201,184; U.S. Pat. Nos. 4,683,202; 4,582,788; and 4,683,194), using primer pairs that are capable of hybridizing to the proximal sequences that define a polymorphism in its double-stranded form.


Methods for typing DNA based on mass spectrometry can also be used. Such methods are disclosed in U.S. Pat. Nos. 6,613,509 and 6,503,710, and references found therein. Polymorphisms in DNA sequences can be detected or typed by a variety of effective methods well known in the art including, but not limited to, those disclosed in U.S. Pat. Nos. 5,468,613, 5,217,863; 5,210,015; 5,876,930; 6,030,787; 6,004,744; 6,013,431; 5,595,890; 5,762,876; 5,945,283; 5,468,613; 6,090,558; 5,800,944; 5,616,464; 7,312,039; 7,238,476; 7,297,485; 7,282,355; 7,270,981 and 7,250,252 all of which are incorporated herein by reference in their entireties. However, the compositions and methods of the present invention can be used in conjunction with any polymorphism typing method to type polymorphisms in genomic DNA samples. These genomic DNA samples used include but are not limited to genomic DNA isolated directly from a plant, cloned genomic DNA, or amplified genomic DNA.


For instance, polymorphisms in DNA sequences can be detected by hybridization to allele-specific oligonucleotide (ASO) probes as disclosed in U.S. Pat. Nos. 5,468,613 and 5,217,863. U.S. Pat. No. 5,468,613 discloses allele specific oligonucleotide hybridizations where single or multiple nucleotide variations in nucleic acid sequence can be detected in nucleic acids by a process in which the sequence containing the nucleotide variation is amplified, spotted on a membrane and treated with a labeled sequence-specific oligonucleotide probe.


Target nucleic acid sequence can also be detected by probe ligation methods as disclosed in U.S. Pat. No. 5,800,944 where sequence of interest is amplified and hybridized to probes followed by ligation to detect a labeled part of the probe.


Microarrays can also be used for polymorphism detection, wherein oligonucleotide probe sets are assembled in an overlapping fashion to represent a single sequence such that a difference in the target sequence at one point would result in partial probe hybridization (Borevitz et al., Genome Res. 13:513-523 (2003); Cui et al., Bioinformatics 21:3852-3858 (2005). On any one microarray, it is expected there will be a plurality of target sequences, which may represent genes and/or noncoding regions wherein each target sequence is represented by a series of overlapping oligonucleotides, rather than by a single probe. This platform provides for high throughput screening a plurality of polymorphisms. A single-feature polymorphism (SFP) is a polymorphism detected by a single probe in an oligonucleotide array, wherein a feature is a probe in the array. Typing of target sequences by microarray-based methods is disclosed in U.S. Pat. Nos. 6,799,122; 6,913,879; and 6,996,476.


Target nucleic acid sequence can also be detected by probe linking methods as disclosed in U.S. Pat. No. 5,616,464, employing at least one pair of probes having sequences homologous to adjacent portions of the target nucleic acid sequence and having side chains which non-covalently bind to form a stem upon base pairing of the probes to the target nucleic acid sequence. At least one of the side chains has a photoactivatable group which can form a covalent cross-link with the other side chain member of the stem.


Other methods for detecting SNPs and Indels include single base extension (SBE) methods. Examples of SBE methods include, but are not limited, to those disclosed in U.S. Pat. Nos. 6,004,744; 6,013,431; 5,595,890; 5,762,876; and 5,945,283. SBE methods are based on extension of a nucleotide primer that is adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. In certain embodiments, the SBE method uses three synthetic oligonucleotides. Two of the oligonucleotides serve as PCR primers and are complementary to sequence of the locus of genomic DNA which flanks a region containing the polymorphism to be assayed. Following amplification of the region of the genome containing the polymorphism, the PCR product is mixed with the third oligonucleotide (called an extension primer) which is designed to hybridize to the amplified DNA adjacent to the polymorphism in the presence of DNA polymerase and two differentially labeled dideoxynucleosidetriphosphates. If the polymorphism is present on the template, one of the labeled dideoxynucleosidetriphosphates can be added to the primer in a single base chain extension. The allele present is then inferred by determining which of the two differential labels was added to the extension primer. Homozygous samples will result in only one of the two labeled bases being incorporated and thus only one of the two labels will be detected. Heterozygous samples have both alleles present, and will thus direct incorporation of both labels (into different molecules of the extension primer) and thus both labels will be detected.


In another method for detecting polymorphisms, SNPs and Indels can be detected by methods disclosed in U.S. Pat. Nos. 5,210,015; 5,876,930; and 6,030,787 in which an oligonucleotide probe having a 5′ fluorescent reporter dye and a 3′ quencher dye covalently linked to the 5′ and 3′ ends of the probe. When the probe is intact, the proximity of the reporter dye to the quencher dye results in the suppression of the reporter dye fluorescence, e.g. by Forster-type energy transfer. During PCR forward and reverse primers hybridize to a specific sequence of the target DNA flanking a polymorphism while the hybridization probe hybridizes to polymorphism-containing sequence within the amplified PCR product. In the subsequent PCR cycle DNA polymerase with 5′→3′ exonuclease activity cleaves the probe and separates the reporter dye from the quencher dye resulting in increased fluorescence of the reporter.


In another embodiment, the locus or loci of interest can be directly sequenced using nucleic acid sequencing technologies. Methods for nucleic acid sequencing are known in the art and include technologies provided by 454 Life Sciences (Branford, Conn.), Agencourt Bioscience (Beverly, Mass.), Applied Biosystems (Foster City, Calif.), LI-COR Biosciences (Lincoln, Nebr.), NimbleGen Systems (Madison, Wis.), Illumina (San Diego, Calif.), and VisiGen Biotechnologies (Houston, Tex.). Such nucleic acid sequencing technologies comprise formats such as parallel bead arrays, sequencing by ligation, capillary electrophoresis, electronic microchips, “biochips,” microarrays, parallel microchips, and single-molecule arrays, as reviewed by R.F. Service Science 2006 311:1544-1546.


The markers to be used in the methods of the present invention should preferably be diagnostic of origin in order for inferences to be made about subsequent populations. Experience to date suggests that SNP markers may be ideal for mapping because the likelihood that a particular SNP allele is derived from independent origins in the extant populations of a particular species is very low. As such, SNP markers appear to be useful for tracking and assisting introgression of QTLs, particularly in the case of Genotypes.


EXAMPLES

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.


Example 1

Marker-assisted backcrossing (MABC) is a common breeding methodology to transfer a gene of interest into a desired recurrent parent. MABC was used to transfer both the dicamba resistance (DMO) transgene (U.S. Patent Appl. US20110067134) and the glyphosate resistant RoundUp Ready 2 Yield™ (RR2Y) CP4 genes (U.S. Pat. No. 7,632,985) into several recurrent parents. The process involved making three backcrosses to the recurrent parent and using genome wide markers to target the recovery of 95% or greater of the recurrent parent genome. In this process, markers were used to confirm the presence of the DMO and RR2Y CP4 genes and the absence of the RR1 CP4 gene. The haplotype at the dicamba tolerance locus for each recurrent parent was known.


Observations on MABC lines whose recurrent parents contained different haplotypes were made. For each MABC, there were several variants, with each variant tracing to a unique BC3F1 plant. The MABC lines were grown in spray trials at two locations throughout the United States with two replications at each location. Each line was planted in a paired, twelve foot plot. Each plot was sprayed at V3 with 0.75 lb a.e./acre of glyphosate and 1.0 lb a.e./acre dicamba followed by the same treatment at V6. Malformation was measured as the percentage of plants within a plot that were malformed. For each MABC, the data were averaged across variants, replications, and locations to place into one the following categories:


1. No malformation: No severe malformation detected


2. Malformation: >20% severe malformation


The data are presented in Table 4. The 6 MABC lines with a CCAATT or TTAATT haplotype all showed malformation whereas the 25 lines with the TTTTCC haplotype showed no malformation. These observations indicated that the presence of certain haplotypes at the dicamba tolerance locus in lines containing the DMO and RR2Y CP4 transgenes leads to malformation following dicamba treatment.









TABLE 4







Recurrent Parent Haplotypes and Malformation Phenotypes in


Response to Dicamba Application.













Recurrent
Number of
M



Response


Parent
Observations
G
M0101742
M0205350
M0102027
to Dicamba





AG3102
24
3
CC
AA
TT
Malformation





AG3603
30
3
CC
AA
TT
Malformation





BBL3606
30
3
CC
AA
TT
Malformation


N0R











BL3307M
30
3
CC
AA
TT
Malformation


2-D0RL











AG4903
36
4
TT
AA
TT
Malformation





AG4907
36
4
CC
AA
TT
Malformation





260744-14
24
0
TT
TT
CC
No Malformation





AFL0506
24
0
TT
TT
CC
No Malformation


C0R











AG0803
24
0
TT
TT
CC
No Malformation





AG0808
24
0
TT
TT
CC
No Malformation





263619-24
24
1
TT
TT
CC
No Malformation





4065735-51
24
1
TT
TT
CC
No Malformation





5463213-25
36
1
TT
TT
CC
No Malformation





AG1002
24
1
TT
TT
CC
No Malformation





AG1403
24
1
TT
TT
CC
No Malformation





AG1406
24
1
TT
TT
CC
No Malformation





CSR1920
36
1
TT
TT
CC
No Malformation





15733-79-59
30
2
TT
TT
CC
No Malformation





5081541-27
12
2
TT
TT
CC
No Malformation





5464705-06
30
2
TT
TT
CC
No Malformation





AG2110
36
2
TT
TT
CC
No Malformation





AG2606
29
2
TT
TT
CC
No Malformation





AG2909
30
2
TT
TT
CC
No Malformation





AG2921V
30
2
TT
TT
CC
No Malformation





AG3021V
30
3
TT
TT
CC
No Malformation





AG3803
30
3
TT
TT
CC
No Malformation





BOX2906
30
3
TT
TT
CC
No Malformation


H0R











AG3803
30
3
TT
TT
CC
No Malformation





DFN3306
24
3
TT
TT
CC
No Malformation


B0R











CSRS478
36
4
TT
TT
CC
No Malformation


2N











GL4807A
36
4
TT
TT
CC
No Malformation


2-D0RN















Example 2: Haplotypes Associated with a Malformation and Sterility Phenotypes for MG 6 and 7 BC2F3:4 Populations Upon Herbicide Application

The effect of different haplotypes on response to dicamba and glyphosate were evaluated by comparing MG6-7 BC2F3:4 lines that contained a CP4 transgene that confers tolerance to glyphosate and a DMO transgene that confers tolerance to dicamba. The recurrent parent of the population was RP1 that had the CCAACC haplotype for markers NS0101742, NS0205350, and NS0102027 markers, respectively. The donor parent of the population was DP1 that had a TTTTCC haplotype. During the breeding process, the haplotype for each line at the dicamba tolerance locus was not known. Markers were used to select for the absence of the RR1 CP4 gene, and for the presence of the RR2Y CP4 gene and the Dicamba resistance DMO gene. Table 5 describes the breeding history for this material.









TABLE 5







Breeding History for Plant Material in Example 2.











Gen.
Season
Year
Location
Breeding Activity





Cross
Winter
2007
Isabella, Puerto Rico
Cross


F1
Summer
2008
Isabella, Puerto Rico
Backcross


BC1F1
Winter
2008
Isabella, Puerto Rico
Backcross


BC2F1
Summer
2009
Isabella, Puerto Rico
Bulk


BC2F2
Winter
2009
Isabella, Puerto Rico
Bulk


BC2F3
Summer
2010
Mount Olive, NC
Single plant selection


BC2F4
Summer
2011
Mount Olive, NC
Progeny row









A total of 360 BC2F3:4 lines were grown in Mount Olive, N.C. in 2011. The lines were grown in a single four foot rows with one replication. The lines were sprayed with 0.75 lb a.e./acre of glyphosate at V3 plant stage followed by the same rate of glyphosate at V6 plant stage plus 0.5 lb a.e./acre of dicamba.


Rating Scales:


Malformation:


A rating of 1: Less than 10% of plants show malformation


A rating of 2: 10-50% of plants show malformation


A rating of 3: Greater than 50% of plants show malformation


Sterility:


A rating of 1: Less than 10% of plants show sterility


A rating of 2: 10-50% of plants show sterility


A rating of 3: Greater than 50% of plants show sterility


Table 6 shows the distribution of lines across the different rating classes.









TABLE 6







Malformation and Sterility Ratings for Soybean Populations.









Malformation Rating











1
2
3










Sterility Rating
Number of lines per rating class















1
154
18
3



2
58
61
52



3
2
2
10









The 51 lines that were rated “1” for malformation and “1” for sterility and the 62 lines that were rated “3” for malformation and “2” or “3” for sterility were genotyped for the three dicamba tolerance markers as shown in Table 7.









TABLE 7







Haplotypes Associated with a


Malformation and Sterility


Ratings for 51 Soybean Lines.









Line
Marker Haplotype
Rating












Number
M0101742
M0205350
M0102027
Malformation
Sterility





123
TT
TT
CC
1
1





124
CC
AA
CC
3
2





126
CC
AA
CC
3
2





128
TT
TT
CC
1
1





135
TT
TT
CC
1
1





136
CC
AA
CC
3
3





140
CC
AA
CC
3
2





141
TT
TT
CC
1
1





143
TT
TT
CC
1
1





144
CC
AA
CC
3
2





145
CC
AA
CC
3
2





149
CT
AT
CC
1
1





151
CC
AA
CC
3
2





154
CC
AA
CC
3
2





156
TT
TT
CC
1
1





157
CT
AT
CC
1
1





159
CC
AA
CC
3
2





160
CC
AA
CC
3
2





164
TT
TT
CC
1
1





171
CT
AT
CC
1
1





173
CC
AA
CC
3
2





184
CC
AA
CC
3
2





189
CC
AA
CC
3
2





193
CC
AA
CC
3
2





200
TT
TT
CC
1
1





201
CC
AA
CC
3
2





203
CC
AA
CC
3
2





204
CT
AT
CC
1
1





212
CC
AA
CC
3
2





213
TT
TT
CC
1
1





214
TT
TT
CC
1
1





216
CC
AA
CC
3
2





217
TT
TT
CC
1
1





218
TT
TT
CC
1
1





222
CT
AT
CC
3
2





223
CC
AA
CC
3
2





225
CT
AT
CC
1
1





228
TT
TT
CC
1
1





230
TT
TT
CC
1
1





234
CC
AA
CC
3
2





235
TT
TT
CC
1
1





243
CC
AA
CC
3
2





246
CC
AA
CC
1
1





251
CC
AA
CC
3
3





260
CC
AA
CC
3
3





261
CT
AT
CC
1
1





262
CT
AT
CC
3
3





264
CT
AT
CC
1
1





268
TT
TT
CC
1
1





274
CC
AA
CC
3
2





277
CC
AA
CC
3
2





280
CC
AA
CC
3
2





281
CC
AA
CC
3
2





290
CC
AA
CC
3
2





309
CC
AA
CC
1
1





314
CC
AA
CC
3
2





316
TT
TT
CC
1
1





317
CC
AA
CC
3
2





318
TT
TT
CC
1
1





319
TT
TT
CC
1
1





324
TT
TT
CC
1
1





329
CC
AA
CC
3
3





330
CC
AA
CC
1
1





331
CC
AA
CC
1
1





333
CC
AA
CC
3
2





334
CC
AA
CC
1
1





336
CC
AA
CC
3
2





337
CC
AA
CC
1
1





338
TT
TT
CC
1
1





340
CC
AA
CC
3
2





347
TT
TT
CC
1
1





348
TT
TT
CC
1
1





350
CT
AT
CC
3
2





352
CC
AA
CC
3
2





353
TT
TT
CC
1
1





362
CC
AA
CC
3
2





379
TT
TT
CC
1
1





380
TT
TT
CC
1
1





381
CC
AA
CC
3
2





382
CT
AT
CC
1
1





384
CC
AA
CC
3
2





385
CC
AA
CC
3
2





393
CT
AT
CC
1
1





396
TT
TT
CC
1
1





398
CC
AA
CC
3
2





399
CC
AA
CC
3
2





400
CC
AA
CC
3
2





408
CC
AA
CC
3
2





409
CC
AA
CC
3
2





411
TT
TT
CC
1
1





412
CC
AA
CC
3
2





417
TT
TT
CC
1
1





421
CC
AA
CC
3
2





433
CT
AT
CC
1
1





434
TT
TT
CC
1
1





435
TT
TT
CC
1
1





440
CC
AA
CC
3
2





446
CC
AA
CC
3
3





449
CC
AA
CC
3
3





452
TT
TT
CC
1
1





457
CC
AA
CC
3
3





460
CC
AA
CC
3
2





467
TT
TT
CC
1
1





468
CC
AA
CC
3
3





470
CC
AA
CC
3
2





488
CC
AA
CC
3
2





490
CC
AA
CC
3
2





494
CC
AA
CC
3
3





495
CC
AA
CC
3
2





500
CC
AA
CC
3
2





505
CC
AA
CC
3
2





510
TT
TT
CC
1
1





512
CC
AA
CC
1
1









The 34 lines with the TTTTCC haplotype had a rating of “1” for malformation and “1” for sterility as summarized in Table 8.









TABLE 8







Summary of Table 7.









No.
Rating











of
Malfor-
Steri-
Marker Haplotype












lines
mation
lity
M0101742
M0205350
M0102027





34
1
1
TT
TT
CC





59
3
2 or 3
CC
AA
CC





 7
1
1








10
1
1
CT
AT
CC





 3
3
2 or 3









Out of the 66 lines with the CCAACC haplotype, 59 had a rating of “3” for malformation and a rating of “2” or “3” for sterility. The 13 lines heterozygous for the markers had a range of ratings for malformation and sterility.


These results support the observations that certain haplotypes at the dicamba tolerance locus in lines containing the RR2Y CP4 and DMO transgenes causes sterility from glyphosate and malformation from dicamba applications made at the V6 plant stage


Example 3. Haplotypes Associated with a Malformation and Sterility Phenotypes for MG 3 and 4 Populations Upon Herbicide Application in Fontezuela, Argentina

The effect of different haplotypes on response to glyphosate were evaluated by measuring observing sterility in MG3 to MG4 lines in glyphosate spray trials in Fontezuela, Argentina in 2012. The lines were from populations known to segregate for markers at the dicamba tolerance locus based on parental haplotypes. During the breeding process, the haplotype for each line at the dicamba tolerance locus was not known. Table 9 describes the breeding history for this material.









TABLE 9







Breeding History for Plant Material in Example 3.











Gen.
Season
Year
Location
Breeding Activity





Cross
Winter or
2010
Isabella, Puerto Rico,
Cross



Summer

or Galena, MD



F1
Summer or
2010
Isabella, Puerto Rico
Bulk



Winter





F2
Winter
2011
Kunia, HI
Bulk


F3
Summer
2011
Stonington, IL
Single plant






selection


F4
Summer
2012
Fontezuela, Argentina
Progeny row









Markers were used to select for the absence of the RR1 CP4 gene, and for the presence of the RR2Y CP4 gene and the Dicamba resistance (DMO) gene. A total of 1,083 F3:4 lines across six populations were planted in 4 foot single row plots. Remnant seed from each line was used for genotyping the lines across two markers at the dicamba tolerance locus. The lines were sprayed with 1.125 lb a.e./acre of glyphosate at V3 plant stage followed by the same rate applied at V6. Sterility ratings were taken at maturity.


A rating of 1: Less than 10% of plants show sterility


A rating of 2: 10-50% of plants show sterility


A rating of 3: Greater than 50% of plants show sterility


The sterility ratings by haplotype class are shown in Table 10.









TABLE 10







Haplotypes Associated with sterility ratings


for Selected Soybean Populations.











Marker
Total
No. lines per



 Haplotype
No. of
 rating class













Population
M0101742
M0205350
Lines
1
2
3





POP1
TT
TT
42
42





CC
AA
27

10
17



CT
AT
25
 1
23
 1





POP2
TT
TT
83
83





TT
AA
23

 8
15



TT
AT
36

11
25





POP3
TT
TT
81
81





CC
AA
89

24
65



CT
AT
40
 4
27
 9





POP4
TT
TT
69
69





CC
AA
43
 1
 2
40



CT
AT
39
 1
27
11



TT
TT
75
75





TT
AA
62

 3
59



TT
AT
44

44






POP5
TT
TT
185 
185 





CC
AA
66

 2
64



CT
AT
54
 4
47
 3





Across
TT
TT
535 
535 
 0
 0


populations
CC
AA
225 
 1
38
186 


(POP1-5)
TT
AA
85
 0
11
74



CT
AT
158 
10
124 
24



TT
AT
80
 0
55
25









Lines with the TTTT haplotype for markers M0101742 and M0205350 did not show sterility across all populations. Nearly all lines with a CĆAA or TTAA haplotype had at least 10% of plants that showed sterility. It is not unexpected that some plants in these lines did no show sterility as some variation in the spray application or other environmental variations can influence the expression of sterility. Lines genotyped as CTAT or TTAT were segregating at the dicamba tolerance locus and progeny from these lines showed a range of response for sterility.


These results support the observations that certain haplotypes at the dicamba tolerance locus in lines containing the RR2Y CP4 and DMO transgenes causes sterility from glyphosate applications made at the V6 plant stage.


Example 4: Exemplary Marker Assays for Detecting Polymorphisms

In one embodiment, the detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods. Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it. Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means. Exemplary primers and probes for amplifying and detecting genomic regions associated with a dicamba tolerance phenotype are given in Table 11.









TABLE 11







Exemplary Assays for Detecting Polymorphisms
















SEQ ID
SEQ ID





Marker

NO
NO
SEQ ID



Marker or
SEQ NO
SNP
Forward
Reverse
NO
SEQ ID NO


Locus Name
ID:
Position
Primer
Primer
Probe 1
Probe 2
















asmbl_11856
1







TC122822
2







BI967232
3







M0205928
4







M01017423
5
1206
24
25
26
27


M0129138
6
218
28
29
30
31


BU551345
7







M0114388
8
502
32
33
34
35


BU551363
9







M02053504
10
148
36
37
38
39


M01020275
11
349
40
41
42
43


BU765955
12







M0093116
13
183
44
45
46
47


M0129925
14
328
48
49
50
51


M0205537
15







M0202715
16







M0206286
17







M0206054
18







M0205375
19







NGMAX008197032
52
201
53
54
55
56









Example 5: Oligonucleotide Probes Useful for Detecting Polymorphisms by Single Base Extension Methods

Oligonucleotides can also be used to detect or type the polymorphisms disclosed herein by single base extension (SBE)-based SNP detection methods. Exemplary oligonucleotides for use in SBE-based SNP detection are provided in Table 12. SBE methods are based on extension of a nucleotide primer that is hybridized to sequences adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. It is also anticipated that the SBE method can use three synthetic oligonucleotides. Two of the oligonucleotides serve as PCR primers and are complementary to the sequence of the locus which flanks a region containing the polymorphism to be assayed. Exemplary extension primers that can be used to type polymorphisms disclosed in this invention are provided in Table 12 in the column labeled “Probe (SBE)”. Following amplification of the region containing the polymorphism, the PCR product is hybridized with an extension primer which anneals to the amplified DNA adjacent to the polymorphism. DNA polymerase and two differentially labeled dideoxynucleoside triphosphates are then provided. If the polymorphism is present on the template, one of the labeled dideoxynucleoside triphosphates can be added to the primer in a single base chain extension. The allele present is then inferred by determining which of the two differential labels was added to the extension primer. Homozygous samples will result in only one of the two labeled bases being incorporated and thus only one of the two labels will be detected. Heterozygous samples have both alleles present, and will thus direct incorporation of both labels (into different molecules of the extension primer) and thus both labels will be detected. Exemplary forward and reverse SBE probes are provided in Table 12.









TABLE 12







Exemplary SBE Probes for Detecting Polymorphisms











Marker or Locus
Marker
SNP

Probe


Name
(SEQ ID NO)
Position
Probe (SBE)
(SEQ ID NO)





M0101742
 5
1206
TGACTAGCATGTATCTAT
26





ATGACTAACATGTATCTAT
27





M0129138
 6
218
TGTGTCCTATATGATCTT
30





TGTCCTGTATGATCTTA
31





M0114388
 8
502
AGTTGGGCTATGCAA
34





TGGGCTGTGCAAGTA
35





M0205350
10
148
AGTTTACACTTACAAATATT
38





AGAGTTTACACTTACATATATT
39





M0102027
11
349
ACCCCCCTTTTTT
42





ATTTTAACCCCCTTTTT
43





M0093116
13
183
CCAACACCAAACTA
46





CAACACCAAACAAA
47





M0129925
14
328
AGTAGTAGCTAGTGAAATA
50





AGCTAGTCAAATATTT
51





NGMAX008197032
52
201
TTGACAGCCTCTGGATAT
55





ACAGCCTCCGGATAT
56









Example 6: Haplotypes Associated with a Malformation and Sterility Phenotypes in MG 4 Populations Upon Herbicide Application

The effect of different haplotypes on response to dicamba and glyphosate were evaluated by comparing genetically similar lines that contained a CP4 transgene that confers tolerance to glyphosate and a DMO transgene that confers tolerance to dicamba. In 2010, two plants from each of fourteen BC1F2:4 lines, or families, across five backcross populations were harvested individually to develop pairs of BC1F4:6 lines from each family. The haplotype of each recurrent parent for each backcross population is shown in Table 13.









TABLE 13







Haplotypes Associated With Listed Recurrent Parent.









Backcross

Recurrent parent haplotype











population
Recurrent parent
M0101742
M0205350
M0102027





1
CBL3606Q0R
CC
AA
TT


2
AG4005
CC
AA
TT


3
CP4408A3-C0RN
CC
AA
TT


4
AG4907
CC
AA
TT


5
AG4630
TT
AA
TT









The donor parent for each population was A3244-RR2Y/A3525-DT that had a TTTTCC haplotype for markers M0101742, M0205350, and M0102027 markers, respectively. During the breeding process, the haplotype for each line at the dicamba tolerance locus was not known. Markers were used to select for the absence of the RR1 CP4 gene, and for the presence of the RR2Y CP4 gene and the Dicamba DMO gene. The BC1F4:5 rows were sprayed with glyphosate at the V6 plant growth stage in Quillota Chile where a pair of lines per family were rated for sterility to glyphosate. Table 14 describes the breeding history for this plant material.









TABLE 14







Breeding History for Plant Material in Example 6.











Gen.
Season
Year
Location
Breeding Activity





Cross
Winter
2007
Isabella, Puerto Rico
Cross


F1
Summer
2008
Isabella, Puerto Rico
Backcross


BC1F1
Winter
2008
Isabella, Puerto Rico
Bulk


BC1F2
Summer
2009
Evansville, IN,
Single plant selection





Stonington, IL, or






Galena, MD



BC1F2:
Summer
2010
Fontezuela, Argentina
Progeny row


3






BC1F2:
Summer
2010
Evansville, IN,
Single plant selection


4


Stonington, IL, or






Galena, MD



BC1F4:
Summer
2011
Quillota, Chile
Progeny row


5






BC1F4:
Summer
2011
Evansville, IN,
Spray trials


6


Stonington, IL,






Galena, MD, and






Stuttgart, AR









DNA was extracted from each line to generate haplotypes across three markers at the dicamba tolerance locus. The lines were evaluated across four locations in the United States (Stuttgart, Ark.; Stonington Ill.; Evansville, Ind.; and Galena, Md.) in 2011. At each location the lines were grown in four to five foot single-row plots replicated two times and one of seven different herbicide treatments were applied at different plant growth stages (V3 or V6) as described in Table 15.









TABLE 15







Herbicide Treatments (Glyphosate and Dicamba) and Concentrations


Applied at Plant Growth Stages (V3 or V6).











Herbicide






Treatment
Glyphosate
Dicamba
Glyphosate
Dicamba


Number
V3
V3
V6
V6





1
none
none
none
none


2
0.75 lb
none
none
none



a.e./acre





3
0.75 lb
none
1.5 lb
none



a.e./acre

a.e./acre



4
none
1.0 lb
none
none




a.e./acre




5
none
1.0 lb
none
1.0 lb




a.e./acre

a.e./acre


6
0.75 lb
1.0 lb
none
none



a.e./acre
a.e./acre




7
0.75 lb
1.0 lb
1.5 lb
1.0 lb



a.e./acre
a.e./acre
a.e./acre
a.e./acre










Rating Scale:


Malformation to dicamba was rated by the percentage of plants showing malformation Sterility to glyphosate was rated as:


A rating scale of 1: Less than 10% of plants show sterility


A rating scale of 2: Less than 10-50% of plants show sterility


A rating scale 3: Greater than 50% of plants show sterility


Data were averaged across replications and locations to place into following classes as described in Table 16.









TABLE 16







Haplotypes Associated with a Malformation and Sterility Phenotypes in Soybean


Sister Line Pedigrees in Response to Herbicide Treatment Protocols.













Reaction to






Glyphosate in

Treatment No.

















Back-cross

Quillota,
Marker haplotype
1
2
3
4
5
6
7













Population
Family
Chile
M0101742
M0205350
M0102027
Response






















1
1.1
N
TT
TT
CC
N
N
N
N
N
N
N




S
CC
AA
TT
N
N
S
N
M
N
M/S





2
2.1
S
CC
AA
TT
N
N
S
N
M
S
M/S




S
CC
AA
TT
N
N
S
N
M
N
M/S





3
3.1
N
TT
TT
CC
N
N
N
N
N
N
N




S
CC
AA
TT
N
N
S
N
M
N
M/S





4
4.1
S
CC
AA
TT
N
N
S
N
M
N
M/S




N
TT
TT
CC
N
N
N
N
N
N
N



4.2
S
CC
AA
TT
N
N
S
N
M
N
M/S




S
CC
AA
TT
N
N
S
N
M
N
M/S



4.3
S
CC
AA
TT
N
N
S
N
M
N
M/S




S
CC
AA
TT
N
N
S
N
M
N
M/S



4.4
S
CC
AA
TT
N
N
S
N
M
N
M/S




S
CC
AA
TT
N
N
S
N
M
N
M/S



4.5
S
CC
AA
TT
N
N
S
N
M
N
M/S




S
CC
AA
TT
N
N
S
N
M
N
M/S



4.6
N
TT
TT
CC
N
N
N
N
N
N
N




N
TT
TT
CC
N
N
N
N
N
N
N



4.7
N
TT
TT
CC
N
N
N
N
N
N
N




S
CC
AA
TT
N
N
S
N
M
N
M/S



4.8
S
CC
AA
TT
N
N
S
N
M
N
M/S




S
CC
AA
TT
N
N
S
N
M
N
M/S



4.9
S
CC
AA
TT
N
N
S
N
M
N
M/S




S
CC
AA
TT
N
N
S
N
M
N
M/S



4.10 
S
CC
AA
TT
N
N
S
N
M
N
M/S




S
CC
AA
TT
N
N
S
N
M
N
M/S





5
5.1
S
TT
AA
TT
N
N
S
N
M
N
M/S




N
TT
TT
CC
N
N
N
N
N
N
N





N = normal response to treatment: Average <1/= 1.25 sterility and/or </= 30% malformation


S = sterility to a glyphosate treatment: Average >1.25


M = malformation to a dicamba treatment >30% malformation


M/S = malformation dicamba and sterility to glyphosate in a combination treatment






Example 7: Selection for Absence of Sterility to Glyphosate Application and Recovery of the Favorable Haplotype

As described in Example 3, marker haplotypes corresponded to reaction to glyphosate application. There were several populations grown in Fontezuela, Argentina where plants sprayed with glyphosate were selected for reproductive tolerance to glyphosate in the absence of haplotype information on each line. Table 17 describes four populations that segregated for the haplotype based on parental haplotypes. Table 18 describes the number of lines grown and the number of lines selected.









TABLE 17







Four soybean populations that segregated for the preferred haplotype


based on parental haplotypes.












Parent 1
Parent 2














NGMAX-
M-
NGMAX-
M-




008197032
0205350
008197032
0205350


Population
Origin
(SEQ ID NO: 52)
(SEQ ID NO: 10)
(SEQ ID NO: 52)
(SEQ ID NO: 10)















1
AG4031/AG38
GG
AA
AA
TT



03-T0BAH









2
AG4130/AG49
AA
TT
GG
AA



07-T0BAH









3
BL3510A9-
AA
TT
GG
AA



D0AAC/AG49







07-T0BAH









4
EI4409C3-
GG
AA
AA
TT



D0YN/GL4807







A2-D0RN-







T0BAH
















TABLE 18







Number of soybean lines grown and the


number of soybean lines selected.









Population
No. Lines Grown
No. Lines Selected












1
165
2


2
92
9


3
200
10


4
260
25


Total
717
46









The 46 selected lines were subsequently genotyped and found to possess the favorable AATT haplotype. In addition, the lines were grown at Stonington, Ill. in 2012 and evaluated for herbicide response. The lines were sprayed with 1.0 lb a.e/acre dicamba and 1.5 lb a.e/acre glyphosate at the V6 plant stage and did not show malformation to dicamba or sterility to glyphosate. These results further support the ability to use glyphosate selection as a means to recover the favorable haplotype and tolerance to both glyphosate and dicamba.


Example 8. Comparison of Dicamba Tolerance in Different Haplotypes Containing a Dicamba Resistance Conferring Transgene

The effect of different haplotypes on response to dicamba was evaluated by comparing F2 families that contained the DMO transgene for dicamba resistance, but that lacked the CP4 transgene for glyphosate resistance. F2 plants across six different populations that were growing in Kunia, Hi. in 2012 were tissue sampled and genotyped for the CP4 and DMO transgenes and for markers NGMAX008197032 and M0205350. F2 plants that were fixed homozygous for the presence of DMO and absence of CP4 and that were fixed homozygous for a haplotype class were selected and harvested individually to create families. Table 19 shows the number of F2 families per haplotype class. The F2 families were evaluated for tolerance to dicamba in a greenhouse environment.









TABLE 19







Six soybean populations that segregated


for the preferred haplotype


based on parental haplotypes.











Haplotype Class












AATT1
GGAA2











Number of


POP
ORIGIN
F2 plants













5
A3525-A3244-BAH/A3431
8
10 





6
DKB31-51/A3525-A3244-BAH
3
3





8
AG4903/A3525-A3244-BAH
0
3





9
AG4907/A3525-A3244-BAH
2
2





12 
AG4903/(AG4903*2/A3525-
0
5



A3244-BAH)







13 
AG4907/GL4911A9-B0BAH
0
5






1An “AA” allele for NGMAX-008197032 (SEQ ID NO: 52) and a “TT” allele for



M020535(SEQ ID NO: 10) (i.e. “favorable” haplotype for dicamba tolerance).



2A “GG” allele for NGMAX-008197032 (SEQ ID NO: 52) and an “AA” allele for



M020535(SEQ ID NO: 10) (i.e. “unfavorable” haplotype for dicamba tolerance).






A comparison of dicamba tolerance in the plants from segregating populations of Table 19 having various “favorable” or “unfavorable” haplotypes of the indicated parental germplasm is provided in FIG. 1. Plants having the favorable haplotypes (i.e. an “AA” allele for NGMAX-008197032 (SEQ ID NO:52) and a “TT” allele for M020535 (SEQ ID NO: 10) showed consistently low dicamba injury (FIG. 1).


Example 9. Selection of Favorable Dicamba Tolerance Haplotypes with One or Two Spray Treatments

A comparison of selections of favorable and unfavorable dicamba tolerance haplotypes based on either one or two spray treatments was made. Transgenic soybean plants containing a dicamba resistance conferring transgene and various favorable or unfavorable haplotypes were treated with dicamba at a rate of 1 pound/acre at either: (a) the V3 and V6 stages; or (b) the V6 stage only. The results of this comparison are shown in FIG. 2. Selection of favorable haplotypes by using a single spray at V6 (dicamba 1 lb/a) was found to be as effective as selections with the combination of aV3 and a V6 spray treatment.


Having illustrated and described the principles of the present invention, it should be apparent to persons skilled in the art that the invention can be modified in arrangement and detail without departing from such principles.


Although the materials and methods of this invention have been described in terms of various embodiments and illustrative examples, it will be apparent to those of skill in the art that variations can be applied to the materials and methods described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.









TABLE 2







of the Specification











Locus/Display

Start
End
ADDITIONAL LOCUS


Name (1)
Source (2)
Base (3)
Base (4)
INFORMATION (5)














asmbl_11856
Vigna_
16426
16586
SEQ ID NO: 1



unguiculata





TA2790_3886
Phaseolus_
16423
17393
ADP-ribosylation factor



coccineus_


[Vigna unguiculata



release_2


(Cowpea)]


TA43459_3847
Glycine_
16434
18055
ADP-ribosylation factor 1



max_release_2


[Oryza sativa (Rice)]


TC276541
GMGI.071508
16434
18076
UniRef100_P36397






Cluster: ADP-ribosylation






factor 1; n = 1; Arabidopsis







thaliana|Rep: ADP-







ribosylation factor 1 -







Arabidopsis thaliana







(Mouse-ear cress) = partial






(38%)


CD392203
Glycine_
16216
18687
ADP-ribosylation factor



max_release_2


[Glycine max (Soybean)]


BQ610865
Glycine_
16327
18667
ADP-ribosylation factor 1



max_release_2


[Oryza sativa (Rice)]


EH046324
Arachis_
16405
18745
Cluster: ADP-ribosylation



stenosperma_


factor 1, n = 1, Arabidopsis



release_5



thaliana|Rep: ADP-







ribosylation factor 1 -







Arabidopsis thaliana







(Mouse-ear cress)


AW202311
Glycine_
16378
19070
ADP-ribosylation factor



max_release_2


[Glycine max (Soybean)]


TC242702
GMGI.071508
16234
20195
UniRef100_Q38JU3






Cluster: ADP ribosylation






factor 002; n = 2; core






eudicotyledons|Rep: ADP






ribosylation factor 002 -







Daucus carota (Carrot) =







complete


BI321678
Glycine_
17384
19066
ADP-ribosylation factor



max_release_2


[Zea mays (Maize)]


AW348317
Glycine_
16355
20097
ADP-ribosylation factor



max_release_2


[Glycine max (Soybean)]


EH042959
Arachis_
16401
20182
Cluster: ADP-ribosylation



stenosperma_


factor 1, n = 2,



release_5



Medicago|Rep: ADP-







ribosylation factor 1 -







Medicago truncatula







(Barrel medic)


TC20337
LJGI.070108
16420
20191
UniRef100_Q5QQ33






Cluster: ADP-ribosylation






factor 1, n = 2,







Medicago|Rep: ADP-







ribosylation factor 1 -







Medicago truncatula







(Barrel medic), complete


EH047563
Arachis_
16430
20182
Cluster: ADP-ribosylation



stenosperma_


factor 1, n = 2,



release_5



Medicago|Rep: ADP-







ribosylation factor 1 -







Medicago truncatula







(Barrel medic)


TA2789_3886
Phaseolus_
16436
20196
ADP-ribosylation factor 1-



coccineus_


like protein [Solanum



release_2



tuberosum (Potato)]



TA43462_3847
Glycine_
16229
20438
ADP-ribosylation factor



max_release_2


[Medicago sativa (Alfalfa)]


TA1120_34305
Lotus_
16522
20191
ADP-ribosylation factor



japonicus_


[Medicago sativa (Alfalfa)]



release_1





TA2306_3848
Glycine_
16442
20440
ADP-ribosylation factor



soja_release_2


[Medicago sativa (Alfalfa)]


TC273941
GMGI.071508
16426
20464
homologue to






UniRef100_Q38JU3






Cluster: ADP ribosylation






factor 002; n = 2; core






eudicotyledons|Rep: ADP






ribosylation factor 002 -







Daucus carota (Carrot) =







complete


TC238119
GMGI.071508
16455
20449
UniRef100_Q38JU3






Cluster: ADP ribosylation






factor 002; n = 2; core






eudicotyledons|Rep: ADP






ribosylation factor 002 -







Daucus carota (Carrot) =







complete


EG373880
Arachis_
17101
20182
Cluster: ADP-ribosylation



hypogaea_


factor 1, n = 2,



release_5



Medicago|Rep: ADP-







ribosylation factor 1 -







Medicago truncatula







(Barrel medic)


BF066818
Glycine_
17081
20378
ADP-ribosylation factor 1



max_release_2


[Populus tomentosa]


BF596154
Glycine_
17083
20397
ADP-ribosylation factor



max_release_2


[Hyacinthus orientalis






(Common hyacinth)]


AW760997
Glycine_
17116
20397
ADP-ribosylation factor



max_release_2


[Hyacinthus orientalis






(Common hyacinth)]


BF424079
Glycine_
17112
20417
ADP-ribosylation factor



max_release_2


[Hyacinthus orientalis






(Common hyacinth)]


AW596022
Glycine_
17121
20415
ADP-ribosylation factor 1



max_release_2


[Populus tomentosa]


TA43446_3847
Glycine_
17106
20436
ADP-ribosylation factor



max_release_2


[Hyacinthus orientalis






(Common hyacinth)]


TA43455_3847
Glycine_
17125
20452
ADP-ribosylation factor



max_release_2


[Hyacinthus orientalis






(Common hyacinth)]


BW595867
Lotus_
17418
20191
ADP-ribosylation factor



japonicus_


[Hyacinthus orientalis



release_1


(Common hyacinth)]


AW507598
Glycine_
17343
20437
ADP-ribosylation factor



max_release_2


[Hyacinthus orientalis






(Common hyacinth)]


TA43447_3847
Glycine_
17343
20445
ADP-ribosylation factor



max_release_2


[Hyacinthus orientalis






(Common hyacinth)]


TA43448_3847
Glycine_
17355
20438
ADP-ribosylation factor 1



max_release_2


[Populus tomentosa]


AW596189
Glycine_
17358
20442
ADP-ribosylation factor 1



max_release_2


[Populus tomentosa]


BI469983
Glycine_
17410
20438
ADP-ribosylation factor 1



max_release_2


[Populus tomentosa]


AW472058
Glycine_
18655
20160
ADP-ribosylation factor 1



max_release_2


[Daucus carota (Carrot)]


CB063805
Glycine_
18623
20432
ADP-ribosylation factor 1



max_release_2


[Populus tomentosa]


BM891090
GMGI.071508
18995
20429
homologue to






UniRef100_A7PRL9






Cluster: Chromosome






chr14 scaffold_27 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_27 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (42%)


BM731935
Glycine_
19949
20444
ADP-ribosylation factor 1



max_release_2


[Populus tomentosa]


AW695591
MTGI.071708
30054
31388
similar to






UniRef100_Q40542






Cluster: NPK2, n = 1,







Nicotiana tabacum|Rep:







NPK2 - Nicotiana tabacum






(Common tobacco), partial






(35%)


TC130040
MTGI.071708
30054
31482
similar to






UniRef100_A7PM42






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(30%)


TC122822
MTGI.071708
30054
34162
Protein kinase, Nuclear






transport factor 2. SEQ






ID NO: 2


Pvcon9203
Phaseolus_
31194
34247
UniRef100_A7PM42



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM42_VITVI






E-0


TA66103_3847
Glycine_
31879
34559
Protein kinase; Nuclear



max_release_2


transport factor 2






[Medicago truncatula






(Barrel medic)]


CA801261
GMGI.071508
33896
34304
similar to






UniRef100_Q40542






Cluster: NPK2; n = 1;







Nicotiana tabacum|Rep:







NPK2 - Nicotiana tabacum






(Common tobacco) = partial






(16%)


TC120073
MTGI.071708
35367
38178
Glycoside hydrolase,






family 28


NP004759
GMGI.071508
34976
39622
GB|AF128266.1|AAD4648






3.1 polygalacturonase PG1


AF128266
Glycine_
34980
39622
Polygalacturonase PG1



max_release_2


[Glycine max (Soybean)]


TA69799_3847
Glycine_
58988
65870
Ubiquitin-associated



max_release_2


[Medicago truncatula






(Barrel medic)]


TA7619_47247
Lotus_
63855
65940
Putative DNA cytosine



corniculatus_


methyltransferase Zmet3



release_1


related cluster


TA8711_34305
Lotus_
63855
65940
UBA-like [Medicago



japonicus_



truncatula (Barrel medic)]




release_1





TC34762
LJGI.070108
65619
65940
NA


Pvcon5587
Phaseolus_
65216
67090
UniRef100_A7PM76



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM76_VITVI






E-0


TA5046_3885
Phaseolus_
65808
67002
UBA-like [Medicago



vulgaris_



truncatula (Barrel medic)]




release_2





asmbl_11857
Vigna_
65951
67042
NA



unguiculata





TA58707_3847
Glycine_
66006
67253
UBA-like [Medicago



max_release_2



truncatula (Barrel medic)]



TC241193
GMGI.071508
66006
67253
similar to






UniRef100_A7PM76






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (38%)


BI967232
Glycine_
66170
67203
UBA-like [Medicago



max_release_2



truncatula (Barrel







medic)]. SEQ ID NO: 3


AV417590
LJGI.070108
66745
67090
similar to






UniRef100_A7PM76






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(19%)


AV768315
Lotus_
66699
67155
UBA-like [Medicago



japonicus_



truncatula (Barrel medic)]




release_1





TC32114
LJGI.070108
66699
67275
similar to






UniRef100_Q76KU6






Cluster: DNA






methyltransferase, n = 1,







Nicotiana tabacum|Rep:







DNA methyltransferase -







Nicotiana tabacum







(Common tobacco), partial






(20%)


TA1535_34305
Lotus_
66745
67277
UBA-like [Medicago



japonicus_



truncatula (Barrel medic)]




release_1





TA2793_47247
Lotus_
66745
67277
DNA methyltransferase



corniculatus_


related cluster



release_1





AV768911
Lotus_
66943
67155
Ubiquitin-associated



japonicus_


[Medicago truncatula



release_1


(Barrel medic)]


CB540531
Phaseolus_
73267
73561
UniRef100_A7PM74



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM74_VITVI






5.00E−27


BE347690
GMGI.071508
73509
73770
similar to






UniRef100_Q5VQL1-2






Cluster: Isoform 2 of






Q5VQL1; n = 1; Oryza







sativa Japonica Group|Rep:







Isoform 2 of Q5VQL1 -







Oryza sativa subsp.








japonica (Rice) = partial







(5%)


BE347690
Glycine_
73509
73822
WW/Rsp5/WWP;



max_release_2


Helicase = C-terminal






[Medicago truncatula






(Barrel medic)]


BE608496
GMGI.071508
73444
73947
similar to






UniRef100_A7PM74






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (16%)


AI416763
GMGI.071508
74073
74520
similar to






UniRef100_Q9SP26






Cluster: P72 DEAD box






protein; n = 1; Pisum







sativum|Rep: P72 DEAD







box protein - Pisum







sativum (Garden pea) =







partial (16%)


AI416763
Glycine_
74073
74743
ATP-dependent RNA



max_release_2


helicase-like protein DB10






[Nicotiana sylvestris (Wood






tobacco)]


BW615083
LJGI.070108
74256
74855
similar to






UniRef100_A7PM74






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(24%)


TA8332_34305
Lotus_
74256
75446
WW/Rsp5/WWP, Helicase,



japonicus_


C-terminal [Medicago



release_1



truncatula (Barrel medic)]



TC27807
LJGI.070108
74343
75446
similar to






UniRef100_Q9SP26






Cluster: P72 DEAD box






protein, n = 1, Pisum







sativum|Rep: P72 DEAD







box protein - Pisum







sativum (Garden pea),







partial (34%)


asmbl_11858
Vigna_
75228
75500
NA



unguiculata





TA60825_3847
Glycine_
74963
75981
P72 DEAD box protein



max_release_2


[Pisum sativum (Garden






pea)]


TC249436
GMGI.071508
74985
75966
similar to






UniRef100_Q9SP26






Cluster: P72 DEAD box






protein; n = 1; Pisum







sativum|Rep: P72 DEAD







box protein - Pisum







sativum (Garden pea) =







partial (12%)


TC269249
GMGI.071508
86882
87576
similar to






UniRef100_A7PM72






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (42%)


TA64136_3847
Glycine_
86882
89066
Putative



max_release_2


phosphate/phosphoenol-






pyruvate translocator






[Arabidopsis thaliana






(Mouse-ear cress)]


CO982132
Glycine_
87225
91497
Phosphate/phosphoenol-



max_release_2


pyruvate translocator






[Nicotiana tabacum






(Common tobacco)]


TC274531
GMGI.071508
87225
91497
similar to






UniRef100_A4UTS3






Cluster: Chloroplast






phosphoenolpyruvate/






phosphate translocator;






n = 1; Pisum sativum|Rep:






Chloroplast phosphoenol-






pyruvate/phosphate






translocator - Pisum







sativum (Garden pea) =







partial (53%)


Pvcon2802
Phaseolus_
87119
92616
UniRef100_A9PD12



vulgaris


Putative uncharacterized






protein n = 1 Tax = Populus







trichocarpa







RepID = A9PD12_POPTR






1.00E−121


TA4406_3885
Phaseolus_
89055
92616
Phosphate/phosphoenol-



vulgaris_


pyruvate translocator



release_2


[Nicotiana tabacum






(Common tobacco)]


TA74766_3847
Glycine_
91397
92725
Phosphoenolpyruvate/



max_release_2


phosphate translocator






[Mesembryanthemum







crystallinum (Common ice







plant)]


TC265023
GMGI.071508
91686
92725
similar to






UniRef100_A7PM71






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (15%)


M0205928
SEQ.
92718
92334
SEQ ID NO: 4



LISTING





BG406195
GMGI.071508
107039
107366



BG406195
Glycine_
107039
107375
NA



max_release_2





M0101742
SEQ.
112189
113483
SEQ ID NO: 5



LISTING





BG550728
GMGI.071508
112663
113757
weakly similar to






UniRef100_A7PM60






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (13%)


BG550728
Glycine_
112663
113867
Receptor-like



max_release_2


serine/threonine kinase






[Arabidopsis thaliana






(Mouse-ear cress)]


CV535605
Phaseolus_
112548
113982
UniRef100_A7PM60



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM60_VITVI






9.00E−79


M0129138
SEQ.
114532
113494
SEQ ID NO: 6



LISTING





BU551345
Glycine_
115956
116339
SEQ ID NO: 7



max_release_2





TA58315_3847
Glycine_
118318
120087
NA



max_release_2





TC236438
GMGI.071508
118318
120087
NA


BE611751
Glycine_
119165
119645
NA



max_release_2





BE611751
GMGI.071508
119229
119645
NA


TA70371_3847
Glycine_
137417
137864
Hypothetical protein



max_release_2


[Medicago truncatula






(Barrel medic)]


TC267549
GMGI.071508
137417
137864
similar to






UniRef100_Q9FI64






Cluster: Genomic DNA =






chromosome 5 = TAC






clone: K21I16; n = 1;







Arabidopsis thaliana|Rep:







Genomic DNA =






chromosome 5 = TAC






clone: K21I16 - Arabidopsis







thaliana (Mouse-ear cress) =







partial (43%)


BG156330
GMGI.071508
155872
156903
similar to






UniRef100_A7PM41






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 2; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (23%)


BG156330
Glycine_
155872
157058
WD40-like [Medicago



max_release_2



truncatula (Barrel medic)]



Pvcon10326
Phaseolus_
155691
157835
UniRef100_A7PM41



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM41_VITVI






3.00E−93


CD397113
Glycine_
157474
157813
NA



max_release_2





TA12653_34305
Lotus_
159489
161341
NADP-specific isocitrate



japonicus_


dehydrogenase [Lupinus



release_1



albus (White lupin)]



TC27381
LJGI.070108
159489
161341
similar to






UniRef100_Q7Y0W7






Cluster: NADP-specific






isocitrate dehydrogenase,






n = 1, Lupinus albus|Rep:






NADP-specific isocitrate






dehydrogenase - Lupinus







albus (White lupin), partial







(25%)


DT084057
Glycine_
161638
162192
NADP-specific isocitrate



soja_release_2


dehydrogenase [Lupinus







albus (White lupin)]



BE661051
Glycine_
170271
172034
Cyclin-like F-box



max_release_2


[Medicago truncatula






(Barrel medic)]


TA11305_34305
Lotus_
170700
172307
Cyclin-like F-box



japonicus_


[Medicago truncatula



release_1


(Barrel medic)]


TC34049
LJGI.070108
170700
172307
similar to






UniRef100_A7PF14






Cluster: Chromosome






chr11 scaffold_13, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr11






scaffold_13, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(32%)


NP7256876
MTGI.071708
171929
173188
GB|AC157983.16|ABE865






10.1 Cyclin-like F-box


TA68495_3847
Glycine_
194920
195696
Oleosin [Sesamum indicum



max_release_2


(Oriental sesame)






(Gingelly)]


TC265354
GMGI.071508
194920
195696
weakly similar to






UniRef100_P29530






Cluster: P24 oleosin






isoform A; n = 1; Glycine







max|Rep: P24 oleosin







isoform A - Glycine max






(Soybean) = partial (40%)


BE658264
Glycine_
195176
195925
Oleosin [Sesamum indicum



max_release_2


(Oriental sesame)






(Gingelly)]


CV539661
Phaseolus_
217885
218101
No significant hit (e-20)



vulgaris





CA912681
Phaseolus_
220374
220748

Arabidopsis thaliana




coccineus_


genomic DNA,



release_2


chromosome 3, P1 clone:






MGF10 [Arabidopsis







thaliana (Mouse-ear cress)]



CA785107
Glycine_
221393
221885
NA



soja_release_2





TC276537
GMGI.071508
221407
222104
weakly similar to






UniRef100_Q4RYK7






Cluster: Chromosome 3






SCAF14975 = whole






genome shotgun sequence;






n = 1; Tetraodon







nigroviridis|Rep:







Chromosome 3






SCAF14975 = whole






genome shotgun sequence -







Tetraodon nigroviridis







(Green puffer) = partial






(21%)


TA71044_3847
Glycine_
221407
222133
NA



max_release_2





CD406643
Glycine_
222113
222297
NA



max_release_






2





AV416316
LJGI.070108
223773
223869
similar to






UniRef100_A7PM35






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(9%)


EC911350
Phaseolus_
224587
225958
UniRef100_A5C233



vulgaris


Putative uncharacterized






protein n = 1 Tax = Vitis







vinifera







RepID = A5C233_VITVI






3.00E−77


BU760697
GMGI.071508
224857
225965
similar to






UniRef100_A7PM35






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (22%)


BU760697
Glycine_
224857
226145
Protein At5g19130



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


TC119982
MTGI.071708
224248
226812
Gaa1-like, GPI






transamidase component


CV541515
Phaseolus_
225934
226374
UniRef100_A7PM35



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM35_VITVI






2.00E−34


TA76349_3847
Glycine_
226118
226768
Protein At5g19130



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


TA12045_47247
Lotus_
226354
226789
GPAA1-like protein related



corniculatus_


cluster



release_1





TA13675_34305
Lotus_
226354
226789
Protein At5g19130



japonicus_


[Arabidopsis thaliana



release_1


(Mouse-ear cress)]


TC29330
LJGI.070108
226354
226789
similar to






UniRef100_A7PM35






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(13%)


NP7254537
MTGI.071708
233411
237212
GB|AC152349.11|ABP03404.1






Protein of unknown






function DUF266, plant


EH256962
GMGI.071508
235306
237649
similar to






UniRef100_A7PM54






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (33%)


CX708677
Glycine_
247269
248145
NA



max_release_2





BW599077
LJGI.070108
255475
261945
similar to






UniRef100_A7QD90






Cluster: Peptidyl-prolyl cis-






trans isomerase, n = 1, Vitis







vinifera|Rep: Peptidyl-







prolyl cis-trans isomerase -







Vitis vinifera (Grape),







partial (18%)


BW625918
LJGI.070108
257810
262980
similar to






UniRef100_Q93YQ8






Cluster: Peptidyl-prolyl cis-






trans isomerase, n = 1,







Arabidopsis thaliana|Rep:







Peptidyl-prolyl cis-trans






isomerase - Arabidopsis







thaliana (Mouse-ear cress),







partial (32%)


DT083826
Glycine_
260886
261121
NA



soja_release_2





CB063628
GMGI.071508
271592
271900
similar to






UniRef100_A7PM52






Cluster: Chromosome






chr14 scaffold_21 whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep: =






partial (2%)


CB063628
Glycine_
271592
271928
NA



max_release_2





TA5835_34305
Lotus_
273868
275906
Vegetative cell wall protein



japonicus_


gp1-like [Oryza sativa



release_1


(japonica cultivar-group)


TC32024
LJGI.070108
275152
275906
similar to






UniRef100_A7PM52






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(9%)


TC252667
GMGI.071508
275739
276506
similar to






UniRef100_A7PM52






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (12%)


AW311416
Glycine_
276269
276455
NA



max_release_2





WmFPC_

99810
475910
NA


Contig850






CV534998
Phaseolus_
288050
288585
UniRef100_A7PM50



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM50_VITVI






6.00E−39


TA75806_3847
Glycine_
288290
290376

Arabidopsis thaliana




max_release_2


genomic DNA =






chromosome 3 = P1 clone:






MGF10 [Arabidopsis







thaliana (Mouse-ear cress)]



TC276120
GMGI.071508
288290
290376
similar to






UniRef100_A7PM50






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (62%)


BI786388
GMGI.071508
291666
292088
similar to






UniRef100_A7PM49






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (7%)


BI786388
Glycine_
291666
292099
NA



max_release_2





TA63308_3847
Glycine_
291633
294397
NA



max_release_2





TC243765
GMGI.071508
293681
294426
weakly similar to






UniRef100_Q0JDM0






Cluster: Os04g0394300






protein; n = 1; Oryza sativa






Japonica Group|Rep:






Os04g0394300 protein -







Oryza sativa subsp.








japonica (Rice) = partial







(3%)


TA6412_34305
Lotus_
293803
294412
NA



japonicus_






release_1





TC24112
LJGI.070108
293803
294412
NA


CA899930
Phaseolus_
294054
294263
NA



coccineus_






release_2





TA3887_3886
Phaseolus_
302301
303033
Hypothetical protein



coccineus_


MJH23.3 [Arabidopsis



release_2



thaliana (Mouse-ear cress)]



AW705271
Glycine_
302299
303855
Hypothetical protein



max_release_2


MJH23.3 [Arabidopsis







thaliana (Mouse-ear cress)]



TC237313
GMGI.071508
303227
306007
similar to






UniRef100_A7PM30






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (54%)


TA61594_3847
Glycine_
303227
306056
Similarity to RNA binding



max_release_2


protein [Arabidopsis







thaliana (Mouse-ear cress)]



asmbl_11859
Vigna_
303952
305921
NA



unguiculata





toGm05
DAGchainer
30059
580791
Ks0.2335


BU544029
Glycine_
305220
305762
NA



max_release_2





TC23280
LJGI.070108
305373
305839
similar to






UniRef100_A7PM30






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(17%)


AI461058
Glycine_
305614
305834
NA



max_release_2





BE555571
Glycine_
305656
306011
NA



max_release_2





NGMAX008197032
SEQ.
314847
315148
SEQ ID NO: 52



LISTING





asmbl_11860
Vigna_
319622
320527
NA



unguiculata





EV270366
GMGI.071508
319893
320575
similar to






UniRef100_P15792






Cluster: Protein kinase






PVPK-1; n = 1; Phaseolus







vulgaris|Rep: Protein kinase







PVPK-1-Phaseolus







vulgaris (Kidney bean)







(French bean) = partial






(34%)


J04555
Phaseolus_
318937
322709
Protein kinase PVPK-1



vulgaris_


[Phaseolus vulgaris



release_2


(Kidney bean) (French






bean)]


TA11578_34305
Lotus_
320355
322024
Protein kinase PVPK-1



japonicus_


[Phaseolus vulgaris



release_1


(Kidney bean) (French






bean)]


TC35252
LJGI.070108
320355
322381
homologue to






UniRef100_P15792






Cluster: Protein kinase






PVPK-1, n = 1, Phaseolus







vulgaris|Rep: Protein kinase







PVPK-1 - Phaseolus







vulgaris (Kidney bean)







(French bean), partial






(48%)


Pvcon4227
Phaseolus_
320098
322709
UniRef100_P15792 Protein



vulgaris


kinase PVPK-1 n = 1






Tax = Phaseolus vulgaris






RepID = KPK1_PHAVU E-0


CA900819
Phaseolus_
325129
325547
Sucrase-like protein



coccineus_


[Arabidopsis thaliana



release_2


(Mouse-ear cress)]


CA900820
Phaseolus_
325119
328122
AT3g27570/MMJ24_12



coccineus_


[Arabidopsis thaliana



release_2


(Mouse-ear cress)]


TC269193
GMGI.071508
325136
329359
weakly similar to






UniRef100_A7PM27






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (47%)


TA4354_3885
Phaseolus_
325476
329154
AT5g40510/MNF13_30



vulgaris_


[Arabidopsis thaliana



release_2


(Mouse-ear cress)]


asmbl_11861
Vigna_
326881
329154
NA



unguiculata





CF920945
Glycine_
326967
329359
AT3g27570/MMJ24_12



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


SATT723

337605
337828



Satt723
ePCR
337605
337828
Map3.0 SSR L/Gm19 cM:






1.5


TC244213
GMGI.071508
354373
354996
similar to






UniRef100_A7PL06






Cluster: Chromosome chr7






scaffold_20 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr7






scaffold_20 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (17%)


BU090380
Glycine_
354683
354871
NA



max_release_2





BP058294
Lotus_
355950
356319
Protein ycf2 [Lotus



japonicus_



japonicus]




release_1





Pvcon2444
Phaseolus_
354593
360732
UniRef100_A7PL07



vulgaris


Chromosome chr7






scaffold_20, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PL07_VITVI






1.00E−144


asmbl_11862
Vigna_
359273
359896
NA



unguiculata





CA800649
Glycine_
377994
379933
AT3g01590/F4P13_13



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


TC245493
GMGI.071508
377994
381638
similar to






UniRef100_A7PM21






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (96%)


CO984617
Glycine_
379899
381537
At5g14500 [Arabidopsis



max_release_2



thaliana (Mouse-ear cress)]



M0114388
SEQ.
381308
380486
SEQ ID NO: 8



LISTING





AW704585
Glycine_
381210
381673
At5g14500 [Arabidopsis



max_release_2



thaliana (Mouse-ear cress)]



TC248588
GMGI.071508
383419
383857
NA


asmbl_11863
Vigna_
383428
384088
NA



unguiculata





TC126554
MTGI.071708
383593
384668
weakly similar to






UniRef100_Q940C3






Cluster:






AT3g27530/MMJ24_7,






n = 2, Arabidopsis







thaliana|Rep:







AT3g27530/MMJ24_7 -







Arabidopsis thaliana







(Mouse-ear cress), partial






(38%)


AJ002216
Pisum_
384088
384751
Emb|CAA07228.1



sativum_


[Arabidopsis thaliana



release_2


(Mouse-ear cress)]


BI702257
GMGI.071508
384067
384789
similar to






UniRef100_Q940C3






Cluster:






AT3g27530/MMJ24_7;






n = 2; Arabidopsis







thaliana|Rep:







AT3g27530/MMJ24_7 -







Arabidopsis thaliana







(Mouse-ear cress) = partial






(14%)


BG451913
MTGI.071708
386353
388007
similar to






UniRef100_Q9LT59






Cluster: Emb|CAA07228.1,






n = 1, Arabidopsis







thaliana|Rep:







Emb|CAA07228.1 -







Arabidopsis thaliana







(Mouse-ear cress), partial






(19%)


CV533025
Phaseolus_
388647
389345
UniRef100_UPI000016357



vulgaris


E GC6 (GOLGIN






CANDIDATE 6) binding/






protein transporter






Tax = n = 1






RepID = UPI000016357E






6.00E−27


AV777312
LJGI.070108
389152
391279
similar to






UniRef100_Q9LT59






Cluster: Emb|CAA07228.1,






n = 1, Arabidopsis







thaliana|Rep:







Emb|CAA07228.1 -







Arabidopsis thaliana







(Mouse-ear cress), partial






(19%)


BM187543
GMGI.071508
394984
395407
similar to






UniRef100_A7PM13






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (36%)


BM187543
Glycine_
394984
395559
Gb|AAF01546.1



max_release_2


[Arabidopsis thaliana






[Mouse-ear cress)]


DN652256
LJGI.070108
395487
395708
similar to






UniRef100_A7P4B1






Cluster: Chromosome chr1






scaffold_5, whole genome






shotgun sequence, n = 1,







Vitis vinifera|Rep:







Chromosome chr1






scaffold_5, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(19%)


DT044393
Arachis_
395462
395746
Cluster: Hypothetical



hypogaea_


protein T23K23.27, n = 1,



release_5



Arabidopsis thaliana|Rep:







Hypothetical protein






T23K23.27 - Arabidopsis







thaliana (Mouse-ear cress)



FD789910
Phaseolus_
395555
395927
UniRef100_A7P4B1



vulgaris


Chromosome chr1






scaffold_5, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7P4B1_VITVI






2.00E−59


EH259382
GMGI.071508
395577
396156
similar to






UniRef100_A7PM13






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (34%)


TA69305_3847
Glycine_
403237
404175
NA



max_release_2





TC243910
GMGI.071508
403237
404175
similar to






UniRef100_A7PM14






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (5%)


CA785084
Glycine_
403526
404055
NA



soja_release_2





CV541170
Phaseolus_
404688
406556
UniRef100_Q9LT57



vulgaris_


Emb|CAB45506.1 n = 1






Tax = Arabidopsis thaliana






RepID = Q9LT57_ARATH






1.00E−113


BF071095
GMGI.071508
406510
407127
similar to






UniRef100_Q9LT57






Cluster: Emb|CAB45506.1;






n = 1; Arabidopsis







thaliana|Rep:







Emb|CAB45506.1 -







Arabidopsis thaliana







(Mouse-ear cress) = partial






(8%)


BF071095
Glycine_
406527
407127
NA



max_release_2





BM270669
Glycine_
409910
410532
NA



max_release_2





BM270669
GMGI.071508
410045
410532
similar to






UniRef100_A7PM16






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (9%)


BG550673
GMGI.071508
421541
422250
similar to






UniRef100_A7PM12






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (26%)


BG550673
Glycine_
421541
422354
Hypothetical protein



max_release_2


F18O22_260 [Arabidopsis







thaliana (Mouse-ear cress)]



BU551363
Glycine_
422150
422745
SEQ ID NO: 9



max_release_2





CD407423
Glycine_
423719
423842
NA



max_release_2





M0205350
SEQ
424095
423776
SEQ ID NO: 10



Listing





EV270239
GMGI.071508
425649
426181
similar to






UniRef100_Q0WVR7






Cluster: TRNA synthase-






like protein; n = 1;







Arabidopsis thaliana|Rep:







TRNA synthase-like






protein - Arabidopsis







thaliana (Mouse-ear cress) =







partial (5%)


BI424448
GMGI.071508
451332
451679
similar to






UniRef100_P82353






Cluster: Non-specific lipid-






transfer protein 2; n = 1;







Prunus armeniaca|Rep:







Non-specific lipid-transfer






protein 2 - Prunus







armeniaca (Apricot) =







partial (68%)


TA49179_3847
Glycine_
451332
451827
Nonspecific lipid-transfer



max_release_2


protein 2 [Prunus







armeniaca (Apricot)]



TC252453
GMGI.071508
451397
451828
weakly similar to






UniRef100_Q43681






Cluster: Probable non-






specific lipid-transfer






protein AKCS9 precursor;






n = 1; Vigna







unguiculata|Rep: Probable







non-specific lipid-transfer






protein AKCS9 precursor -







Vigna unguiculata







(Cowpea) = partial (86%)


BE609938
Glycine_
451607
451756
Probable lipid transfer



max_release_2


protein family protein






[Tamarix androssowii]


BQ612382
Glycine_
451777
452217
NA



max_release_2





M0102027

466228
466889
SEQ ID NO: 11


Pvcon7917
Phaseolus_
466120
467338
UniRef100_A5C9E2



vulgaris


Putative uncharacterized






protein n = 1 Tax = Vitis







vinifera







RepID = A5C9E2_VITVI






6.00E−44


asmbl_11864
Vigna_
467520
468191
NA



unguiculata





TA49596_3847
Glycine_
470086
472059
Methionine aminopeptidase



max_release_2


2B [Arabidopsis thaliana






(Mouse-ear cress)]


TC255857
GMGI.071508
470086
476828
homologue to






UniRef100_A7PXX3






Cluster: Methionine






aminopeptidase; n = 1; Vitis







vinifera|Rep: Methionine







aminopeptidase - Vitis







vinifera (Grape) = partial







(91%)


FD792539
Phaseolus_
472774
475674
UniRef100_A7PXX3



vulgaris


Methionine aminopeptidase






n = 1 Tax = Vitis vinifera






RepID = A7PXX3_VITVI






5.00E−56


TA3829_3848
Glycine_
471918
476623
Methionine aminopeptidase



soja_release_2


2B [Arabidopsis thaliana






(Mouse-ear cress)]


BU765955
Glycine_
472787
475846
Methionine



max_release_2


aminopeptidase 2B






[Arabidopsis thaliana






(Mouse-ear cress)]. SEQ






ID NO: 12


EG530516
Arachis_
472835
476690
Cluster: Methionine



hypogaea_


aminopeptidase 2B, n = 1,



release_5



Arabidopsis thaliana|Rep:







Methionine aminopeptidase






2B - Arabidopsis thaliana






(Mouse-ear cress)


AV425234
LJGI.070108
475562
475924
homologue to






UniRef100_A7PXX3






Cluster: Methionine






aminopeptidase, n = 1, Vitis







vinifera|Rep: Methionine







aminopeptidase - Vitis







vinifera (Grape), partial







(22%)


TA49598_3847
Glycine_
474794
476709
Methionine aminopeptidase



max_release_2


2B [Arabidopsis thaliana






(Mouse-ear cress)]


FD797260
Phaseolus_
475768
476654
UniRef100_A7PXX3



vulgaris


Methionine aminopeptidase






n = 1 Tax = Vitis vinifera






RepID = A7PXX3_VITVI






6.00E−55


BE823844
Glycine_
475751
476828
Methionine aminopeptidase



max_release_2


2B [Arabidopsis thaliana






(Mouse-ear cress)]


BG726070
Glycine_
476668
476807
NA



max_release_2





BQ080926
GMGI.071508
480002
480636
similar to






UniRef100_A7PY54






Cluster: Chromosome






chr15 scaffold_37 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr15






scaffold_37 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (39%)


TA69442_3847
Glycine_
480002
481069
Hypothetical protein



max_release_2


F22I13.40 [Arabidopsis







thaliana (Mouse-ear cress)]



TC262427
GMGI.071508
480002
481069
similar to






UniRef100_A7P8Q6






Cluster: Chromosome chr3






scaffold_8 = whole genome






shotgun sequence; n = 1;







Vitis vinifera|Rep:







Chromosome chr3






scaffold_8 = whole genome






shotgun sequence - Vitis







vinifera (Grape) = partial







(20%)


BU548976
Glycine_
481474
481970
Multi antimicrobial



max_release_2


extrusion protein MatE






[Medicago truncatula






(Barrel medic)]


CX547082
Glycine_
481345
482173
Multi antimicrobial



max_release_2


extrusion protein MatE






[Medicago truncatula






(Barrel medic)]


TC236122
GMGI.071508
481300
482612
NA


TA57759_3847
Glycine_
481300
482627
Multi antimicrobial



max_release_2


extrusion protein MatE






[Medicago truncatula






(Barrel medic)]


AV420909
LJGI.070108
481846
482201
weakly similar to






UniRef100_A7QTE8






Cluster: Chromosome






undetermined scaffold_167,






whole genome shotgun






sequence, n = 1, Vitis







vinifera|Rep: Chromosome







undetermined scaffold_167,






whole genome shotgun






sequence - Vitis vinifera






(Grape), partial (24%)


AW597322
Glycine_
481965
482825
Multi antimicrobial



max_release_2


extrusion protein MatE






[Medicago truncatula






(Barrel medic)]


BM270610
Glycine_
482034
483008
Multi antimicrobial



max_release_2


extrusion protein MatE






[Medicago truncatula






(Barrel medic)]


BI972603
GMGI.071508
482632
483190
weakly similar to






UniRef100_A7P3G6






Cluster: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence; n = 1;







Vitis vinifera|Rep:







Chromosome chr1






scaffold_5 = whole genome






shotgun sequence - Vitis







vinifera (Grape) = partial







(20%)


BI972603
Glycine_
482632
484113
Multi antimicrobial



max_release_2


extrusion protein MatE






[Medicago truncatula






(Barrel medic)]


TA66198_3847
Glycine_
482595
484230
Multi antimicrobial



max_release_2


extrusion protein MatE






[Medicago truncatula






(Barrel medic)]


TC253566
GMGI.071508
482648
484405
weakly similar to






UniRef100_A7QTE8






Cluster: Chromosome






undetermined






scaffold_167 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome undetermined






scaffold_167 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (44%)


asmbl_11865
Vigna_
482937
484289
NA



unguiculata





BG881371
Glycine_
483075
484230
Multi antimicrobial



max_release_2


extrusion protein MatE






[Medicago truncatula






(Barrel medic)]


WmFPC_

384071
598745
NA


Contig7443






AW695419
MTGI.071708
491367
494466
similar to






UniRef100_A7PU69






Cluster: Chromosome chr7






scaffold_31, whole genome






shotgun sequence, n = 1,







Vitis vinifera|Rep:







Chromosome chr7






scaffold_31, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(11%)


BF645755
MTGI.071708
494870
497474
similar to






UniRef100_A7PU69






Cluster: Chromosome chr7






scaffold_31, whole genome






shotgun sequence, n = 1,







Vitis vinifera|Rep:







Chromosome chr7






scaffold_31, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(14%)


BE475242
GMGI.071508
497000
497327
similar to






UniRef100_A7NWE7






Cluster: Chromosome chr5






scaffold_2 whole genome






shotgun sequence; n = 1;







Vitis vinifera|Rep: = partial







(1%)


BE475242
Glycine_
497000
497549
Hypothetical protein



max_release_2


At3g23590/MDB19_8






[Arabidopsis thaliana






(Mouse-ear cress)]


BW611072
LJGI.070108
497387
497795
similar to






UniRef100_A7PU69






Cluster: Chromosome chr7






scaffold_31, whole genome






shotgun sequence, n = 1,







Vitis vinifera|Rep:







Chromosome chr7






scaffold_31, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(10%)


BQ613050
Glycine_
497409
498014
ORF protein [Arabidopsis



max_release_2



thaliana (Mouse-ear cress)]



CV541244
Phaseolus_
500143
500464
UniRef100_A9PGX2



vulgaris


Putative uncharacterized






protein n = 1 Tax = Populus







trichocarpa







RepID = A9PGX2_POPTR






3.00E−28


CX856527
Glycine_
501517
501735
NA



max_release_2





BG839076
Glycine_
503126
505209
F2P3.12 protein



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


FD790090
Phaseolus_
503370
505191
No significant hit (e-20)



vulgaris





TC236383
GMGI.071508
503107
505675
similar to






UniRef100_O82505






Cluster: Elongation factor






Ts; n = 1; Arabidopsis







thaliana|Rep: Elongation







factor Ts - Arabidopsis







thaliana (Mouse-ear cress) =







partial (32%)


TA56246_3847
Glycine_
503107
505848
Ethylene-responsive



max_release_2


elongation factor EF-Ts






precursor [Lycopersicon







esculentum (Tomato)]



TC239475
GMGI.071508
503126
506560
similar to






UniRef100_Q9SWW0






Cluster: Ethylene-






responsive elongation






factor EF-Ts precursor;






n = 1; Solanum







lycopersicum|Rep:







Ethylene-responsive






elongation factor EF-Ts






precursor Solanum







lycopersicum (Tomato)







(Lycopersicon







esculentum) = partial (74%)



TA56245_3847
Glycine_
505512
506546
Ethylene-responsive



max_release_2


elongation factor EF-Ts






precursor [Lycopersicon







esculentum (Tomato)]



BG839060
Glycine_
505661
506530
At4g11120 [Arabidopsis



max_release_2



thaliana (Mouse-ear cress)]



CV543527
Phaseolus_
508539
508771
Eukaryotic translation



vulgaris_


initiation factor 5



release_2


[Phaseolus vulgaris






(Kidney bean) (French






bean)]


CD393454
Glycine_
510651
511000
Ribosomal protein L22



max_release_2


[Glycine max (Soybean)]


TC245517
GMGI.071508
510651
511270
homologue to






UniRef100_O48879






Cluster: Ribosomal protein






L22; n = 1; Glycine







max|Rep: Ribosomal







protein L22 - Glycine max






(Soybean) = partial (80%)


asmbl_11866
Vigna_
510868
511269
NA



unguiculata





TA51206_3847
Glycine_
510702
512712
Ribosomal protein L22



max_release_2


[Glycine max (Soybean)]


TC249077
GMGI.071508
510771
512771
homologue to






UniRef100_O48879






Cluster: Ribosomal protein






L22; n = 1; Glycine







max|Rep: Ribosomal







protein L22 - Glycine max






(Soybean) = partial (98%)


BG316244
Glycine_
511015
512722
Ribosomal protein L22



max_release_2


[Glycine max (Soybean)]


BQ155270
MTGI.071708
513084
514936
similar to






UniRef100_A7PR59






Cluster: Chromosome






chr14 scaffold_26, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_26, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(52%)


TC30151
LJGI.070108
514647
516395
similar to






UniRef100_A7PR59






Cluster: Chromosome






chr14 scaffold_26, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_26, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(29%)


BP044357
Lotus_
514647
516409
S-locus protein 8 [Brassica



japonicus_



campestris (Field mustard)]




release_1





CB540591
Phaseolus_
514839
516355
No significant hit (e-20)



vulgaris





TA65114_3847
Glycine_
523413
524053
At1g22990/F19G10_22



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


TC259745
GMGI.071508
523413
524067
similar to






UniRef100_A7P3I8






Cluster: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence; n = 2;







Vitis vinifera|Rep:







Chromosome chr1






scaffold_5 = whole genome






shotgun sequence - Vitis







vinifera (Grape) = partial







(56%)


TA4332_47247
Lotus_
529321
530051
Actin-11 related cluster



corniculatus_






release_1





TA6031_34305
Lotus_
529321
530051
Actin [Striga asiatica]



japonicus_






release_1





TC32457
LJGI.070108
529321
530051
homologue to






UniRef100_P30167






Cluster: Actin-58, n = 1,







Solanum tuberosum|Rep:







Actin-58 - Solanum







tuberosum (Potato), partial







(39%)


AW351005
Glycine_
529380
530095
Actin [Striga asiatica]



max_release_2





TA43521_3847
Glycine_
529306
530175
Actin-11 [Arabidopsis



max_release_2



thaliana (Mouse-ear cress)]



asmbl_11867
Vigna_
529342
530189
NA



unguiculata





AU240079
LJGI.070108
529747
530013
homologue to






UniRef100_P93372






Cluster: Actin-66, n = 1,







Nicotiana tabacum|Rep:







Actin-66 - Nicotiana







tabacum (Common







tobacco), partial (25%)


AU240079
Lotus_
529747
530039
Actin-11 [Arabidopsis



japonicus_



thaliana (Mouse-ear cress)]




release_1





EE127018
Arachis_
529933
530285
Cluster: Hypothetical



hypogaea_


protein, n = 1, Oryza sativa



release_5


(indica cultivar-group)|Rep:






Hypothetical protein -







Oryza sativa subsp. indica







(Rice)


TC240040
GMGI.071508
529306
531078
homologue to






UniRef100_P02581






Cluster: Actin-1; n = 1;







Glycine max|Rep: Actin-1 -








Glycine max (Soybean) =







complete


AW666288
Glycine_
529980
530789
Actin [Phaseolus acutifolius



max_release_


(Tepary bean)]



2





TA43509_3847
Glycine_
529888
530911
Actin [Glycine max



max_release_2


(Soybean)]


TA6074_34305
Lotus_
530031
531095
Actin-1 [Sorghum bicolor



japonicus_


(Sorghum) (Sorghum



release_1



vulgare)]



TC26188
LJGI.070108
530031
531095
homologue to






UniRef100_A1Y2A0






Cluster: Actin, n = 1,







Aegiceras








corniculatum|Rep: Actin -








Aegiceras corniculatum,







partial (81%)


BM142797
Glycine_
530212
531095
Actin [Trifolium pratense



max_release_2


(Red clover)]


BP036880
Lotus_
530235
531095
Actin/actin-like [Medicago



japonicus_



truncatula (Barrel medic)]




release_1





AW349632
Glycine_
533113
533701
NA



max_release_2





AI900119
Glycine_
533044
534995
NA



max_release_2





TA51800_3847
Glycine_
533054
535063
NA



max_release_2





TC241826
GMGI.071508
533055
535063
similar to






UniRef100_Q2Z1Y5






Cluster: Pm52 protein; n = 1;







Prunus mume|Rep: Pm52







protein - Prunus mume






(Japanese flowering






apricot) = partial (73%)


BU494245
LJGI.070108
533191
534994
weakly similar to






UniRef100_Q2Z1Y5






Cluster: Pm52 protein, n = 1,







Prunus mume|Rep: Pm52







protein - Prunus mume






(Japanese flowering






apricot), partial (59%)


AI440735
Glycine_
534517
535020
NA



max_release_2





AI440735
GMGI.071508
534522
535020
similar to






UniRef100_Q2Z1Y5






Cluster: Pm52 protein; n = 1;







Prunus mume|Rep: Pm52







protein - Prunus mume






(Japanese flowering






apricot) = partial (41%)


TC250013
GMGI.071508
536842
537680
UniRef100_Q8L7J4






Cluster: Pyruvate kinase;






n = 1; Glycine max|Rep:






Pyruvate kinase - Glycine







max (Soybean) = partial







(29%)


TA10574_34305
Lotus_
537149
537628
Pyruvate kinase [Glycine



japonicus_



max (Soybean)]




release_1





TC26632
LJGI.070108
537149
537628
homologue to






UniRef100_Q42806






Cluster: Pyruvate kinase,






cytosolic isozyme, n = 1,







Glycine max|Rep: Pyruvate







kinase, cytosolic isozyme -







Glycine max (Soybean),







partial (26%)


CV536725
Phaseolus_
537147
537846
Pyruvate kinase = cytosolic



vulgaris_


isozyme [Glycine max



release_2


(Soybean)]


asmbl_11868
Vigna_
537127
538325
NA



unguiculata





TC25282
LJGI.070108
537149
538489
homologue to






UniRef100_Q8L7J4






Cluster: Pyruvate kinase,






n = 1, Glycine max|Rep:






Pyruvate kinase - Glycine







max (Soybean), partial







(29%)


TA47094_3847
Glycine_
536842
539314
Pyruvate kinase [Glycine



max_release_2



max (Soybean)]



Pvcon4373
Phaseolus_
537147
539113
UniRef100_Q42806



vulgaris


Pyruvate kinase, cytosolic






isozyme n = 1 Tax = Glycine







max







RepID = KPYC_SOYBN E-0


TC124922
MTGI.071708
537491
538783
homologue to






UniRef100_Q42806






Cluster: Pyruvate kinase,






cytosolic isozyme, n = 1,







Glycine max|Rep: Pyruvate







kinase, cytosolic isozyme -







Glycine max (Soybean),







partial (64%)


BF598352
Glycine_
538308
538971
Pyruvate kinase [Citrus



soja_release_2



sinensis (Sweet orange)]



BG044770
Glycine_
538624
539149
Pyruvate kinase [Citrus



soja_release_2



sinensis (Sweet orange)]



TC249941
GMGI.071508
538549
539314
UniRef100_Q8L7J4






Cluster: Pyruvate kinase;






n = 1; Glycine max|Rep:






Pyruvate kinase - Glycine







max (Soybean) = partial







(37%)


BE608312
Glycine_
542536
544875
Hypothetical protein



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


TC253996
GMGI.071508
542045
546856
similar to






UniRef100_A7QNQ5






Cluster: Chromosome






undetermined






scaffold_133 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome undetermined






scaffold_133 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (80%)


TC258772
GMGI.071508
548268
548805
NA


CV533614
Phaseolus_
548540
548638
No significant hit



vulgaris





TA57756_3847
Glycine_
548268
551375
Putative microtubule-



max_release_2


severing protein subunit






[Oryza sativa (japonica






cultivar-group)]


TC239891
GMGI.071508
548323
551375
similar to






UniRef100_A7QNQ6






Cluster: Chromosome






undetermined






scaffold_133 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome undetermined






scaffold_133 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (12%)


EH221990
GMGI.071508
550796
551633
weakly similar to






UniRef100_A7QNQ6






Cluster: Chromosome






undetermined






scaffold_133 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome undetermined






scaffold_133 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (7%)


EV263369
GMGI.071508
552842
553615
similar to






UniRef100_A8D2Q2






Cluster: ATP synthase






protein 8; n = 1; Caranx







ignobilis|Rep: ATP







synthase protein 8 - Caranx







ignobilis = partial (37%)



BU964969
Glycine_
556336
556943
NA



max_release_2





BU964969
GMGI.071508
556494
556943
similar to






UniRef100_Q9MYM4






Cluster: Lysosomal alpha-






glucosidase precursor; n = 1;







Bos taurus|Rep: Lysosomal







alpha-glucosidase = partial






(1%)


EH221989
GMGI.071508
562783
563692
homologue to






UniRef100_A7QNQ6






Cluster: Chromosome






undetermined






scaffold_133 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome undetermined






scaffold_133 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (3%)


AW831441
GMGI.071508
573069
573567
NA


AW831441
Glycine_
573069
573639
NA



max_release_2





TA6761_34305
Lotus_
573706
580487
Sphingosine kinase [Lotus



japonicus_



japonicus]




release_1





TC20288
LJGI.070108
573706
580487
UniRef100_Q5KR50






Cluster: Sphingosine






kinase, n = 1, Lotus







japonicus|Rep: Sphingosine







kinase - Lotus japonicus,






complete


TC122322
MTGI.071708
574490
580620
homologue to






UniRef100_Q5KR50






Cluster: Sphingosine






kinase, n = 1, Lotus







japonicus|Rep: Sphingosine







kinase - Lotus japonicus,






partial (66%)


BI701010
Glycine_
577145
579375
Sphingosine kinase [Lotus



max_release_2



japonicus]



Pvcon3123
Phaseolus_
577107
580468
UniRef100_Q5KR50



vulgaris


Sphingosine kinase n = 1






Tax = Lotus japonicus






RepID = Q5KR50_LOTJA






E-0


TA49258_3847
Glycine_
579511
580791
Sphingosine kinase [Lotus



max_release_2



japonicus]



TC235674
GMGI.071508
579511
580791
homologue to






UniRef100_Q5KR50






Cluster: Sphingosine






kinase; n = 1; Lotus







japonicus|Rep: Sphingosine







kinase - Lotus japonicus =






partial (26%)


BI969866
Glycine_
579600
580756
Sphingosine kinase [Lotus



max_release_2



japonicus]



EH043869
Arachis_
579729
580660
Cluster: Sphingosine



stenosperma_


kinase, n = 1, Lotus



release_5



japonicus|Rep: Sphingosine







kinase - Lotus japonicus


BQ786742
Glycine_
580594
580719
NA



max_release_






2





BM108235
Glycine_
581688
582006
NA



max_release_2





AW508189
Glycine_
581725
582244
Hypothetical protein



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


TC238711
GMGI.071508
581688
582562
similar to






UniRef100_A7QNQ7






Cluster: Chromosome






undetermined






scaffold_133 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome undetermined






scaffold_133 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (50%)


TA46155_3847
Glycine_
581745
582556
Hypothetical protein



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


AW278369
GMGI.071508
581988
582389
similar to






UniRef100_A7QNQ7






Cluster: Chromosome






undetermined






scaffold_133 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome undetermined






scaffold_133 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (44%)


AW278369
Glycine_
581988
582418
Hypothetical protein



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


CD394810
Glycine_
582134
582328
NA



max_release_2





BG047332
Glycine_
591288
592013
OSJNBb0065L13.3 protein



max_release_2


[Oryza sativa (japonica






cultivar-group)]


TC272805
GMGI.071508
591358
592013
similar to






UniRef100_A7NXM8






Cluster: Chromosome chr5






scaffold_2 = whole genome






shotgun sequence; n = 1;







Vitis vinifera|Rep:







Chromosome chr5






scaffold_2 = whole genome






shotgun sequence - Vitis







vinifera (Grape) = partial







(15%)


BW599171
LJGI.070108
593399
593875
weakly similar to






UniRef100_A7PT63






Cluster: Chromosome chr8






scaffold_29, whole genome






shotgun sequence, n = 1,







Vitis vinifera|Rep:







Chromosome chr8






scaffold_29, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(24%)


BE057829
Glycine_
606858
607008
NA



max_release_2





TC275159
GMGI.071508
606858
607456
NA


BE612118
GMGI.071508
615853
616253
weakly similar to






UniRef100_A7GPV4






Cluster: Citrate transporter;






n = 1; Bacillus cereus subsp.






cytotoxis NVH 391-98|Rep:






Citrate transporter -







Bacillus cereus subsp.







cytotoxis (strain NVH 391-






98) = partial (5%)


BE612118
Glycine_
615869
616269
NA



max_release_2





CA910895
Phaseolus_
622174
622531

Arabidopsis thaliana




coccineus_


genomic DNA,



release_2


chromosome 5, P1






clone: MPO12 [Arabidopsis







thaliana (Mouse-ear cress)]



BU763992
Glycine_
625192
625591
NA



max_release_2





TA51978_3847
Glycine_
625330
626304
Putative ethylene-



max_release_2


responsive protein [Oryza







sativa (japonica cultivar-







group)]


TC236117
GMGI.071508
625330
626304
similar to






UniRef100_A7PM86






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (43%)


TC263881
GMGI.071508
625192
627651
similar to






UniRef100_A7PM86






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (76%)


TA51979_3847
Glycine_
625252
627642
Putative ethylene response



max_release_2


protein [Capsicum chinense






(Scotch bonnet) (Bonnet






pepper)]


TC236300
GMGI.071508
625318
627642
similar to






UniRef100_A7PM86






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (98%)


CA910548
Phaseolus_
625559
627607
Putative ethylene response



coccineus_


protein [Capsicum chinense



release_2


(Scotch bonnet) (Bonnet






pepper)]


Pvcon5808
Phaseolus_
625567
627610
UniRef100_A7PM86



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM86_VITVI






2.00E−77


EV269595
GMGI.071508
627204
627569
similar to






UniRef100_A7PM86






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (29%)


BI273677
Glycine_
637550
637816
NA



max_release_2





BP049107
Lotus_
647584
649419
Cinnamoyl CoA reductase-



corniculatus_


like protein related cluster



release_1





TC258382
GMGI.071508
646415
652371
weakly similar to






UniRef100_A7PM88






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (72%)


TA50222_3847
Glycine_
646722
652222
Cinnamoyl CoA reductase-



max_release_2


like protein [Arabidopsis







thaliana (Mouse-ear cress)]



SATT495

650288
650531



Satt495
ePCR
650288
650531
Map3.0 SSR L/Gm19 cM:






2.7


AW099618
GMGI.071508
649276
652222
weakly similar to






UniRef100_A7PM88






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (23%)


TA50296_3847
Glycine_
674409
676421
NA



max_release_2





BQ629031
Glycine_
674669
676494
NA



max_release_2





BM520842
Glycine_
674685
676538
NA



soja_release_2





TC264557
GMGI.071508
674741
676494
NA


BU765059
Glycine_
674828
676698
NA



max_release_2





BU765059
GMGI.071508
674925
676698
weakly similar to






UniRef100_A7L4B0






Cluster: Protein kinase;






n = 1; Carica papaya|Rep:






Protein kinase Carica







papaya (Papaya) = partial







(6%)


TC264815
GMGI.071508
674409
678111
weakly similar to






UniRef100_A7L4B0






Cluster: Protein kinase;






n = 1; Carica papaya|Rep:






Protein kinase - Carica







papaya (Papaya) = partial







(14%)


asmbl_11869
Vigna_
676473
676672
NA



unguiculata





TA50295_3847
Glycine_
674775
678957
NA



max_release_2





Pvcon1987
Phaseolus_
674506
679702
UniRef100_A7L4B0



vulgaris


Protein kinase n = 1






Tax = Carica papaya






RepID = A7L4B0_CARPA






1.00E−127


BM528477
Glycine_
676507
678111
NA



max_release_2





TA11531_47247
Lotus_
676692
678714
Protein kinase-like protein



corniculatus_


related cluster



release_1





TA13031_34305
Lotus_
676692
678714
Hypothetical protein



japonicus_


At5g14720 [Arabidopsis



release_1



thaliana (Mouse-ear cress)]



TC31122
LJGI.070108
676701
678714
similar to






UniRef100_A7L4B0






Cluster: Protein kinase,






n = 1, Carica papaya|Rep:






Protein kinase - Carica







papaya (Papaya), partial







(14%)


TC255388
GMGI.071508
679127
681361
homologue to






UniRef100_A7PM90






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (44%)


TC124284
MTGI.071708
679117
681419
homologue to






UniRef100_A7PM90






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(48%)


DV565290
Phaseolus_
681368
681460
No significant hit (e-20)



vulgaris





toGm05
DAGchainer
603011
803108
Ks0.2166


NP7265365
MTGI.071708
703588
713159
GB|AC124951.19|ABE84834.1






ATPase, E1-E2 type,






Peptidase M, neutral zinc






metallopeptidases, zinc-






binding site


BF325038
Glycine_
711165
712911
ATPase = E1-E2 type;



max_release_2


Peptidase M = neutral zinc






metallopeptidases = zinc-






binding site [Medicago







truncatula (Barrel medic)]



FE897117
Phaseolus_
715539
715874
UniRef100_Q93VL6 NBS-



vulgaris


LRR resistance-like protein






J78 n = 1 Tax = Phaseolus







vulgaris







RepID = Q93VL6_PHAVU






2.00E−47


TC264844
GMGI.071508
731939
732440
weakly similar to






UniRef100_A7PD05






Cluster: Chromosome






chr17 scaffold_12 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr17






scaffold_12 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (13%)


TA67235_3847
Glycine_
731939
733078
NA



max_release_2





CD404253
GMGI.071508
732439
733078
homologue to






UniRef100_A7PM92






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (8%)


BU091162
GMGI.071508
737876
738292
NA


BU091162
Glycine_
737876
738363
NA



max_release_2





asmbl_11870
Vigna_
740144
741401
NA



unguiculata





BI470779
GMGI.071508
740189
741746
similar to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase; n = 1; Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata) =






partial (30%)


TA43150_3847
Glycine_
740126
742524
Carbonic anhydrase



max_release_2


[Phaseolus aureus(Mung






bean) (Vigna radiata)]


BG509786
GMGI.071508
740265
742434
homologue to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase; n = 1; Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata) =






partial (34%)


BG509786
Glycine_
740265
742656
Carbonic anhydrase [Zea



max_release_2



mays (Maize)]




2





DT083317
Glycine_
740299
742670
Carbonic anhydrase [Zea



soja_release_2



mays (Maize)]



AW781596
Glycine_
740182
742860
Carbonic anhydrase



max_release_2


[Phaseolus aureus (Mung






bean) (Vigna radiata)]


BU089680
Glycine_
741070
742671
Carbonic anhydrase [Zea



max_release_2



mays (Maize)]



BM887226
Glycine_
741037
742852
Carbonic anhydrase [Zea



max_release_2



mays (Maize)]



BU089600
Glycine_
741070
742891
Carbonic anhydrase [Zea



max_release_2



mays (Maize)]



TC23104
LJGI.070108
740127
744319
similar to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase, n = 1, Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata),






partial (98%)


TA2934_3885
Phaseolus_
739932
744687
Carbonic anhydrase [Zea



vulgaris_



mays (Maize)]




release_2





TC238511
GMGI.071508
740118
744639
homologue to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase; n = 1; Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata) =






complete


TA377_34305
Lotus_
740127
744704
Carbonic anhydrase [Zea



japonicus_



mays (Maize)]




release_1





Pvcon229
Phaseolus_
740125
744728
UniRef100_Q9XQB0



vulgaris


Carbonic anhydrase n = 1






Tax = Vigna radiata var.






radiata






RepID = Q9XQB0_PHAAU






1.00E−176


TA2935_3885
Phaseolus_
740178
744687
Carbonic anhydrase [Zea



vulgaris_



mays (Maize)]




release_2





TA2376_3848
Glycine_
740118
744805
Carbonic anhydrase



soja_release_2


[Phaseolus aureus (Mung






bean) (Vigna radiata)]


TA43157_3847
Glycine_
740117
744844
Carbonic anhydrase [Zea



max_release_2



mays (Maize)]



TA43160_3847
Glycine_
741051
744186
Carbonic anhydrase =



max_release_2


chloroplast precursor (EC






4.2.1.1) (Carbonate






dehydratase) [Contains:






Carbonic anhydrase = 27






kDa isoform; Carbonic






anhydrase = 25 kDa






isoform] [Pisum sativum






(Garden pea)]


TC135779
MTGI.071708
741364
744530
homologue to






UniRef100_P17067






Cluster: Carbonic






anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27






kDa isoform, Carbonic






anhydrase, 25 kDa






isoform], n = 1, Pisum







sativum|Rep: Carbonic







anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27






kDa isoform, Carbonic






anhydrase, 25 kDa isoform] -







Pisum sativum (Garden







pea), partial (79%)


TA4174_3848
Glycine_
742624
743398
Carbonic anhydrase



soja_release_2


[Phaseolus aureus (Mung






bean) (Vigna radiata)]


Pvcon228
Phaseolus_
741374
744687
UniRef100_Q9XQB0



vulgaris


Carbonic anhydrase n = 1






Tax = Vigna radiata var.






radiata






RepID = Q9XQB0_PHAAU






1.00E−137


TA43163_3847
Glycine_
741381
744770
Carbonic anhydrase [Zea



max_release_2



mays (Maize)]



TC247359
GMGI.071508
741381
744770
homologue to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase; n = 1; Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata) =






partial (62%)


BG045644
Glycine_
742643
743622
Carbonic anhydrase =



soja_release_2


chloroplast precursor (EC






4.2.1.1) (Carbonate






dehydratase) [Contains:






Carbonic anhydrase = 27






kDa isoform; Carbonic






anhydrase = 25 kDa






isoform] [Pisum sativum






(Garden pea)]


Pvcon227
Phaseolus_
741681
744687
UniRef100_Q9XQB0



vulgaris


Carbonic anhydrase n = 1






Tax = Vigna radiata var.






radiata






RepID = Q9XQB0_PHAAU






1.00E−133


TC124201
MTGI.071708
741922
744665
homologue to






UniRef100_P17067






Cluster: Carbonic






anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27






kDa isoform, Carbonic






anhydrase, 25 kDa






isoform], n = 1, Pisum







sativum|Rep: Carbonic







anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27






kDa isoform, Carbonic






anhydrase, 25 kDa isoform] -







Pisum sativum (Garden







pea), partial (57%)


CB543710
Phaseolus_
742464
744532
Carbonic anhydrase



vulgaris_


[Phaseolus aureus (Mung



release_2


bean) (Vigna radiata)]


CB539509
Phaseolus_
742480
744557
Carbonic anhydrase [Zea



vulgaris_



mays (Maize)]




release_2





TC126947
MTGI.071708
742434
744665
homologue to






UniRef100_P17067






Cluster: Carbonic






anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27






kDa isoform, Carbonic






anhydrase, 25 kDa






isoform], n = 1, Pisum







sativum|Rep: Carbonic







anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27






kDa isoform, Carbonic






anhydrase, 25 kDa isoform] -







Pisum sativum (Garden







pea), partial (51%)


asmbl_11871
Vigna_
742823
744369
NA



unguiculata





asmbl_11872
Vigna_
742628
744687
NA



unguiculata





asmbl_11874
Vigna_
742641
744687
NA



unguiculata





TA43165_3847
Glycine_
742658
744772
Carbonic anhydrase



max_release_2


[Phaseolus aureus (Mung






bean) (Vigna radiata)]


TC241035
GMGI.071508
742658
744772
homologue to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase; n = 1; Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata) =






partial (38%)


TA480_3888
Pisum_
742823
744641
Carbonic anhydrase,



sativum_


chloroplast precursor (EC



release_2


4.2.1.1) (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27






kDa isoform, Carbonic






anhydrase, 25 kDa isoform]






[Pisum sativum (Garden






pea)]


TC240357
GMGI.071508
742650
744828
homologue to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase; n = 1; Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata) =






partial (38%)


BE346766
Glycine_
743636
744227
Carbonic anhydrase =



max_release_2


chloroplast precursor (EC






4.2.1.1) (Carbonate






dehydratase) [Contains:






Carbonic anhydrase = 27






kDa isoform; Carbonic






anhydrase = 25 kDa






isoform] [Pisum sativum






(Garden pea)]


AW596246
Glycine_
743636
744243
Carbonic anhydrase



max_release_2


[Phaseolus aureus (Mung






bean) (Vigna radiata)]


BE807206
Glycine_
743636
744244
Carbonic anhydrase



max_release_2


[Phaseolus aureus (Mung






bean) (Vigna radiata)]


CB280659
Phaseolus_
743613
744419
Carbonic anhydrase



vulgaris_


[Phaseolus aureus (Mung



release_2


bean) (Vigna radiata)]


asmbl_11875
Vigna_
743587
744642
NA



unguiculata





DT083076
Glycine_
743565
744678
Carbonic anhydrase



soja_release_2


[Phaseolus aureus (Mung






bean) (Vigna radiata)]


TC29040
LJGI.070108
743565
744702
similar to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase, n = 1, Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata),






partial (31%)


TA134_47247
Lotus_
743568
744704
Carbonic anhydrase related



corniculatus_


cluster



release_1





TA378_34305
Lotus_
743568
744704
Carbonic anhydrase,



japonicus_


prokaryotic and plant



release_1


[Medicago truncatula






(Barrel medic)]


TC24201
LJGI.070108
743584
744704
similar to






UniRef100_Q9XQB0






Cluster: Carbonic






anhydrase, n = 1, Vigna







radiata var. radiata|Rep:







Carbonic anhydrase -







Phaseolus aureus (Mung







bean) (Vigna radiata),






partial (25%)


CB539196
Phaseolus_
743626
744687
Carbonic anhydrase



vulgaris_


[Phaseolus aureus (Mung



release_2


bean) (Vigna radiata)]


AV413187
LJGI.070108
744089
744647
similar to






UniRef100_P27140






Cluster: Carbonic






anhydrase, chloroplast






precursor, n = 4, Arabidopsis







thaliana|Rep: Carbonic







anhydrase, chloroplast






precursor - Arabidopsis







thaliana (Mouse-ear cress),







partial (17%)


AV413187
Lotus_
744089
744672
Carbonic anhydrase,



japonicus_


chloroplast precursor



release_1


[Arabidopsis thaliana






(Mouse-ear cress)]


CD860850
Pisum_
744145
744641
Carbonic anhydrase,



sativum_


chloroplast precursor



release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


CD403834
Glycine_
744076
744732
Carbonic anhydrase =



max_release_2


chloroplast precursor






[Arabidopsis thaliana






(Mouse-ear cress)]


CD415400
Glycine_
744251
744691
NA



max_release_2





asmbl_11873
Vigna_
744448
744649
NA



unguiculata





CB541850
Phaseolus_
747218
747570
No significant hit (e-20)



vulgaris





BM953717
Glycine_
747199
748912
Peptidase S1 and S6 =



max_release_2


chymotrypsin/Hap






[Medicago truncatula






(Barrel medic)]


EH256926
GMGI.071508
747192
749279
homologue to






UniRef100_A7Q7E6






Cluster: Chromosome






chr18 scaffold_59 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr18






scaffold_59 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (21%)


TA51716_3847
Glycine_
747191
749327
Putative DegP protease



max_release_2


[Oryza sativa (japonica






cultivar-group)]


TC243148
GMGI.071508
747199
749327
homologue to






UniRef100_A7Q7E6






Cluster: Chromosome






chr18 scaffold_59 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr18






scaffold_59 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (25%)


AV768772
LJGI.070108
747281
749288
homologue to






UniRef100_O22609






Cluster: Protease Do-like 1,






chloroplast precursor, n = 1,







Arabidopsis thaliana|Rep:







Protease Do-like 1,






chloroplast precursor -







Arabidopsis thaliana







(Mouse-ear cress), partial






(23%)


BE807421
Glycine_
748776
749688
Peptidase S1 and S6 =



max_release_2


chymotrypsin/Hap






[Medicago truncatula






(Barrel medic)]


TA51715_3847
Glycine_
747251
752927
Peptidase S1 and S6 =



max_release_2


chymotrypsin/Hap






[Medicago truncatula






(Barrel medic)]


TC260884
GMGI.071508
747251
752942
homologue to






UniRef100_A7Q7E6






Cluster: Chromosome






chr18 scaffold_59 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr18






scaffold_59 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (80%)


BE474482
Glycine_
751068
752387
Peptidase S1 and S6 =



max_release_2


chymotrypsin/Hap






[Medicago truncatula






(Barrel medic)]


BE474482
GMGI.071508
751070
752387
homologue to






UniRef100_A7Q7E6






Cluster: Chromosome






chr18 scaffold_59 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr18






scaffold_59 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (19%)


TC261290
GMGI.071508
755656
757218
similar to






UniRef100_A7PM96






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (33%)


BG646067
MTGI.071708
756996
759297
similar to






UniRef100_A7PM96






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(33%)


BE555567
Glycine_
757210
762134
Hypothetical protein



max_release_2


[Medicago truncatula






(Barrel medic)]


BE555567
GMGI.071508
757746
762134
similar to






UniRef100_A7PM96






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (31%)


BE058948
Glycine_
762117
763784
Hypothetical protein



max_release_2


[Medicago truncatula






(Barrel medic)]


BE058948
GMGI.071508
762818
763784
similar to






UniRef100_A7PM96






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (25%)


TC138874
MTGI.071708
768876
770881
similar to






UniRef100_Q40318






Cluster: Coil protein, n = 1,







Medicago sativa|Rep: Coil







protein - Medicago sativa






(Alfalfa), partial (60%)


TC124470
MTGI.071708
768770
771318
similar to






UniRef100_Q1RU40






Cluster: Lipolytic enzyme,






G-D-S-L, n = 1, Medicago







truncatula|Rep: Lipolytic







enzyme, G-D-S-L -







Medicago truncatula







(Barrel medic), partial






(77%)


TC268582
GMGI.071508
768733
771727
weakly similar to






UniRef100_A7PMA0






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (89%)


BE059369
Glycine_
770328
771326
Lipolytic enzyme = G-D-S-



max_release_2


[Medicago truncatula






(Barrel medic)]


BE329784
GMGI.071508
770783
771236
similar to






UniRef100_Q1RU40






Cluster: Lipolytic enzyme =






G-D-S-L; n = 1; Medicago







truncatula|Rep: Lipolytic







enzyme = G-D-S-L -







Medicago truncatula







(Barrel medic) = partial






(27%)


BE329784
Glycine_
770783
771288
Lipolytic enzyme = G-D-S-



max_release_2


L [Medicago truncatula






(Barrel medic)]


TA68573_3847
Glycine_
773983
774836
Putative kinesin light chain



max_release_2


[Oryza sativa (japonica






cultivar-group)]


TC259227
GMGI.071508
773983
774836
similar to






UniRef100_A7PD12






Cluster: Chromosome






chr17 scaffold_12 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr17






scaffold_12 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (13%)


AI759741
Glycine_
774118
774822
Putative kinesin light chain



max_release_2


[Oryza sativa (japonica






cultivar-group)]


asmbl_11876
Vigna_
774030
774978
NA



unguiculata





TC139308
MTGI.071708
774935
775598
similar to






UniRef100_A7PMA1






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(34%)


AW186182
Glycine_
775276
775796
Similarity to kinesin light



max_release_2


chain [Arabidopsis thaliana






(Mouse-ear cress)]


AW186182
GMGI.071508
775464
775796
similar to






UniRef100_A7PD12






Cluster: Chromosome






chr17 scaffold_12 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr17






scaffold_12 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (16%)


BF010272
GMGI.071508
783671
784035
UniRef100_Q00K67






Cluster: Major surface






antigen; n = 1; Hepatitis B






virus|Rep: Major surface






antigen - Hepatitis B virus






(HBV) = partial (5%)


TA54422_3847
Glycine_
783644
784982
Alcohol dehydrogenase



max_release_2


superfamily = zinc-






containing [Medicago







truncatula (Barrel medic)]



BI971258
Glycine_
783921
784926
Auxin-induced protein



max_release_2


[Vigna radiata]


CV542673
Phaseolus_
784213
785346
Quinone oxidoreductase-



vulgaris_


like protein [Helianthus



release_2



annuus (Common







sunflower)]


TC239445
GMGI.071508
783904
786356
similar to






UniRef100_O23939






Cluster: Ripening-induced






protein; n = 1; Fragaria







vesca|Rep: Ripening-







induced protein - Fragaria







vesca (Woodland







strawberry) = partial (84%)


TA3037_3848
Glycine_
784204
786191
Quinone oxidoreductase-



soja_release_2


like protein [Helianthus







annuus (Common







sunflower)]


BG045149
Glycine_
784943
785469
Quinone oxidoreductase



soja_release_2


[Fragaria ananassa






(Strawberry)]


TA54423_3847
Glycine_
784420
786354
Quinone oxidoreductase-



max_release_2


like protein [Helianthus







annuus (Common







sunflower)]


BG046280
Glycine_
786163
786344
NA



soja_release_2





CA901808
Phaseolus_
800890
801759
Alcohol dehydrogenase



coccineus_


superfamily, zinc-



release_2


containing [Medicago







truncatula (Barrel medic)]



TA14086_34305
Lotus_
800932
801745
Alcohol dehydrogenase



japonicus_


superfamily, zinc-



release_1


containing [Medicago







truncatula (Barrel medic)]



TC23841
LJGI.070108
800932
801745
similar to






UniRef100_Q43677






Cluster: Auxin-induced






protein, n = 1, Vigna







radiata|Rep: Auxin-induced







protein - Vigna radiata,






partial (40%)


M0093116
SEQ.
805373
805788
SEQ ID NO: 13



Listing





TC252650
GMGI.071508
805357
806601
similar to






UniRef100_Q43677






Cluster: Auxin-induced






protein; n = 1; Vigna







radiata|Rep: Auxin-induced







protein - Vigna radiata =






partial (54%)


BARC-039375-
ePCR&blat
805660
806532
Map3.0 SNP L/Gm19 cM:


07304



3.4


TA65006_3847
Glycine_
805357
807089
Quinone oxidoreductase-



max_release_2


like protein [Helianthus







annuus (Common







sunflower)]


TA65005_3847
Glycine_
806611
807310
Alcohol dehydrogenase



max_release_2


superfamily = zinc-






containing [Medicago







truncatula (Barrel medic)]



TC274718
GMGI.071508
806611
807310
similar to






UniRef100_Q43677






Cluster: Auxin-induced






protein; n = 1; Vigna







radiata|Rep: Auxin-induced







protein - Vigna radiata =






partial (30%)


AW397551
Glycine_
811245
811796
Auxin-induced protein



max_release_2


[Vigna radiata]


Pvcon4580
Phaseolus_
811330
813524
UniRef100_Q43677 Auxin-



vulgaris


induced protein n = 1






Tax = Vigna radiata






RepID = Q43677_9FABA






1.00E−133


asmbl_11877
Vigna_
812523
812779
NA



unguiculata





BE608172
Glycine_
821487
822389
Protein farnesyltransferase



max_release_2


subunit beta [Pisum







sativum (Garden pea)]



BQ273477
Glycine_
821559
822383
NA



max_release_2





TC246895
GMGI.071508
821516
822443
similar to






UniRef100_Q04903






Cluster: Protein






farnesyltransferase subunit






beta; n = 1; Pisum







sativum|Rep: Protein







farnesyltransferase subunit






beta - Pisum sativum






(Garden pea) = partial






(15%)


TC241767
GMGI.071508
824186
828116
similar to






UniRef100_Q7XHJ0






Cluster: Formate






dehydrogenase; n = 1;







Quercus robur|Rep:







Formate dehydrogenase -







Quercus robur (English







oak) = partial (97%)


TA40711_3847
Glycine_
824209
828372
Formate dehydrogenase



max_release_2


[Quercus robur (English






oak)]


AI522957
Glycine_
826883
827087
Formate dehydrogenase



max_release_2


[Quercus robur (English






oak)]


BG044450
Glycine_
826544
827461
Formate dehydrogenase =



soja_release_2


mitochondrial precursor






[Solanum tuberosum






(Potato)]


asmbl_11878
Vigna_
826586
827463
NA



unguiculata





CA800817
Glycine_
826705
827869
Formate dehydrogenase



soja_release_2


[Quercus robur (English






oak)]


TC240429
GMGI.071508
826957
828379
similar to






UniRef100_Q9ZRI8






Cluster: Formate






dehydrogenase =






mitochondrial precursor;






n = 1; Hordeum vulgare|Rep:






Formate dehydrogenase =






mitochondrial precursor -







Hordeum vulgare (Barley) =







partial (40%)


AW350528
Glycine_
826986
828379
Formate dehydrogenase 1 =



max_release_2


mitochondrial precursor






[Oryza sativa (Rice)]


BG882062
Glycine_
827372
828284
Formate dehydrogenase 1 =



max_release_2


mitochondrial precursor






[Oryza sativa (Rice)]


BE347639
Glycine_
827443
828262
Formate dehydrogenase 1 =



max_release_2


mitochondrial precursor






[Oryza sativa (Rice)]


CA782711
Glycine_
827371
828357
Formate dehydrogenase 1 =



soja_release_2


mitochondrial precursor






[Oryza sativa (Rice)]


TA40821_3847
Glycine_
829640
832253
Formate dehydrogenase



max_release_2


[Quercus robur (English






oak)]


BE330555
Glycine_
829875
832057
Formate dehydrogenase =



max_release_2


mitochondrial precursor






[Solanum tuberosum






(Potato)]


BU090495
Glycine_
829863
832082
Formate dehydrogenase



max_release_


[Quercus robur (English



2


oak)]


BG044406
Glycine_
829915
832082
Formate dehydrogenase



soja_release_


[Quercus robur (English



2


oak)]


AW508186
GMGI.071508
830914
831336
similar to






UniRef100_A7PMA5






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (15%)


M0129925
SEQ
830552
831704
SEQ ID NO: 14



LISTING





AW508186
Glycine_
830914
831970
Formate dehydrogenase =



max_release_2


mitochondrial precursor






[Solatium tuberosum






(Potato)]


AW508145
Glycine_
830909
832061
Formate dehydrogenase



max_release_2


[Quercus robur (English






oak)]


TA40373_3847
Glycine_
830863
832118
Formate dehydrogenase



max_release_2


[Quercus robur (English






oak)]


AW397259
Glycine_
831219
832141
Formate dehydrogenase



max_release_2


[Quercus robur (English






oak)]


TC261330
GMGI.071508
829795
833576
similar to






UniRef100_Q7XHJ0






Cluster: Formate






dehydrogenase; n = 1;







Quercus robur|Rep:







Formate dehydrogenase -







Quercus robur (English







oak) = partial (96%)


TC249502
GMGI.071508
830866
832529
similar to






UniRef100_Q7XHJ0






Cluster: Formate






dehydrogenase; n = 1;







Quercus robur|Rep:







Formate dehydrogenase -







Quercus robur (English







oak) = partial (72%)


TA40376_3847
Glycine_
830879
833356
Formate dehydrogenase



max_release_2


[Quercus robur (English






oak)]


asmbl_11879
Vigna_
831735
833050
NA



unguiculata





AW569072
GMGI.071508
832471
832890
similar to






UniRef100_Q7XHJ0






Cluster: Formate






dehydrogenase; n = 1;







Quercus robur|Rep:







Formate dehydrogenase -







Quercus robur (English







oak) = partial (9%)


AW569072
Glycine_
832471
832929
Formate dehydrogenase



max_release_2


[Quercus robur (English






oak)]


TA40339_3847
Glycine_
832130
833531
Formate dehydrogenase 1 =



max_release_2


mitochondrial precursor






[Oryza sativa (Rice)]


TA5191_3885
Phaseolus_
832192
833517
Formate dehydrogenase



vulgaris_


[Quercus robur (English



release_2


oak)]


FD790937
Phaseolus_
833039
833412
UniRef100_A6N0B2



vulgaris


Mitochondrial formate






dehydrogenase 1






(Fragment) n = 1 Tax = Oryza







sativa Indica Group







RepID = A6N0B2_ORYSI






3.00E−30


CA913454
Phaseolus_
841331
841722
NA



coccineus_






release_2





TA70199_3847
Glycine_
841305
841824
NA



max_release_2





asmbl_11880
Vigna_
841326
841889
NA



unguiculata





TA3611_3848
Glycine_
841347
842640
Hypothetical protein



soja_release_2


OJ1593_C11.11 [Oryza







sativa (japonica cultivar-







group)]


TA5381_34305
Lotus_
841455
842700
Calcium homeostasis



japonicus_


regulator CHoR1 [Solanum



release_1



tuberosum (Potato)]



TC20706
LJGI.070108
841455
842700
weakly similar to






UniRef100_Q5QTN8






Cluster: Calcium






homeostasis regulator






CHoR1, n = 1, Solanum







tuberosum|Rep: Calcium







homeostasis regulator






CHoR1 - Solanum







tuberosum (Potato), partial







(52%)


Pvcon2378
Phaseolus_
841347
843522
UniRef100_A7PMA9



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMA9_VITVI






4.00E−94


TC252755
GMGI.071508
841305
843655
similar to






UniRef100_A7PMA9






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (74%)


EX305183
Phaseolus_
841682
843613
UniRef100_A7PMA9



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMA9_VITVI






1.00E−67


BI498351
GMGI.071508
844582
845168
NA


TA66563_3847
Glycine_
844582
847078
Hypothetical protein



max_release_2


[Ipomoea trifida (Morning






glory)]


TC247953
GMGI.071508
844582
847220
similar to






UniRef100_A7Q5T8






Cluster: Chromosome






chr14 scaffold_54 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_54 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (58%)


TA3593_3848
Glycine_
844668
847194
Hypothetical protein



soja_release_2


[Ipomoea trifida (Morning






glory)]


TA56324_3847
Glycine_
854425
856413
Similarity to intracellular



max_release_2


protein [Arabidopsis







thaliana (Mouse-ear cress)]



TC235843
GMGI.071508
854425
856413
similar to






UniRef100_A7PMB1






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (40%)


CD406351
Glycine_
855627
856402
Similarity to intracellular



max_release_2


protein [Arabidopsis







thaliana (Mouse-ear cress)]



TC276442
GMGI.071508
855627
856402
similar to






UniRef100_A7PMB1






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (14%)


TC273993
GMGI.071508
863632
864262
homologue to






UniRef100_A7PMB2






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (26%)


BU082700
Glycine_
863841
864449
Hypothetical protein



max_release_2


OJ1126_B10.9 [Oryza







sativa (japonica cultivar-







group)]


AW459960
Glycine_
863632
865288
Hypothetical protein



max_release_2


F4P13.4 [Arabidopsis







thaliana (Mouse-ear cress)]



AL385435
MTGI.071708
863952
865397
homologue to






UniRef100_A7PD25






Cluster: Chromosome






chr17 scaffold_12, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr17






scaffold_12, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(37%)


AI856244
GMGI.071508
864500
864958
UniRef100_A7PMB2






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (6%)


asmbl_11881
Vigna_
863829
865710
NA



unguiculata





TC238318
GMGI.071508
863970
865869
homologue to






UniRef100_A7PMB2






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (34%)


TA63907_3847
Glycine_
864500
865869
Hypothetical protein



max_release_2


F4P13.4 [Arabidopsis







thaliana (Mouse-ear cress)]



BW598574
LJGI.070108
865265
865656
similar to






UniRef100_Q8LES3






Cluster: Protein kinase,






n = 1, Arabidopsis







thaliana|Rep: Protein kinase -








Arabidopsis thaliana







(Mouse-ear cress), partial






(9%)


BW598574
Lotus_
865265
865674
Protein kinase [Arabidopsis



japonicus_



thaliana (Mouse-ear cress)]




release_1





CD400016
Glycine_
870972
871184
NA



max_release_






2





CD399245
Glycine_
870876
871427
Putative Peptidyl-prolyl cis-



max_release_2


trans isomerase =






chloroplast [Oryza sativa






(japonica cultivar-group)]


TC242592
GMGI.071508
870943
872827
similar to






UniRef100_A6MZC4






Cluster: Peptidyl-prolyl cis-






trans isomerase; n = 2; Oryza







sativa|Rep: Peptidyl-prolyl







cis-trans isomerase - Oryza







sativa subsp. indica (Rice) =







partial (60%)


CB543642
Phaseolus_
871229
872777
Peptidyl-prolyl cis-trans



vulgaris_


isomerase = chloroplast



release_2


precursor [Spinacia







oleracea (Spinach)]



TA52959_3847
Glycine_
870943
873450
Poly(A) polymerase [Pisum



max_release_2



sativum (Garden pea)]



CB539263
Phaseolus_
871195
873325
Poly(A) polymerase [Pisum



vulgaris_



sativum (Garden pea)]




release_2





Pvcon1578
Phaseolus_
870946
876143
UniRef100_O22636



vulgaris


Poly(A) polymerase n = 1






Tax = Pisum sativum






RepID = O22636_PEA E-0


TA10487_34305
Lotus_
873266
875963
Poly(A) polymerase [Pisum



japonicus_



sativum (Garden pea)]




release_1





TA6667_47247
Lotus_
873266
875963
Poly(A) polymerase related



corniculatus_


cluster



release_1





TC34747
LJGI.070108
873266
875963
similar to






UniRef100_O22636






Cluster: Poly(A)






polymerase, n = 1, Pisum







sativum|Rep: Poly(A)







polymerase - Pisum







sativum (Garden pea),







partial (57%)


BG363373
Glycine_
874357
874944
Poly(A) polymerase [Pisum



max_release_2



sativum (Garden pea)]



TC251420
GMGI.071508
874369
876078
similar to






UniRef100_O22636






Cluster: Poly(A)






polymerase; n = 1; Pisum







sativum|Rep: Poly(A)







polymerase - Pisum







sativum (Garden pea) =







partial (37%)


CA901088
Phaseolus_
874490
876191
Poly(A) polymerase [Pisum



coccineus_



sativum (Garden pea)]




release_2





asmbl_11882
Vigna_
886629
890018
NA



unguiculata





TA68870_3847
Glycine_
886534
893419
Senescence-associated



max_release_2


protein-like [Oryza sativa






(japonica cultivar-group)]


TC270337
GMGI.071508
886672
893419
weakly similar to






UniRef100_A7PD28






Cluster: Chromosome






chr17 scaffold_12 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr17






scaffold_12 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (86%)


M0205537
SEQ.
890458
890051
SEQ ID NO: 15



Listing





BM732054
Glycine_
899859
901015
NA



max_release_2





BM732054
GMGI.071508
900006
901015
similar to






UniRef100_Q04TD2






Cluster: MviN-related






protein; n = 1; Leptospira







borgpetersenii serovar







Hardjo-bovis JB197|Rep: =






partial (2%)


toGm13
DAGchainer
816170
1014875
Ks0.1202


M0202715
SEQ.
921233
921630
SEQ ID NO: 16



Listing





TA46168_3847
Glycine_
921047
924660
Homeodomain leucine



max_release_2


zipper protein HDZ3






[Phaseolus vulgaris






(Kidney bean) (French






bean)]


TC260016
GMGI.071508
921056
924739
homologue to






UniRef100_Q93XA3






Cluster: Homeodomain






leucine zipper protein






HDZ3; n = 1; Phaseolus







vulgaris|Rep:







Homeodomain leucine






zipper protein HDZ3 -







Phaseolus vulgaris (Kidney







bean) (French bean) =






complete


Pvcon1101
Phaseolus_
921086
924758
UniRef100_Q93XA3



vulgaris


Homeodomain leucine






zipper protein HDZ3






(Fragment) n = 1






Tax = Phaseolus vulgaris






RepID = Q93XA3_PHAVU






1.00E−124


TA3604_3885
Phaseolus_
921111
924754
Homeodomain leucine



vulgaris_


zipper protein HDZ3



release_2


[Phaseolus vulgaris






(Kidney bean) (French






bean)]


asmbl_11883
Vigna_
921538
924758
NA



unguiculata





BG041631
Glycine_
923015
923340
Homeobox-leucine zipper



soja_release_2


protein HAT5 [Arabidopsis







thaliana (Mouse-ear cress)]



AV421688
LJGI.070108
923118
924180
similar to






UniRef100_Q93XA3






Cluster: Homeodomain






leucine zipper protein






HDZ3, n = 1, Phaseolus







vulgaris|Rep:







Homeodomain leucine






zipper protein HDZ3 -







Phaseolus vulgaris (Kidney







bean) (French bean), partial






(25%)


TC235979
GMGI.071508
923000
924768
similar to






UniRef100_Q93XA3






Cluster: Homeodomain






leucine zipper protein






HDZ3; n = 1; Phaseolus







vulgaris|Rep:







Homeodomain leucine






zipper protein HDZ3 -







Phaseolus vulgaris (Kidney







bean) (French bean) =






partial (86%)


TA46165_3847
Glycine_
923000
924779
Homeodomain leucine



max_release_2


zipper protein HDZ3






[Phaseolus vulgaris






(Kidney bean) (French






bean)]


AW351287
Glycine_
923128
924720
Homeodomain leucine



max_release_2


zipper protein HDZ3






[Phaseolus vulgaris






(Kidney bean) (French






bean)]


CA785782
Glycine_
925713
925880
NA



soja_release_2





Pvcon8364
Phaseolus_
925735
926609
UniRef100_A7PMB7



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMB7_VITVI






1.00E−27


BE248998
MTGI.071708
926978
927524
similar to






UniRef100_Q7F8S7






Cluster: PHD finger-like






protein, n = 1, Oryza sativa






Japonica Group|Rep: PHD






finger-like protein - Oryza







sativa subsp. japonica







(Rice), partial (4%)


TC35470
LJGI.070108
928423
929804
similar to






UniRef100_A7PMB8






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(9%)


TA11035_34305
Lotus_
928423
929825
PHD finger-like protein



japonicus_


[Oryza sativa (japonica



release_1


cultivar-group)]


CA911004
Phaseolus_
934882
939256
T13O15.10 protein



coccineus_


[Arabidopsis thaliana



release_2


(Mouse-ear cress)]


AI856399
GMGI.071508
937577
938041
NA


AI856399
Glycine_
937577
938106
NA



max_release_2





AW348703
Glycine_
963043
963750
NA



max_release_2





TC276191
GMGI.071508
963049
964044
weakly similar to






UniRef100_A7PZY3






Cluster: Chromosome chr8






scaffold_41 = whole






genome shotgun sequence; n = 1;







Vitis vinifera|Rep:







Chromosome chr8






scaffold_41 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (21%)


BQ628183
Glycine_
963625
964044
NA



max_release_2





BQ080193
Glycine_
963695
967475
NA



max_release_2





TA52645_3847
Glycine_
963720
967461
NA



max_release_2





TC256882
GMGI.071508
963774
967475
weakly similar to






UniRef100_A7PZY3






Cluster: Chromosome chr8






scaffold_41 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr8






scaffold_41 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (45%)


BG156825
Glycine_
971121
971284
NA



max_release_2





BG156825
GMGI.071508
971125
971284
NA


BU545761
Glycine_
971300
971901
NA



max_release_2





BU550718
Glycine_
971255
973578
NA



max_release_2





TA72701_3847
Glycine_
972120
972806
NA



max_release_2





TC271942
GMGI.071508
972201
972806
NA


TC269989
GMGI.071508
971255
973827
similar to






UniRef100_A7P2M9






Cluster: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence; n = 1;







Vitis vinifera|Rep:







Chromosome chr1






scaffold_5 = whole genome






shotgun sequence - Vitis







vinifera (Grape) = partial







(63%)


BI317782
Glycine_
971510
973827
NA



max_release_2





BI893512
Glycine_
971537
973848
NA



max_release_2





BI893512
GMGI.071508
971671
973848
similar to






UniRef100_A7P2M9






Cluster: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence; n = 1;







Vitis vinifera|Rep:







Chromosome chr1






scaffold_5 = whole genome






shotgun sequence - Vitis







vinifera (Grape) = partial







(54%)


CO985587
Glycine_
974859
976255
Putative GTP-binding



max_release_2


membrane protein LepA






[Oryza sativa (japonica






cultivar-group)]


AW596868
Glycine_
976346
976856
NA



max_release_2





AW596868
GMGI.071508
976412
976856
similar to






UniRef100_A2Q5T1






Cluster: Tetratricopeptide-






like helical; n = 1; Medicago







truncatula|Rep:







Tetratricopeptide-like






helical - Medicago







truncatula (Barrel medic) =







partial (5%)


CA901672
Phaseolus_
983905
984264
Aldehyde dehydrogenase 1



coccineus_


precursor [Lotus



release_2



corniculatus (Bird's-foot







trefoil)


WmFPC_

899736
1068750
NA


Contig4169






FE898889
Phaseolus_
983908
984989
UniRef100_A7PD33



vulgaris


Chromosome chr17






scaffold_12, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PD33_VITVI






2.00E−79


TC273361
GMGI.071508
984396
986122
similar to






UniRef100_P93344






Cluster: Aldehyde






dehydrogenase; n = 1;







Nicotiana tabacum|Rep:







Aldehyde dehydrogenase -







Nicotiana tabacum







(Common tobacco) = partial






(37%)


BE473475
Glycine_
984960
986122
Aldehyde dehydrogenase



max_release_2


[Nicotiana tabacum






(Common tobacco)]


CV539672
Phaseolus_
985959
987101
UniRef100_P93344



vulgaris


Aldehyde dehydrogenase






(NAD+) n = 1






Tax = Nicotiana tabacum






RepID = P93344_TOBAC






7.00E−50


AV410805
LJGI.070108
987592
987888
similar to






UniRef100_A7PMC7






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(6%)


TC265505
GMGI.071508
1011306
1012664
similar to






UniRef100_A7PMD1






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (28%)


TA51641_3847
Glycine_
1011306
1013783
Putative high-affinity



max_release_2


potassium transporter






protein 1 [Nicotiana







tabacum (Common







tobacco)]


CB540416
Phaseolus_
1012333
1013531
UniRef100_A7PMD1



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMD1_VITVI






5.00E−97


BM891067
GMGI.071508
1012675
1013617
similar to






UniRef100_A7PMD1






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (22%)


TC131883
MTGI.071708
1012665
1014070
similar to






UniRef100_A7PMD1






Cluster: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence,






n = 1, Vitis vinifera|Rep:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(34%)


asmbl_11884
Vigna_
1012674
1014123
NA



unguiculata





BE330787
Glycine_
1013888
1014305
Putative high-affinity



max_release_2


potassium transporter






protein [Phytolacca







esculenta (Food







pokeberry)]


FD792954
Phaseolus_
1013779
1014573
UniRef100_A7PMD1



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMD1_VITVI






3.00E−57


TC244134
GMGI.071508
1014004
1014793
similar to






UniRef100_A7PMD1






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (15%)


TA51642_3847
Glycine_
1013926
1014875
Putative high-affinity



max_release_2


potassium transporter 1






[Nicotiana rustica (Aztec






tobacco)]


TC242106
GMGI.071508
1013926
1014875
similar to






UniRef100_A7PMD1






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (15%)


BI970123
Glycine_
1014128
1014721
Putative potassium



max_release_2


transporter HAK1p






[Mesembryanthemum







crystallinum (Common ice







plant)]


BQ080303
Glycine_
1018604
1019142
NA



max_release_2





TC270109
GMGI.071508
1018604
1019142
weakly similar to






UniRef100_UPI0000196D3






9 Cluster: NHL repeat-






containing protein; n = 1;







Arabidopsis thaliana|Rep:







NHL repeat-containing






protein - Arabidopsis







thaliana = partial (4%)



BQ080219
Glycine_
1018604
1019579
NA



max_release_2





TA62145_3847
Glycine_
1021347
1023221
NA



max_release_2





TC245123
GMGI.071508
1021347
1023221
similar to






UniRef100_A7PMD2






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (31%)


asmbl_11885
Vigna_
1022417
1022510
NA



unguiculata





CA784724
Glycine_
1046117
1047384
NA



max_release_2





CA784724
GMGI.071508
1046400
1047384
similar to






UniRef100_A7Q2E7






Cluster: Chromosome chr1






scaffold_46 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr1






scaffold_46 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (17%)


Pvcon4015
Phaseolus_
1047011
1048610
UniRef100_A5ATC1



vulgaris


Putative uncharacterized






protein n = 1 Tax = Vitis







vinifera







RepID = A5ATC1_VITVI






1.00E−146


BQ742289
Glycine_
1048650
1048767
NA



max_release_2





BF068315
GMGI.071508
1057203
1057316
similar to






UniRef100_Q8MIG1






Cluster: Skinkine; n = 1; Sus







scrofa|Rep: Skinkine - Sus








scrofa (Pig) = partial (12%)



BF068315
Glycine_
1057203
1057506
NA



max_release_2





BU083500
GMGI.071508
1058026
1058431
UniRef100_Q2R023






Cluster: Expressed protein;






n = 1; Oryza sativa Japonica






Group|Rep: Expressed






protein - Oryza sativa =






partial (2%)


TA74227_3847
Glycine_
1058026
1059408
NA



max_release_2





BI423963
GMGI.071508
1058432
1059275
similar to






UniRef100_Q2QDD6






Cluster: Nodulin-like






protein; n = 1; Gossypium







hirsutum|Rep: Nodulin-like







protein - Gossypium







hirsutum (Upland cotton)







(Gossypium mexicanum) =






partial (22%)


TC237120
GMGI.071508
1063015
1063972
UniRef100_Q39819






Cluster: Hsp22.3; n = 1;







Glycine max|Rep: Hsp22.3 -








Glycine max (Soybean) =







complete


CA802234
Glycine_
1061477
1067499
Similarity to nodulin



soja_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


BI425574
GMGI.071508
1065519
1066854
weakly similar to






UniRef100_A7PMD8






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (21%)


BI425574
Glycine_
1065519
1066940
Hypothetical protein



max_release_2


[Medicago truncatula






(Barrel medic)]


AU251786
LJGI.070108
1066790
1067424
weakly similar to






UniRef100_A7Q2G7






Cluster: Chromosome chr1






scaffold_46, whole genome






shotgun sequence, n = 1,







Vitis vinifera|Rep:







Chromosome chr1






scaffold_46, whole genome






shotgun sequence - Vitis







vinifera (Grape), partial







(7%)


Pvcon8451
Phaseolus_
1065511
1068752
UniRef100_A7PMD8



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMD8_VITVI






7.00E−91


TC260900
GMGI.071508
1065796
1069134
weakly similar to






UniRef100_A7PMD8






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (41%)


TA63020_3847
Glycine_
1067436
1069134
NA



max_release_2





CA783703
Glycine_
1068257
1068879
NA



soja_release_2





TA58065_3847
Glycine_
1074998
1076541
AT3g28050/MMG15_6



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


TC251785
GMGI.071508
1074998
1076541
similar to






UniRef100_Q8L9I2






Cluster: Nodulin MtN21-






like protein; n = 1;







Arabidopsis thaliana|Rep:







Nodulin MtN21-like






protein - Arabidopsis







thaliana (Mouse-ear cress) =







partial (16%)


CB280623
Phaseolus_
1075036
1076540
AT3g28050/MMG15_6



vulgaris_


[Arabidopsis thaliana



release_2


(Mouse-ear cress)]


EH043320
Arachis_
1075056
1077422
Cluster: Hypothetical



stenosperma_


protein, n = 1, Medicago



release_5



truncatula|Rep:







Hypothetical protein -







Medicago truncatula







(Barrel medic)


asmbl_11886
Vigna_
1075036
1077585
NA



unguiculata





BQ094260
Glycine_
1075548
1077551
Nodulin-like protein



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


BF598290
Glycine_
1075557
1077593
Nodulin-like protein



soja_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


Pvcon6314
Phaseolus_
1075036
1078733
UniRef100_A7PMD8



vulgaris


Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMD8_VITVI






1.00E−105


TA58064_3847
Glycine_
1075337
1079189
AT3g28050/MMG15_6



max_release_2


[Arabidopsis thaliana






(Mouse-ear cress)]


TC255833
GMGI.071508
1075337
1079189
weakly similar to






UniRef100_A7PMD8






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (64%)


BG042956
Glycine_
1078885
1079014
NA



soja_release_2





TC263589
GMGI.071508
1086875
1091139
similar to






UniRef100_A7PME0






Cluster: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence;






n = 1; Vitis vinifera|Rep:






Chromosome chr14






scaffold_21 = whole






genome shotgun sequence -







Vitis vinifera (Grape) =







partial (35%)


TA50577_3847
Glycine_
1086875
1094082
Alpha-dioxygenase [Pisum



max_release_2



sativum (Garden pea)]



asmbl_11887
Vigna_
1089135
1092345
NA



unguiculata





CA410123
Lupinus_
1092182
1092694
Alpha-dioxygenase [Pisum



albus_release_2



sativum (Garden pea)



Pvcon4974
Phaseolus_
1091225
1093836
UniRef100_Q5GQ66



vulgaris


Alpha-dioxygenase n = 1






Tax = Pisum sativum






RepID = Q5GQ66_PEA E-0


TC243973
GMGI.071508
1091177
1094141
similar to






UniRef100_Q5GQ66






Cluster: Alpha-






dioxygenase; n = 1; Pisum







sativum|Rep: Alpha-







dioxygenase - Pisum







sativum (Garden pea) =







partial (61%)


asmbl_11888
Vigna_
1092518
1093829
NA



unguiculata





M0206286
SEQ.
1209562
1210392
SEQ ID NO: 17



Listing





M0206054
SEQ.
1465522
1465187
SEQ ID NO: 18



Listing





M0205375
SEQ.
2010060
2009541
SEQ ID NO: 19



Listing





toGm13
DAGchainer
1046081
4647877
Ks0.2059


NA
Glyma1
1
50600000
NA









Sequences for the genes provided above can be obtained from the World Wide Web (or Internet) using the identifiers provided in Column 1 (Locus/Display Name) or Column 5 (ADDITIONAL LOCUS INFORMATION) from the following internet locations: “soybase.org” (described in Grant et al., Nucleic Acids Research, 2010, Vol. 38, Database issue D843-D846) or soybase.org/gbrowse/cgi-bin/gbrowse/gmax1.01/ (see Hyten D L, Choi I-Y, Song Q, Specht J E, Carter T E et al. (2010) A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping. Crop Science 50:960-968. (Crop Science); and Hyten D L, Cannon S B, Song Q, Weeks N, Fickus E W et al. (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11(1): 38);














“phytozome.net” or “phytozome.net/cgi-bin/gbrowse/soybean/


?name=Gm09”;


“www.plantgdb.org” or “plantgdb.org/GmGDB/(Assembly version


Glyrnal.170 (Apr 2009)” ; and,


“ncbi.nlm.nih.gov/sites/entrez” and subsites “ncbi.nlm.nih.gov/nucest”,


“ncbi.nlm.nih.gov/dbEST”, “ncbi.nlm.nih.gov/genbank/”,


“.ncbi.nlm.nih.gov/sites/genome”,


“ncbi.nlm.nih.gov/unigene”, and “ncbi.nlm.nih.gov/UniGene/


UGOrg.cgi?TAXID=3847”.








Claims
  • 1. A method for producing a soybean plant comprising in its genome an introgressed favorable dicamba tolerance locus haplotype and a transgene that confers resistance to dicamba, the method comprising the steps of: (a) crossing a first soybean plant comprising a favorable dicamba tolerance locus haplotype with a second soybean plant comprising an unfavorable dicamba tolerance locus haplotype associated with dicamba-mediated malformation;(b) obtaining a population of soybean plants from progeny of the cross of step (a) that are segregating for the favorable dicamba tolerance locus haplotype;(c) genotyping soybean plants in the population of step (b) with respect to at least one polymorphic nucleic acid marker in each of at least two linkage group L genomic regions selected from: i) a first linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6), wherein the region comprises the locus of M0101742 (SEQ ID NO: 5);(ii) a second linkage group L genomic region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12), wherein the region comprises the loci M0205350 (SEQ ID NO:10) and M0102027 (SEQ ID NO: 11); and(iii) a third linkage group L genomic region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8), wherein the region comprises the locus NGMAX008197032 (SEQ ID NO: 52); and(d) selecting a soybean plant from said population based on the genotype determined in step (c), said selected plant comprising the allelic states associated with the favorable dicamba tolerance locus haplotype in at least two of (i), (ii), and (iii), wherein the selected soybean plant comprises a transgene that confers resistance to dicamba or wherein the transgene that confers resistance to dicamba is introduced into the selected soybean plant or progeny thereof, thereby obtaining a soybean plant comprising in its genome an introgressed favorable dicamba tolerance locus haplotype and the transgene that confers resistance to dicamba.
  • 2. The method of claim 1, wherein said selected soybean plant and/or progeny of the selected soybean plant is exposed to a dosage of dicamba sufficient to cause dicamba-mediated malformation in a soybean plant comprising in its genome the unfavorable dicamba tolerance locus haplotype and a transgene that confers resistance to dicamba.
  • 3. The method of claim 1, wherein the method further comprises the step (e) of performing one or more backcrosses of the selected plant of step (d) to a recurrent parent second soybean plant comprising the unfavorable dicamba tolerance locus haplotype and repeating steps (b), (c), and (d).
  • 4. The method of claim 1, wherein the favorable dicamba tolerance locus haplotype comprises: a TT or an AT allele located at nucleotide 148 of nucleic acid marker M0205350 (SEQ ID NO: 10), located within the second linkage group L genomic region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12);a TT allele or a CT allele located at nucleotide 1206 of nucleic acid marker M0101742 (SEQ ID NO: 5), located within the first linkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6);a CC allele located at nucleotide 349 of nucleic acid marker M0102027 (SEQ ID NO: 11), located within the second linkage group L genomic region that is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12); andan AA allele located at nucleotide 201 of nucleic acid marker NGMAX008197032 (SEQ ID NO: 52), located within the third linkage group L genomic region that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8).
  • 5. The method of claim 4, wherein said haplotype is determined by genotyping in step (c) the SNPs located at nucleotides 148, 349, and 201 of nucleic acid markers M0205350 (SEQ ID NO: 10), M0102027 (SEQ ID NO: 11), and marker NGMAX008197032 (SEQ ID NO: 52), respectively.
  • 6. The method of claim 4, wherein said haplotype is determined by genotyping a SNP in nucleic acid marker M0101742 (SEQ ID NO: 5).
  • 7. The method of claim 1, wherein the method further comprises three backcrosses to the second soybean plant as a recurrent parent and wherein genome wide nucleic acid markers are used to recover 95% or greater of the recurrent parent second soybean plant genome in the soybean plant comprising in its genome the introgressed favorable dicamba tolerance locus haplotype.
  • 8. The method of claim 1, wherein said soybean plants are genotyped in step (c) with respect to the SNPs in nucleic acid markers M0205350 (SEQ ID NO: 10), M0101742 (SEQ ID NO: 5), and M0102027 (SEQ ID NO: 11).
  • 9. The method of claim 3, wherein at least 90% of the genomic sequences in the soybean plant comprising the introgressed favorable dicamba tolerance locus haplotype carry markers characteristic of the second soybean plant.
CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a 35 U.S.C. § 371 National Phase of International Patent Application No. PCT/US2013/042349, filed May 23, 2013 and incorporated herein by reference in its entirety, which claims the benefit of U.S. Patent Application No. 61/779,739, filed Mar. 13, 2013; U.S. Patent Application No. 61/753,725, filed Jan. 17, 2013; U.S. Patent Application No. 61/753,693, filed Jan. 17, 2013; U.S. Patent Application No. 61/650,869, filed May 23, 2012; and U.S. Patent Application No. 61/650,852, filed May 23, 2012, each of which is incorporated herein by reference in its entirety.

PCT Information
Filing Document Filing Date Country Kind
PCT/US2013/042349 5/23/2013 WO 00
Publishing Document Publishing Date Country Kind
WO2013/177356 11/28/2013 WO A
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Related Publications (1)
Number Date Country
20150143577 A1 May 2015 US
Provisional Applications (5)
Number Date Country
61650869 May 2012 US
61650852 May 2012 US
61753725 Jan 2013 US
61753693 Jan 2013 US
61779739 Mar 2013 US