GENE CONTROLLING CHASMOGAMY/CLEISTOGAMY OF PLANT AND USE THEREOF

TECHNICAL FIELD

The present invention relates to a gene controlling chasmogamy/cleistogamy of a plant, as well as relates to determination of chasmogamy/cleistogamy of a plant and production of a cleistogamous plant using the gene.

BACKGROUND ART

World's important cereals such as rice, wheat, and barley are all crop plants whose seeds (embryos and albumens) are eaten, and are each a self-pollinating crop plant which produces seeds in such a manner that a stamen and a pistil develop in each single flower, and undergo self-pollination. Flowers of these crop plants generally open at pollination, and anthers of the flowers generally project to the outside (chasmogamy). However, it is known that, since self-pollination inside the flowers is possible and open-flowering is not necessarily required for fructification, flowers of these crop plants may undergo closed-flower pollination (cleistogamy), where pollination occurs without opening of the flowers, depending on environmental conditions (NPL1). Meanwhile, it has been known from the past that some barley varieties do not open their flowers, and undergo closed-flower pollination, genetically (NPL 2).

Recently, the cleistogamy of barley has been shown to be associated with a gene effective for improvement of resistance to Fusarium ear blight of barley, and it has been revealed that introduction of cleistogamy is extremely effective means for preventing infection of barley with Fusarium ear blight (NPL 3). Fusarium ear blight is the most important disease among plants of the subfamily Pooideae, and the enhancement of resistance against Fusarium ear blight has been sought. Accordingly, the introducing of cleistogamy is necessary for quality improvement of barley.

Conventional breeding of a crop plant has required a large farm field, a lot of man power, and a considerable period, because it is necessary to mate a cultivar, a wild species, or the like having a target trait, actually raise many individuals, select individuals having the target trait, and genetically fix the target trait. For example, when the target trait is chasmogamy/cleistogamy, it is necessary to specify individuals to be selected, by raising a selection target population, and investigating at anthesis whether each individual is chasmogamous or cleistogamous.

In this respect, breeding methods based on selection using a genetic marker as an index have been used recently in order to shorten the breeding period and to reduce manpower and the farm field area. The breeding based on such a genetic marker enables easy estimation about the presence or absence of the target trait on the basis of the genotype of the marker, and hence enables selection at a seed or seedling stage. Breeding of a cleistogamous variety using a marker is proposed also for barley (PTLs 1 and 2).

However, the breeding of a cleistogamous variety using a marker is inferior in specificity (accuracy) to the breeding using a gene controlling the target trait itself as a target. Hence, it is necessary to identify a gene controlling the chasmogamy/cleistogamous trait in order to conduct more efficient breeding.

For this reason, the identifying of a gene controlling the closed-flower pollination character of barley has been attempted over years, but the gene is yet to be identified, for example, because genomic analysis information on barley is insufficient.

CITATION LIST
Patent Literature

[PTL 1] Japanese Unexamined Patent Application Publication No. 2004-180570

[PTL 2] Japanese Unexamined Patent Application Publication No. 2005-229854

Non Patent Literature

[NPL 1] Hoshikawa Kiyochika, “The Growing Rice Plant”, Rural Culture Association Japan, 1975, p 249 to 252

[NPL 2] Briggs D. E., “Barley”, Chapman and Hall, London, ISBN: 041211870X, 1978, p. 45

[NPL 3] Yoshida Megumi, Kawada Naoyuki, Tohnooka Takuji, Breeding Research 4 (Suppl. 2), p. 303, (2002), (proceedings of 102nd Meeting of Japanese Society of Breeding; Japanese Society of Breeding)

SUMMARY OF INVENTION
Technical Problem

The present invention has been made in view of such circumstances, and an object of the present invention is to identify a novel gene controlling chasmogamy/cleistogamy of a plant such as barley, and elucidate the mechanism of development of chasmogamy/cleistogamy. Moreover, another object of the present invention is to provide a method for efficiently determining chasmogamy/cleistogamy of a plant on the basis of the elucidated mechanism of development of chasmogamy/cleistogamy. Still another object of the present invention is to provide a method for efficiently producing a plant having a closed-flower pollination trait on the basis of the elucidated mechanism of development of chasmogamy/cleistogamy.

Solution to Problem

To achieve the above-described objects, the present inventors have attempted to identify a gene controlling chasmogamy/cleistogamy of barley by a positional cloning approach. Here, the situation was that it was extremely difficult to identify a target gene from only the known genomic information regarding barley, because the entire genomic base sequence was not determined for barley. Hence, the present inventors first built, by a unique approach, comparative genetic maps between chromosome 4 of rice and chromosome 2H of barley (Patent Document 1) in which the presence of the target gene was suggested (FIG. 1). Subsequently, by use of markers on the genetic map, an analysis was conducted on a large-scale F2 segregation population of a chasmogamous barley variety “Azumamugi” and a cleistogamous barley variety “Kanto Nakate Gold.” Thus, a candidate region in which the cleistogamy gene cly1 seemed to be present was narrowed to a region of approximately 0.7 cM (FIG. 2 and FIG. 3A). The approximately 0.7-cM genome region corresponded to a 90-kb genome region of rice (FIG. 2 and FIG. 3A). The present inventors found 11 genes within the genomic region of rice, and presumed that, of these genes, a gene encoding a transcription factor having two AP2 domains was a gene corresponding to a chasmogamy gene Cly1 of barley.

EST base sequences partially encoding the barley gene corresponding to the AP2 gene of rice were extracted from databases, and a BAC library of a chasmogamous variety Morex was screened by use of markers created based on the sequence information. The base sequences of selected BAC clones were determined, and new markers were prepared based on the information concerning the base sequences. Then, by use of the markers, a large-scale F2 segregation population analysis was conducted. As a result, the candidate region in which cly1 seemed to be present was narrowed to a region of approximately 7 kb (FIG. 3A). Since any gene other than the AP2 gene was present in the 7-kb region, it was supported that cly1 encoded AP2.

A comparison was made among base sequences of AP2 genes of barley varieties. As a result, only one single-nucleotide polymorphism associated with chasmogamy/cleistogamy of barley was found among the microRNA (miR172) target sites of the AP2 genes (FIG. 3B). For this reason, it was conceivable that this single-nucleotide polymorphism caused the difference in affinity between miR172 and the mRNA of the AP2 gene. In addition, mRNAs of AP2 genes (Cly1 ) of chasmogamous types underwent cleavage at the target site of microRNA, whereas mRNAs of the AP2 genes (cly1) of cleistogamous types did not undergo cleavage (FIGS. 5D and 5E). These facts revealed that the presence or absence of cleavage of the mRNA of the AP2 gene determines the deference in chasmogamous/cleistogamous phenotype of barley. The base sequence of the miR172 target site is highly conserved also in chasmogamous plants in addition to barley, and these chasmogamous plants have base sequences which undergo cleavage with miR172 (FIG. 6). Accordingly, the present inventors have found that, by analyzing the base sequences of AP2 genes of plants including barley, it is possible to determine an open-flower pollination character or a closed-flower pollination character of the plants. Moreover, the present inventors have found that, by use of a cleistogamous-type AP2 gene (cly1), it is possible to impart a cleistogamous trait to plants including barley.

Accordingly, the present invention relates to a gene controlling chasmogamy/cleistogamy of a plant, as well as determination of chasmogamy/cleistogamy of a plant and production of a cleistogamous plant, which make use of the gene. More specifically, the present invention provides the following:

(1) A DNA which does not undergo cleavage with a microRNA comprising the base sequence of SEQ ID NO: 10, and which imparts cleistogamy to a plant, wherein the DNA is described in any one of the following (a) to (c):

(a) a DNA comprising a coding region of the base sequence shown in SEQ ID NO: 1, 2, 4, or 5;

(b) a DNA comprising a base sequence in which one or a plurality of bases are substituted, deleted, added, and/or inserted in a coding region of the base sequence shown in SEQ ID NO: 1, 2, 4, 5, 7, or 8; and

(c) a DNA which hybridizes with a DNA comprising the base sequence shown in SEQ ID NO: 1, 2, 4, 5, 7, or 8 under stringent conditions.

(2) The DNA according to (1), which has a microRNA target site comprising a base sequence in which one or several bases are substituted in comparison with the base sequence shown in SEQ ID NO: 11.

(3) The DNA according to (2), wherein the substitution of the bases in the microRNA target site does not involve change in any encoded amino acid.

(4) The DNA according to (2), wherein the substitution of the bases in the microRNA target site is substitution of at least one base selected from the group consisting of “a” at position 2, “a” at position 8, and “a” at position 14 in the base sequence shown in SEQ ID NO: 11.

(5) A vector comprising the DNA according to any one of (1) to (4).

(6) A plant cell into which the DNA according to any one of (1) to (4) is introduced.

(7) A plant comprising the cell according to (6).

(8) A plant which is a progeny or a clone of the plant according to (7).

(9) A propagation material of the plant according to (7) or (8).

(10) A method for producing a plant having a cleistogamous trait, comprising a step of introducing the DNA according to any one of (1) to (4) into a plant.

(11) An agent for imparting a cleistogamous trait to a plant, comprising the DNA according to (1) to (4) or a vector into which the DNA is inserted.

(12) A method for determining chasmogamy/cleistogamy of a plant, comprising:

analyzing a base sequence of a DNA of a test plant; and

comparing the analyzed base sequence with a reference base sequence, wherein

the DNA is described in any one of the following (a) to (c):

(a) a DNA comprising a coding region of the base sequence shown in SEQ ID NO: 1, 2, 4, 5, 7, or 8;

(c) a DNA which hybridizes with a DNA comprising the base sequence shown in SEQ ID NO: 1, 2, 4, 5, 7, or 8 under stringent conditions.

(13) A method for determining chasmogamy/cleistogamy of a plant, comprising detecting cleavage, with a microRNA comprising the base sequence shown in SEQ ID NO: 10, of a transcription product of the DNA according to any one of (1) to (4) of a test plant.

(14) A method for breeding a cleistogamous plant, comprising the steps of:

(a) mating a cleistogamous plant variety with any variety;

(b) determining, by the method according to (12) or (13), chasmogamy/cleistogamy of individuals which are obtained by the mating in step (a); and

Note that, in the present invention, the “chasmogamy” means a phenotype in which an anther projects from a glumous flower at anthesis, and the “cleistogamy” means a phenotype in which an anther does not project from a glumous flower at anthesis.

Advantageous Effects of Invention

According to the present invention, a novel gene Cly1/cly1 controlling chasmogamy/cleistogamy of a plant was identified, and the position of the gene on the chromosome, the structure of the gene, and the mechanism of chasmogamy/cleistogamy development were elucidated. As a result, provided are a method for determining chasmogamy/cleistogamy of a plant, targeting the Cly1/cly1 gene, and a method for breeding a cleistogamous plant, using the determination method. Moreover, a method for producing a cleistogamous plant variety, using the cly1 gene, is provided. The Cly1/cly1 gene controlling chasmogamy/cleistogamy is focused in the determination of chasmogamy/cleistogamy of a plant and the production and the breeding of a cleistogamous plant variety according to the present invention. Hence, these are more accurate than conventional methods using markers linked with the gene. For this reason, these methods make it possible to determine chasmogamy/cleistogamy of a plant, to produce or breed a cleistogamous plant variety more specifically and more efficiently than conventional methods.

BRIEF DESCRIPTION OF DRAWINGS

[FIG. 1] FIG. 1 shows comparative maps of Cly1/cly1 genes.

[FIG. 2] FIG. 2 shows high resolution maps of the Cly1/cly1 genes.

[FIG. 3] FIG. 3 shows positional cloning of the Cly1/cly1 genes, where A is a genetic map constructed from an Azumamugi (AZ)×Kanto Nakate Gold (KNG) F2 population, and B shows sequence comparisons between alleles of the miR712 target site.

[FIG. 4] FIG. 4 shows phylogeny of AP2 homologs from A. thaliana, rice, maize, wheat, and barley.

[FIG. 5] FIG. 5 shows expression of the Cly1/cly1 gene, where A shows the 3′ end of the gene, including Exon 10 which has the miR172 target site, B is a photograph showing gene expression in an immature spike at the awn primordium stage of Azumamugi (AZ), C is a photograph of electrophoresis showing gene expression in an immature spike throughout a series of developmental stages, D is a photograph of electrophoresis showing results of detection of transcription products cleaved by modified 5′RACE, and E shows a cleavage site of miR172.

[FIG. 6] FIG. 6 is a diagram showing miR172 target sites of Cly1/cly1 homologs of grass species.

[FIG. 7] FIG. 7 is a diagram showing a phylogenetic analysis of the Cly1/cly1 gene sequence of barley.

[FIG. 8] FIG. 8 is a diagram showing polymorphic sites in the Cly1/cly1 gene sequence of barley.

[FIG. 9] FIG. 9 shows photographs showing lodicules of chasmogamous barley and cleistogamous barley, where A is a photograph showing a morphology in which a lodicule (lo) located at the base of a stamen (st) opens a spikelet by pushing apart a lemma (le) and a palea (pa), B shows a spike of chasmogamous barley at anthesis, C shows a spike of cleistogamous barley at anthesis, D shows a lodicule of chasmogamous barley, E shows a lodicule of cleistogamous barley, F shows a section of a spikelet of chasmogamous barley, G shows a section of a spikelet of cleistogamous barley, and carpels (cp) are surrounded by other flower organs.

DESCRIPTION OF EMBODIMENTS

The present invention provides a DNA (hereinafter referred to as “cleistogamous-type DNA”) encoding which imparts a cleistogamous trait to a plant. A cly1 DNA of the present invention does not undergo cleavage with miR172 (a microRNA comprising the base sequence shown in SEQ ID NO: 10), and, when expressed in a plant, imparts a cleistogamous trait to the plant.

A base sequence of the cly1 cDNA derived from a cleistogamous barley variety “Kanto Nakate Gold” is shown in SEQ ID NO: 1, abase sequence of a cly1 genomic DNA derived therefrom is shown in SEQ ID NO: 2, and an amino acid sequence of a protein encoded by these DNAs is shown in SEQ ID NO: 3. These sequences were identified by the present inventors. In addition, a base sequence of a cly1 cDNA derived from a cleistogamous barley variety “SV230” is shown in SEQ ID NO: 4, a base sequence of a cly1 genomic DNA derived therefrom is shown in SEQ ID NO: 5, and an amino acid sequence of a protein encoded by these DNAs is shown in SEQ ID NO: 6. These sequences were also identified by the present inventors. Meanwhile, a base sequence of a Cly1 cDNA derived from a chasmogamous barley variety “Azumamugi” is shown in SEQ ID NO: 7, a base sequence of a Cly1 genomic DNA derived therefrom is shown in SEQ ID NO: 8, and an amino acid sequence of a protein encoded by these DNAs is shown in SEQ ID NO: 9. These sequences were also identified by the present inventors.

An embodiment of the cleistogamous-type DNA of the present invention is a DNA comprising a coding region of the base sequence shown in SEQ ID NO: 1 or 2). Another embodiment of the cleistogamous-type DNA of the present invention is a DNA comprising a coding region of the base sequence shown in SEQ ID NO: 4 or 5). Moreover, the cleistogamous-type DNA of the present invention encompasses DNAs (various DNAs based on degeneracy of codons) encoding a protein comprising the amino acid sequence shown in SEQ ID NO: 3 and DNAs (various DNAs based on degeneracy of codons) encoding a protein comprising the amino acid sequence shown in SEQ ID NO: 6, as long as these DNAs encode transcription products which do not undergo cleavage with miR172, and impart a cleistogamous trait to a plant.

As shown in Examples, a comparison between the base sequence of the cly1 gene derived from the chasmogamous barley variety “Azumamugi” and the base sequence of the cly1 gene derived from the cleistogamous barley variety “Kanto Nakate Gold” shows that a base at a single position in the miR172 target site is different between them (FIG. 3B). In addition, a comparison between the base sequence of the Cly1 gene derived from the chasmogamous barley variety “Azumamugi” and the base sequence of the cly1 gene derived from the cleistogamous barley variety “SV230” shows that bases at two positions in the miR172 target site are different between them (FIG. 3B). Other barley varieties whose miR172 target sites have the same base sequence as that of “Azumamugi” exhibit a chasmogamous trait, whereas other barley varieties whose miR172 target sites have the same base sequence as that of “Kanto Nakate Gold” or “SV230” exhibit a cleistogamous trait. Hence, it is conceivable that the base variation in the miR172 target site influences the cleavage of the transcription product (mRNA) with miR172, and determines chasmogamy/cleistogamy of barley. Actually, the cleavage of the transcription product of the cly1 gene of “Kanto Nakate Gold” with miR172 is suppressed when compared with that of the transcription product of the Cly1 gene of “Azumamugi” (FIG. 5D and 5E).

Under the current state of the art, those skilled in the art can carry out a modification of a base sequence of a Cly1 DNA of a specific chasmogamous barley variety (for example, Azumamugi) so that the cleavage of the transcription product of the base sequence with miR172 can be suppressed. It is also possible to carry out various modifications of a base sequence of a cly1 DNA of a specific cleistogamous barley variety (for example, Kanto Nakate Gold, SV230), as long as the suppression of the cleavage of the transcription product of the base sequence with miR172 is maintained. In addition, mutation in the base sequence may occur even in the natural world. Accordingly, the present invention encompasses a DNA comprising a base sequence in which one or a plurality of bases are substituted, deleted, added, and/or inserted in a coding region of the base sequence (SEQ ID NO: 1, 2, 4, 5, 7, or 8) of the Cly1 /cly1 gene of Azumamugi, Kanto Nakate Gold, or SV230, as long as the cleavage with miR172 is suppressed, and the DNA imparts a cleistogamous trait to a plant. Here, the term “a plurality” means generally 50 bases or less, preferably 30 bases or less, further preferably 10 bases or less, and several bases or less (for example, 5 bases or less, 3 bases or less, 2 bases or less, and 1 base) in the entire base sequence in the coding region of the gene.

The cleistogamous-type DNA of the present invention is preferably a DNA having a miR172 target site comprising a base sequence in which one or several bases are substituted in comparison with the base sequence shown in SEQ ID NO: 11 (the target sequence which undergoes cleavage with miR172). Here, the term “several bases” represents the number of bases in a range within which the cleavage with miR172 is suppressed, and is generally several bases or less (for example, 5 bases or less, 3 bases or less, 2 bases or less, or 1 base). The substitution of the bases in the miR172 target site is preferably one which does not involve change in any encoded amino acid. The substitution of the bases is, for example, substitution of at least one base selected from the group consisting of “a” at position 2, “a” at position 8, and “a” at position 14 in the base sequence shown in SEQ ID NO: 11. For example, the base sequence of the miR172 target sites in the cly1 genes of MG, GP, SV002, SV235, SV241, SV242, SV237, and SV235 is a base sequence in which “a” at position 8 is substituted with “g” in the base sequence shown in SEQ ID NO: 11 (FIG. 3B), as in the case with Kanto Nakate Gold. Meanwhile, for example, the base sequence of the miR172 target sites in the cly1 genes of SV223, SV253, and SV255 is abase sequence in which both “a”s at positions 2 and 14 are substituted with “c”s in the base sequence shown in SEQ ID NO: 11 (FIG. 3B), as in the case with SV230. The present invention encompasses the cly1 DNAs derived from these varieties.

Moreover, under the current state of the art, when a Cly1/cly1 gene is obtained from a specific barley variety (for example, Azumamugi, Kanto Nakate Gold, or SV230), those skilled in the art can obtain a DNA (hereinafter referred to as “homologous DNA”) encoding a homologous gene controlling chasmogamy/cleistogamy from other plant by utilizing the base sequence information of the gene. Moreover, it is also possible to prepare a DNA which imparts a cleistogamous trait to a plant by modification of the base sequence of the obtained homologous DNA. Examples of the plant used to obtain such a homologous DNA include grass species such as barley, wheat, rye, Triticale, oat, rice, maize, and A. thaliana. The plant is preferably a plant of the family Poaceae such as barley, wheat, rye, Triticale, oat, rice, or maize, more preferably a plant of the subfamily Pooideae such as barley, wheat, rye, Triticale, or oat, and most preferably barley. In general, the obtained homologous DNA is capable of hybridizing with a DNA encoding a Cly1/cly1 gene of a specific barley variety (for example, Azumamugi, Kanto Nakate Gold, or SV230) under stringent conditions. Hence, the present invention also encompasses a DNA which hybridizes with a Cly1/cly1 DNA (SEQ ID NO: 1, 2, 4, 5, 7, or 8) of Azumamugi, Kanto Nakate Gold, or SV230 under stringent conditions, as long as the cleavage with miR172 is suppressed, and the DNA imparts a cleistogamous trait to a plant.

Whether or not a mutant DNA or a homologous DNA of the present invention undergoes cleavage with miR172 can be determined, for example, by an RNA ligase-mediated 5′RACE method described in Example (see Example 5(2)). Meanwhile, whether or not a mutant DNA or a homologous DNA imparts cleistogamy to a plant can be determined, for example, by recombining a cly1 gene of a chasmogamous variety with the DNA, producing a plant having the DNA in a homozygous manner, and checking whether or not a cleistogamous trait is imparted to the produced plant. The chasmogamy/cleistogamy of a plant can be determined by visually investigating whether or not an anther projects from a glumous flower at anthesis. Specifically, a plant can be determined to be chasmogamous, when an anther projects from a glumous flower at anthesis, whereas a plant can be determined to be cleistogamous, when an anther does not project from a glumous flower at anthesis. The chasmogamy/cleistogamy can also be determined by measuring a lodicule size at anthesis, because such deference in chasmogamy/cleistogamy is based on the difference in lodicule size. Specifically, a plant can be determined to be chasmogamous, when a lodicule swells and increases in size at anthesis, whereas a plant can be determined to be cleistogamous, when a lodicule remains small at anthesis (FIG. 9).

The cleistogamous-type DNA of the present invention is an agent for imparting a cleistogamous trait to a plant, in a sense that the introduction of the cleistogamous-type DNA makes it possible to impart a cleistogamous trait to a plant.

Note that the introduction of artificial mutation into a DNA for preparing the above-described mutant DNA can be carried out by, for example, the site-directed mutagenesis method (Kramer, W. & Fritz, H J., Methods Enzymol, 1987, 154, 350).

Meanwhile, examples of a method for isolating the above-described homologous DNA include the hybridization technology (Southern, E. M., J. Mol. Biol., 98: 503, 1975) and the polymerase chain reaction (PCR) technology (Saiki, R. K., et al. Science, 230: 1350-1354, 1985, Saiki, R. K. et al. Science, 239: 487-491, 1988). In order to isolate a homologous DNA, a hybridization reaction is carried out under stringent conditions, in general. Examples of the stringent hybridization conditions include conditions of 6 M urea, 0.4% SDS, and 0.5×SSC, and hybridization conditions with similar stringency. When more stringent conditions, for example, conditions of 6 M urea, 0.4% SDS, and 0.1×SSC, are employed, isolation of a DNA with a higher homology can be expected. The isolated DNA has a sequence identity of at least 50% or higher, further preferably 70% or higher, further preferably 90% or higher (for example, 95%, 96%, 97%, 98%, or 99% or higher) at the nucleic acid level or the amino acid sequence level. The sequence homology can be determined by use of a program (Altschul et al. J. Mol. Biol., 215: 403-410, 1990) of BLASTN (nucleic acid level) or BLASTX (amino acid level). These programs are based on the algorithm BLAST by Karlin and Altschul (Proc. Natl. Acad. Sci. USA, 87:2264-2268, 1990, Proc. Natl. Acad. Sci. USA, 90: 5873-5877, 1993). When a base sequence is analyzed by BLASTN, parameters are set to, for example, score=100, and wordlength=12. Meanwhile, when an amino acid sequence is analyzed by BLASTX, parameters are, for example, set to score=50, and wordlength=3. When an amino acid sequence is to be analyzed by use of the Gapped BLAST program, the analysis can be conducted as described in Altschul et al., (Nucleic Acids Res. 25: 3389-3402, 1997). When BLAST and Gapped BLAST programs are used, the default parameters of the programs are used. The specific procedures of these analysis methods are known.

The form of the cleistogamous-type DNA of the present invention is not particularly limited, and the cleistogamous-type DNA encompasses genomic DNAs and chemically synthesized DNAs in addition to cDNAs. These DNAs can be prepared by routine methods for those skilled in the art. A genomic DNA can be prepared, for example, by extracting genomic DNAs from a plant, constructing a genomic library (a plasmid, a phage, a cosmid, a BAC, a PAC or the like can be used as the vector), spreading the genomic library, and conducting colony hybridization or plaque hybridization by use of a probe prepared based on a base sequence of a Cly1/cly1 gene (for example, the DNA shown in any one of SEQ ID NOs: 1, 2, 4, 5, 7, and 8). Alternatively, a genomic DNA can also be prepared by preparing a primer specific to a Cly1/cly1 gene, and conducting PCR using the primer. Meanwhile, a cDNA can be prepared, for example, by synthesizing cDNAs based on mRNAs extracted from a plant, inserting the cDNAs into a vector such as λZAP to prepare a cDNA library, spreading the cDNA library, and conducting colony hybridization or plaque hybridization in the similar manner as described above, or conducting PCR. In addition, if a commercially available DNA synthesizer is used, a desired DNA can be prepared by synthesis.

<Vector, Transformed Sorghum Cell, Transgenic Sorghum Plant>

The present invention also provides a vector comprising the above-described cleistogamous-type DNA of the present invention, a plant cell into which the above-described cleistogamous-type DNA of the present invention or a vector comprising the cleistogamous-type DNA of the present invention is introduced, a plant comprising the plant cell, a plant which is a progeny or a clone of the plant, and propagation materials of these plants.

The vector of the present invention is not particularly limited, as long as the vector is capable of expressing the inserted gene in a plant cell. The vector of the present invention may comprise a promoter for constitutive or inducible expression of the DNA of the present invention. Examples of the promoter for constitutive expression include the 35S promoter of cauliflower mosaic virus, the actin promoter of rice, the ubiquitin promoter of maize, and the like. Meanwhile, examples the promoter for inducible expression include promoters which are known to initiate expression in response to external factors such as infection with or invasion of filamentous fungi•bacteria•viruses, low-temperature, high-temperature, dryness, ultraviolet irradiation, and spraying of particular compounds. Examples of these promoters include the promoter of the rice chitinase gene and the promoter of the tobacco PR protein gene, which are expressed by infection with or invasion of filamentous fungi•bacteria•viruses, the promoter of the rice lip19 gene, which is induced by low-temperature, the promoters of the rice hsp80 gene and hsp72 gene which are induced by high-temperature, the promoter of the A. thaliana rab16 gene, which is induced by dryness, the promoter of the parsley chalcone synthase gene, which is induced by ultraviolet irradiation, the promoter of the maize alcohol dehydrogenase gene, which is induced under anaerobic conditions, and the like. In addition, the promoter of the rice chitinase gene and the promoter of the tobacco PR protein gene are also induced by specific compounds such as salicylic acid, and the rab16 is also induced by spreading of a plant hormone, abscisic acid.

The present invention also provides a plant cell into which the vector of the present invention is introduced. The plant from which the plant cell is derived is not particularly limited, and examples thereof include grass species such as barley, wheat, rye, Triticale, oat, rice, maize, and A. thaliana. Plants of the family Poaceae such as barley, wheat, rye, Triticale, oat, rice, and maize are preferable, plants of the subfamily, Pooideae such as barley, wheat, rye, Triticale, and oat are more preferable, and barley is most preferable. The plant cell of the present invention also encompasses cells in plants, in addition to cultured cells. In addition, the plant cell of the present invention encompasses plant cells in various forms, such as suspended cultured cells, protoplasts, leaf slices, calluses, immature embryos, and pollen. For introducing the vector into a plant cell, it is possible to use various methods known to those skilled in the art such as the polyethylene glycol method, electroporation, the Agrobacterium mediated method, and the particle gun method.

Regeneration of plants from transformed plant cells can be carried out by a method known to those skilled in the art which depends on the kind of the plant cells. For example, examples of methods for producing a transgenic barley plant include the methods described in Tingay et al., (Tingay S. et al. Plant J. 11: 1369-1376, 1997), Murray et al., (Murray F et al. Plant Cell Report 22: 397-402, 2004), and Travalla et al., (Travalla S et al. Plant Cell Report 23: 780-789, 2005). Meanwhile, the following are several technologies which are already established as methods for producing a transgenic rice plant, and which have been widely used in the technical field of the invention of the present application: a method in which a plant is regenerated by introducing a gene into a protoplast with polyethylene glycol (Datta, S. K. In Gene Transfer To Plants(Potrykus I and Spangenberg Eds.) pp. 66-74, 1995), a method in which a plant is regenerated by introducing a gene into a protoplast with an electric pulse (Toki et al. Plant Physiol. 100, 1503-1507, 1992), a method in which a plant is regenerated by directly introducing a gene into a cell by the particle gun method (Christou et al. Bio/technology, 9: 957-962, 1991), and a method in which a plant is regenerated by introducing a gene with Agrobacterium (Hiei et al. Plant J. 6: 271-282, 1994), and the like. Meanwhile, an example of a method for producing a transgenic A. thaliana plant is the method of Akama et al., (Akama et al. Plant Cell Reports 12: 7-11, 1992). In the present invention, these methods can be used suitably.

Once a transgenic plant whose genome has the cleistogamous-type DNA of the present invention introduced therein is obtained, a progeny can be obtained from the plant by sexual reproduction or asexual reproduction. Moreover, it is also possible to obtain a propagation material (for example, seeds, fruits, cut-spikes, stubbles, calluses, protoplasts, or the like) from the plant or a progeny or clone thereof, and then to mass produce the plant from the propagation material. The present invention encompasses plant cells into which the DNA of the present invention is introduced, plants comprising the cells, progenies and clones of the plants, propagation materials of the plants and progenies and clones thereof.

The present invention also provides a method for producing a plant to which a cleistogamous trait is imparted, comprising introducing the cleistogamous-type DNA of the present invention into a plant. The cleistogamous-type DNA of the present invention can be introduced into a plant as an exogenous DNA, and also can be introduced into a plant by mating with a variety having the cleistogamous-type DNA of the present invention. The “introduction” in the present invention encompasses both of these modes. In addition, in the present invention, “to impart” a cleistogamous trait to a plant has a meaning including not only to give a cleistogamy to a variety having a chasmogamous trait, but also to further enhance cleistogamy of a variety already having certain cleistogamy. In order to impart a cleistogamous trait to a plant, both cly1 alleles in an individual are preferably converted into cleistogamous-type DNAs. The introduction of the cleistogamous-type DNA of the present invention into a plant genome can be carried out by, for example, mating or homologous recombination. A plant to which a cleistogamous trait is imparted is, for example, excellent in ability to prevent infection with Fusarium ear blight, or excellent in ability to suppress pollen dispersal, in comparison with plants having no such a trait.

—Analysis of Base Sequence of Cly1/cly1 Gene—

The present invention also provides a method for determining chasmogamy/cleistogamy of a plant. An embodiment of the determination method of the present invention is a method comprising: analyzing a base sequence of a Cly1/cly1 gene in a plant; and comparing the analyzed base sequence with a reference base sequence. The Cly1/cly1 gene in the plant is typically a gene comprising any one of the following DNAs, because it is conceivable that the Cly1/cly1 gene in the plant is generally homologous to a Cly1/cly1 gene of a specific barley variety (for example, Azumamugi, Kanto Nakate Gold, or SV230):

(a) a DNA comprising a coding region of the base sequence shown in SEQ ID NO: 1, 2, 4, 5, 7, or 8;

(c) a DNA which hybridizes with a DNA comprising the base sequence shown in SEQ ID NO: 1, 2, 4, 5, 7, or 8 under stringent conditions

Here, the definitions of the terms “a plurality of” and “stringent conditions” are as described above. The meaning of the “analyzing a base sequence of a gene” includes not only analysis of the entire length of the base sequence of the gene, but also analysis of the base sequence of a specific part of the gene. The base sequence of the specific part preferably comprises a base sequence of a miR172 target site of the gene.

For analysis of the base sequence of the Cly1/cly1 gene, an amplification product obtained by amplifying a DNA of the Cly1/cly1 gene by PCR can be used. In the case where PCR is carried out, a primer used is not particularly limited, as long as the primer is capable of specifically amplifying the Cly1/cly1 gene. The primer can be designed as appropriate on the basis of the sequence information of the Cly1/cly1 gene (for example, the base sequence shown in SEQ ID NO: 1, 2, 4, 5, 7, or 8, a base sequences shown in FIG. 8). It is possible to use not only a primer amplifying the entire length of the DNA of the Cly1/cly1 gene, but also a primer amplifying a DNA of a specific part. The primer is preferably one at least capable of amplifying a DNA comprising a base sequence of a miR172 target site.

The “reference base sequence” to be compared with the base sequence of the Cly1/cly1 gene in the test plant is typically a base sequence of a Cly1/cly1 gene for which whether the Cly1/cly1 gene is of a chasmogamous-type or of a cleistogamous-type has already been determined. The “reference base sequence” may be the base sequence of the Cly1/cly1 gene (for example, the base sequence shown in SEQ ID NO: 1, 2, 4, 5, 7, or 8, the base sequence shown in FIG. 8) already identified by the present inventors. Preferably, the “reference base sequence” is a base sequence of a miR172 target site of a Cly1/cly1 gene (for example, the base sequence shown in FIG. 6).

A comparison between a determined base sequence of the gene in the test plant and the reference base sequence enables a judgment as to whether the gene in the test plant is of a chasmogamous-type or of a cleistogamous-type. For example, a probability that the gene of the test plant is of a chasmogamous-type is determined to be high, when the base sequence of the gene is substantially identical to a base sequence of a Cly1 gene of a chasmogamous-type variety (for example, the base sequence shown in SEQ ID NO: 7 or 8, the Cly1a base sequence shown in FIG. 8) (particularly when a base sequence of a miR172 target site is identical, or when the difference in a base sequence of a miR172 target site is so small that it is conceivable that cleavage of a transcription product with miR172 is not suppressed). On the other hand, the probability that the gene in the test plant is of a cleistogamous-type is determined to be high, when the base sequence of the gene is substantially identical to a base sequence of a cly1 gene of a cleistogamous-type variety (for example, the base sequence shown in SEQ ID NO: 1, 2, 4, or 5, the cly1b or cly1c base sequence shown in FIG. 8) (particularly when a base sequence of a miR172 target site is identical or when the difference in a base sequence of a miR172 target site is so small that is conceivable that cleavage of a transcription product with miR172 is suppressed).

Whether or not the base sequence of the gene in the test plant is different from the reference base sequence can be indirectly analyzed by various methods, besides the above-described direct determination of the base sequence. Examples of these methods include the PCR-SSCP (single-strand conformation polymorphism) method, the RFLP method and the PCR-RFLP method which make use of restriction fragment length polymorphism (RFLP), denaturant gradient gel electrophoresis (DGGE), the allele specific oligonucleotide (ASO) hybridization method, and the ribonuclease A mismatch cleavage method.

Note that, in the determination method of the present invention, the preparation of the DNA from the test plant can be conducted by an ordinary method, for example, by the CTAB method. The source from which the DNA is obtained is not particularly limited, and the DNA can be extracted from any tissue of the plant. For example, the DNA can be extracted from spikes, leaves, roots, stems, seeds, albumen portions, embryos, or the like. For the preparation of the DNA, not only grown plants, but also plant seeds and seedlings can be used. Hence, it is possible to determine chasmogamy/cleistogamy of a plant at an early stage.

In addition, the base sequencing can be carried out by an ordinary method, for example, the dideoxy method, the Maxam-Gilbert method, or the like. For the base sequencing, a commercially available sequencing kit and sequencer can be used.

—Detection of Cleavage of Transcription Product of Gene with miR172—

Another embodiment of the determination method of the present invention is a method comprising detecting cleavage, with miR172, of a transcription product of a gene of a test plant. The detection of the cleavage, with miR172, of a transcription product of a gene can be carried out by detecting a transcription product shortened by the cleavage. For example, the RNA ligase-mediated 5′ RACE method described in Example can be used for the detection of the shortened transcription product. Specifically, an RNA oligomer which binds to only the 5′end of a cleaved transcription product (a fragment on the 3′ side) is caused to act on total RNA extracted from a plant, and then a nested PCR is performed by use of a primer for the RNA oligomer and a reverse primer specific to the cleaved transcription product (the fragment on the 3′ side). Thus, the transcription product cleaved with miR172 can be detected specifically. A commercially available kit (for example, GeneRacer Kit (Invitrogen)) can be used for this method.

It is conceivable that, once the transcription product of the gene is cleaved with miR172, a subsequent translation process is suppressed. Hence, the detection of cleavage, with miR172, of a transcription product of a gene can also be carried out by detecting a translation product of the gene, besides the above-described direct detection method of a transcription product. The detection of the translation product of the gene can be carried out by an ordinary method, for example, by the Western blotting method. An antibody used for the Western blotting may be a polyclonal antibody or a monoclonal antibody. Preparation methods of these antibodies are well-known to those skilled in the art. For example, a protein comprising the amino acid sequence shown in SEQ ID NO: 3, 6, or 9 or a partial peptide thereof can be used as an antigen used to prepare the antibody.

The probability that the test plant is chasmogamous is determined to be high, when cleavage, with miR172, of a transcription product of a gene is detected for the test sample, as a result of the above-described method. On the other hand, the probability that the test plant is cleistogamous is determined to be high, when no cleavage is detected.

The present invention also provides a method for breeding a cleistogamous plant. The breeding method of the present invention comprises the methods of:

(a) mating a chasmogamous plant variety with any plant variety;

(b) determining, by the above-described determination method of the present invention, chasmogamy/cleistogamy of individuals which are obtained by the mating; and

Examples of the “any plant variety” to be mated with the chasmogamous plant variety include cleistogamous varieties, and individuals obtained by mating a cleistogamous variety with a chasmogamous variety, but the “any plant variety” is not limited to these. The use of the breeding method of the present invention makes it possible to select cleistogamous plants at the seed stage or the seedling stage. Hence, development of a variety having a cleistogamous trait can be performed in a short time. Moreover, it can be said that the breeding method is highly accurate, because the selection is carried out by not employing a linkage marker molecule as a target, but employing the gene controlling chasmogamy/cleistogamy of a plant as a direct target.

EXAMPLES

Hereinafter, the present invention will be described more specifically on the basis of Examples. However, the present invention is not limited to Examples below.

Example 1
Construction of Comparative Genetic Maps Between Barley and Rice

One hundred and thirty seven barley EST sequences were matched with sequences on chromosome 4 of rice. As a result, 24 sequences were able to be mapped to chromosome 2H of barley. Of the 24 sequences, 18 sequences were converted to STS markers, 4 sequences were converted to SNP markers, and the remaining two sequences were converted to SSR markers (Table 1).

TABLE 1

Allele pattern

Marker
Primer F
Primer R
A.T.^a
Size
Restriction
(size bp)^b
Marker

name
(5′-3′)
(5′-3′)
° C.
bp
enzyme
A
K
M
S
type

BJ457596
AAAACGGTAAAGACGTGCAGG
CTAGAAGAGGAACCCGTCAAGC
58.0
700
MseI
480
700
—
—
STS

BU999268
TTCGCATCAGCCGAAGTTGG
GAACTGCCCTTGCTGCTTGC
58.0
1200
HaeIII
140
210
—
—
STS

BJ478159
GCACGAGGTTCCTTTGGATGC
GTGGATGGTAAATACAACCCGA
55.6
1700
—
—
1700
—
—
STS

C

GBM1149^c,d
GCAGCAACGAGCTGTGACTA
CTGTACATGAAGACGTCGCTG
55.0
220
—
220
116
220
220
SSR

TC80749^e
GCTCTCGTCAAGATGCTGCTGG
GCCTTCTCGATGAGCTCCAGG
62.5
1300
ClyI
1300
800
—
—
STS

TC77480
CATCGGCCTGTGCGCCTTCG
GCCGCTGAGAAGCATGGTGC
62.7
700
SacII
700
450
—
—
STS

CD662417
AACCAAATACTGGGCGGCAG
TGCTCACCACTTCATCCAAAGG
55.0
380
—
380
380
380
380
SNP

TC126660
AAGGTCTGAGCCGGTTTTGG
ATCAAAGGAGCGAATGCGTG
56.0
1500
MspA1I
—
—
1500
1000
STS

TC124907
GAAAGGATGCCCGAAAAACC
CCTCTGGGTCACGGTCAGGAG
56.4
1510
HhoI
—
—
1510
1490
STS

TC153299
GGCTGCTTTGAAATTCCGAC
CTGTACGACCATCTCGACGTGC
55.5
1200
MboI
600
700
—
—
STS

TC137028
ACGAGCTCCACTTGGGATACC
GCCTTGATCCCCAAACGTGC
56.0
700
NlaIII
180
250
—
—
STS

BU990250
TTCGGAAATACAGCAAGGAGC
TCCTTTCAAATAGTTCGCAACG
55.0
2000
—
2000
2000
2000
2000
SNP

AJ465833
CAGTTCGCAGTCGAGGGCTG
AAATGGCAACTCGATCCTTCC
56.0
850
AluI
750
170
170
750
STS

AV932221
GGAGCGTAACATCAAGGCATCC
ATGCAAAAGCAAATTTGGTGG
58.6
800
—
800
800
800
800
SNP

GBM1498^c,d
TGCTCCAACCCAAAAGCTAC
GAAGACGACGAGCGGTACTC
55.0
170
—
170
160
160
160
SSR

TC123870
GGCGATTACTTCGAAATCGAG
CCGTCTGGTAGATGGCAACTCC
58.0
1000
MspA1I
500
800
—
—
STS

BI25378^e
TGAAAATAAATGACAAACCATT
TATCAGATTTTGGTATGGCAAGG
55.0
900
MluI
900
600
—
—
STS

GG

BI779462^e
GGTGCTCAGCGCCCCATACC
GCTAGCAGATCATCCCTTGGTC
57.5
700
Fnu4HI
450
700
—
—
STS

TC145553
TCACAAGTTGTCGAGGCCTGG
AGTAGCCTGGAACGCATGAGG
57.0
450
AvaI
250
450
—
—
STS

AV946002
CAACGGGGAGCAGAGCCCTC
TATCGACCAGATCGCCGTGG
60.0
620
HpaII
190
120
120
190
STS

CA018688
TCGTCTTCTACCTCTCGCTTCC
TCTTTATCAAAGAGCGCGTAGC
58.0
2100
DdeI
—
—
350
600
STS

CA032173
GCAGACATCCAGGGCAACACG
TTGCATTTCTGAGCCCCCAC
60.0
700
—
—
—
700
700
SNP

TC110372
TAAGCGCATGCCTGAGCCAG
CATAGTCTCGGCTATTCCCCAC
58.4
3000
Fnu4HI
—
3000
—
—
STS

e11m19-
TTTTCACTTCAGTACTTCGCATC
ACAGCATACTTTGTGGATGGCTG
55.0
800
MseI
700
800
800
700
STS

3STS^f
G

^aAnnealing temperature

^bA-Azumamugi, K-Kanto Nakate Gold, M-Misato Golden, S-Satsuki Nijo

^cHomology GBM1149 (BQ466807), GBM1498 (CA002095), BI25378 (DN183702), and BI779462 (ABC153).

^dDeveloped by Varshney et al

^eDNA sequences of amplicons for ‘TC’ markers are available in ESM 1.

^fDeveloped by Turuspekov et al, (2004), and modified in this study.

FIG. 1 shows a comparison between a physical map of chromosome 4 of rice and genetic maps of barley, which are created by the present inventors. Among Kanto Nakate Gold (KNG)×Azumamugi (AZ) individuals, cly1 co-segregated from MSU21, e11m19-3STS, AJ465833, and GBM1498. A BLAST search of these sequences against the genomic sequence of chromosome 4 of rice revealed that GBM1498 and AJ465833 are homologous to RM1153 and C1016, respectively. Meanwhile, neither MSU21 nor e11m19-3STS was related to any genomic sequence of rice. Sequences between 30.13 Mb and 34.68 Mb of chromosome 4 of rice were co-linearly arranged in barley, whereas the region from 31.66 Mb to 33.52 Mb was inverted in barley. Several other disruptions in gene order were detected.

Example 2
Genotypic Analysis of F2 Population

By a genetic analysis of a large-scale KNG×AZ F2 population (2652 individuals), the cly1 gene locus was mapped to a position 0.66 cM distal from AV932221 and 0.15 cM proximal from CA002095 (FIG. 3A). AV932221 and CA002095 were homologous to Os04g0650000 and Os04g0648900 of rice, respectively, and 11 genes were found between these two loci (http://rapdb.dna.affrc.go.jp/). It was speculated, on the basis of a partial cDNA sequence, that one of these, Os04g0649100, encoded an AP2 protein. BF623536 was a barley EST homologous to Os04g0649100. On the assumption that BF623536 was a part of Cly1, the Morex BAC library (Yu Y, et al., Theor Appl Genet 101: 1093-1099, 2000) was PCR-screened with the sequence of BF623536 to identify the full genomic sequence of Cly1. As a result, five clones (M060H23, M191K21, M601E22, M799P16, and M796024) were selected, and the base sequences of two (M191K21 and M601E22) of the five clones were determined. On the basis of the sequences of these two BAC clones, further five new markers were prepared (Table 2), and mapped (FIG. 3A).

TABLE 2

Barley

EST BAC
Rice

Marker
clone
orthologue
Source
Primer sequence

HV1091
NIAS_
Os04g0649700
NIAS
F GCGCCGGCCATCCACCCTCTC

Hv1091M03_F

R CCCGGCGAGGCCCGAGATCGT

HV2058
NIAS_
Os04g0649600
NIAS
F CGCTCCTCGACGCCGCCTTCT

Hv2058M22_F

R GGGACGCTCTCTGCAATGAAT

C4dCAPS
BE454122,
Os04g0649200
http://rapdb.
F TCAAAGGATTACAGTAGCAAGCT

AJ478153

dna.affrc
R AATGCTTTATGATAGTTTCCCTC

.go.jp

M601E22A8
M601E22
—
This study
F AATCCCAATGCTCGGTGT

R GGCTTTCGGGAGGAATCG

M601E22I
M601E22
—
This study
F TGCTAAGTTGATGTGATGCCAGTGA

R GCGAGAAGAAGAAATATGCGACGTA

M191K21A11
M191K21
—
This study
F CACTGTGGATTCCATCGGCTT

R GAACCACCCATGCCGAGTAAA

P22AP23*
M191K21
—
This study
F CAACTGCAAGCCCCCCACATG

R CGTCTTCTTGGGGAACTCTGC

P101AP35*
M191K21
—
This study
F CCAGCCAACGAGAGCAGAGCC

R ACCTGCTTGCCGCAATCCCTG

BF623536
BF623536
Os04g0649100
http://rapdb.
F CCCGGGGGAGCTCCAAGTACA

dna.affrc
R GCTGCCCCTCTTGTTCGACGC

.go.jp

CA002095
CA002095
Os04g0648900
http://rapdb.
F CGCAGCCGCAGCCGCCGTGGA

dna.affrc
R TTCCGGCACGCGGCAGGGAGGTGAG

.go.jp

CA002095
CA002095
Os04g0648900
http://rapdb.
F GCTACTCCTCCTTCCGGCACG

dna.affrc
R ACGTTGTGCTCCTCCTTGGCC

.go.jp

BU985214
BU985214
Os04g064880
http://rapdb.
F TGAGGAACAACTCCCGAACTATGGAA

dna.affrc
C

.go.jp
R TGTCTCATGTTTAGTGCAGAGTCAGG

G

PCR reaction conditions

Annealing

Restrition

MgCL
DMSO
temp.
Extension

Marker
enzyme

Marker
(mM)
(%)
(° C.)
(S)
Cycles
type
AZxKNG
KNGxOUH602

HV1091
2.5
10
70-55*
30
35
CAPS
BttEII
BttEII

HV2058
2.5

70-55*
20
35
dCAPS
Mono
Hpy188I

C4dCAPS
4.0

55
30
30
dCAPS
Mono
HindIII

M601E22A8
1.5

65
60
35
CAPS
Mono
MspI

M601E22I
2.0

65
60
35
CAPS
Mono
AvaI

M191K21A11
2.0

6*
30
30
SSR
—
—

P22AP23*
2.5
10
60
60
40
SNP
—
—

P101AP35*
2.5
10
60
60
32
CAPS
Trpr45I
Trp45I

BF623536
1.5

64
30
30
CAPS
Mono
AvaI

CA002095
2.5
10
70-55*
30
35
dCAPS
AvaII
—

CA002095
2.5
10
70-55*
30
35
ALP
—
—

BU985214
3.0

65
30
30
CAPS
Mono
BsmI

*Touch down PCR: The annealing temperature was reduced by 1° C. in every cycle from 70° C. to 55° C., followed by 20 cycles at 55° C.

A single recombination event (0.02 cM) separated P101AP25′ from cly1, and two recombination events (0.04 cM) separated M191K21A11 from cly1. These results narrowed the genomic region containing cly1 to 7 kbp. The DNA region included most of the coding region of Cly1, and no other genes were present in the DNA region. A sequence (Cly1.a) in AZ differed from a sequence (cly1.b) of KNG at two base positions.

Example 3
Analysis of Gene Base Sequence

The Cly1 gene had 2691 by from the start codon to the stop codon, had a GC content of 60.8%, and was divided into 10 exons and 9 introns (FIG. 3A). The coding sequence had 1464 bp, and flanked by a 5′UTR (480 bp) and a 3′UTR (346-368 bp). The Cly1 encoded a 487-residue polypeptide having two AP2 domains (Jofuku K D, et al., Plant Cell 6: 1211-1225, 1994, Okamuro J K, et al., Proc Natl Acad Sci USA 94: 7076-7081, 1997). One of the AP2 domains was present between positions 112 and 178, and the other one was present between positions 203 and 270. A putative miR172 target sequence was present in Exon 10 (FIG. 3A), and the sequence is also present in many AP2 genes (Aukerman M J, Sakai H 15: 2730-2741, 2003, Chen X Science 303: 2022-2025, 2004). Two auxin-response elements (Guilfoyle T. et al., How does auxin turn on genes? Plant Physiol 118: 341-347, 1998) were present upstream of the start codon (one was present within 3 k by upstream, and the other was present within 2 k by upstream). The base sequence of the Cly1 gene resembled those of Arabidopsis. thaliana (A. thaliana) AP2 (AT4G36920.1) and TOES (AT5G67180.1), and belonged to the euAP2 Glade (FIG. 4). The transcription product was highly homologous to the rice AP2-like gene Os04g0649100. The single-nucleotide polymorphism at P22AP23′ (present in the putative miR172 target sequence within Exon 10) does not involve change in any amino acid.

Example 4
Polymorphism Analysis of miR172 Target Site

The sequence polymorphism of the miR172 target site was associated with lodicule size and cleistogamy. Sequence variation among 274 barley lines was found at three base positions within the miR172 target sequence (FIG. 3B and Tables 3 to 7).

TABLE 3

Ear density

SV ID
OU ID
Variety name
Origin
Row-type
mm*
Flowering type
SNP1
SNP2
SNP3

SV001
A002
Compana (CI 5438)
CDA
2
3.4
+
A
A
A

SV002
A008
Sanalta (CI 6087)
CDA
2
2.6
Cleistogamous
.
G
.

SV003
A321
Olympia (CI 6107)
USA
6
3.7
+
.
.
.

SV004
A604
Vantage (CI 7324)
CDA
6
3.5
+
C
.
.

SV005
A607
Peatland (CI 5267)
USA
6
3.3
+
C
.
.

SV006
B008
Libia
NAF
6
3.7
+
.
.
.

SV007
B015
Rabat
MRC
6
3.9
+
.
.
.

SV008
B033
Morocco
TNS
6
4.3
+
.
.
.

SV009
B069
Giza 117
EGP
6
3.5
+
.
.
.

SV010
B318
Macha
AGA
6
3.5
+
.
.
.

SV011
B327
Tunis (CI 1383)
TNS
6
2.6
+
.
.
.

SV012
B349
Giza 68
EGP
6
3.1
+
.
.
.

SV013
B369
Cairo 1 (14)
EGP
6
3.6
+
.
.
.

SV014
B623
Algiers
AGA
6
4.5
+
.
.
.

SV015
B669
Suez (84)
EGP
6
2.6
+
.
.
.

SV016
B670
Palmella Blue
NAF
2
2.9
+
.
.
.

SV017
C001
Vladivostok
CHN
6
3.2
+
.
.
.

SV018
C018
Pukou 1
CHN
6
4.0
+
.
.
.

SV019
C040
Chiaochuang 1
CHN
6
3.2
+
.
.
.

SV020
C043
Chengchou 3
CHN
6
3.4
+
.
.
.

SV021
C045
Chengchou 1
CHN
6
3.1
+
.
.
.

SV022
C059
Tibet Violet 1
CHN
6
3.1
+
C
.
.

SV023
C302
Manchuria Native 1
CHN
6
NT
+
.
.
.

SV024
C304
Sanchiang Fuchin
CHN
6
3.1
+
.
.
.

SV025
C319
Chihchou
CHN
6
4.4
+
.
.
.

SV026
C328
Titienchiao 2
CHN
6
1.4
+
.
.
.

SV027
C331
Tayeh 1
CHN
6
1.5
+
.
.
.

SV028
C336
Paoanchen 1
CHN
6
3.9
+
.
.
.

SV029
C346
Shanghai 1
CHN
6
2.8
+
C
.
.

SV030
C616
Tinghsien
CHN
6
2.8
+
C
.
.

SV031
C619
Wuhu
CHN
6
NT
+
.
.
.

SV032
C621
Takungkuan
CHN
6
2.9
+
.
.
.

SV033
C624
Tawangmiao 1
CHN
6
3.7
+
.
.
.

SV034
C627
Mushinchiang 3
CHN
6
4.2
+
.
.
.

SV035
C656
Tibet White 4
CHN
6
2.6
+
C
.
.

SV036
E216
Debre Zeit 1 (1-5-17a)
ETP
6
2.2
+
.
.
.

SV037
E245
Addis Ababa 40 (12-24-84)
ETP
L
3.8
+
.
.
.

SV038
E254
Sululta 1 (1-8-11)
ETP
6
4.0
+
.
.
.

SV039
E269
Mota 1 (1-24-10)
ETP
D
3.9
+
.
.
.

SV040
E278
Dabat 1 (1-27-25)
ETP
6
3.2
+
.
.
.

SV041
E284
Molale 1 (2-8-4a)
ETP
L
3.4
+
.
.
.

SV042
E285
Debra Birhan 1 (2-8-18)
ETP
6
2.3
+
.
.
.

SV043
E525
Debre Zeit 29 (1-5-35)
ETP
D
3.0
+
.
.
.

SV044
E550
Addis Ababa 56 (3-10-1b)
ETP
6
3.5
+
.
.
.

SV045
E559
Nazareth 1 (1-10-1a)
ETP
D
3.0
+
.
.
.

SV046
E560
Asbe Tafari 1 (1-11-19)
ETP
6
3.6
+
.
.
.

SV047
E574
Gondar 1 (1-27-1)
ETP
6
4.3
+
.
.
.

SV048
E581
Qutha 1 (2-3-73)
ETP
D
3.8
+
.
.
.

SV049
E589
Dembi 1 (2-20-51)
ETP
L
3.3
+
.
.
.

SV050
E821
Debre Zeit 18 (1-5-28a)
ETP
L
3.8
+
.
.
.

SV051
E832
Addis Ababa 3 (12-24-9)
ETP
6
3.5
+
.
.
.

SV052
E862
Jijiga 2 (1-13-20)
ETP
6
1.7
+
.
.
.

SV053
E863
Kulubi 3 (1-14-38b)
ETP
L
3.7
+
.
.
.

SV054
E864
Deder 1 (1-16-27)
ETP
L
2.6
+
.
.
.

SV055
E872
Glyorgi 1 (1-24-21a)
ETP
D
3.8
+
.
.
.

SV056
E879
Adi Abun 1 (1-28-2)
ETP
D
3.6
+
.
.
.

SV057
E883
Dessie 1 (2-4-22)
ETP
6
3.3
+
.
.
.

SV058
F001
Ammora 1 (99-1)
ETP
6
NT
+
.
.
.

SV059
F003
Zeggi 1 (137-1)
ETP
D
NT
+
.
.
.

SV060
F035
Quesi (471)
ETP
D
NT
+
.
.
.

TABLE 4

Ear density

SV ID
OU ID
Variety name
Origin
Row-type
mm*
Flowering type
SNP1
SNP2
SNP3

SV061
F037
Palagi (499)
ETP
6
NT
+
.
.
.

SV062
F038
Adigrat 3 (508-2)
ETP
L
NT
+
.
.
.

SV063
F313
Fiche 1 (212a-1)
ETP
L
NT
+
.
.
.

SV064
F318
Sheki 2 (260-2)
ETP
6
NT
+
.
.
.

SV065
F322
Sombo 1 (281-1)
ETP
L
NT
+
.
.
.

SV066
F324
Asella 1 (372a-1)
ETP
D
NT
+
.
.
.

SV067
F336
Mai Chew 1 (495)
ETP
L
NT
+
.
.
.

SV068
F606
Debra Markos 1 (181-1)
ETP
L
NT
+
.
.
.

SV069
F619
Jimma 2 (265-1)
ETP
6
NT
+
.
.
.

SV070
F629
Shashamane 1 (415)
ETP
6
NT
+
.
.
.

SV071
F635
Meki 2 (481-2)
ETP
L
NT
+
.
.
.

SV072
F639
Adigrat 8 (520c-2)
ETP
L
NT
+
.
.
.

SV073
I003
Ballia
IND
6
4.3
+
.
.
.

SV074
I012
Kabul 1
AFG
6
1.7
+
.
.
.

SV075
I024
Iraq Black Barley
IRQ
2
3.3
+
.
.
.

SV076
I027
Aleppo 1 (438)
SAR
2
3.5
+
.
.
.

SV077
I032
Esfahan 1 (152 III)
IRN
6
3.2
+
.
.
.

SV078
I036
Gorgan 1 (225A I)
IRN
6
3.7
+
.
.
.

SV079
I166
Khanaqin 2 (KUH 5305)
IRQ
2
NT
+
.
.
.

SV080
I167
Khanaqin 5 (KUH 5308)
IRQ
2
NT
+
.
.
.

SV081
I170
Arbat 1 (KUH 5317)
IRQ
2
NT
+
.
.
.

SV082
I173
Chamchamal 1 (KUH 5326)
IRQ
2
NT
+
.
.
.

SV083
I174
Samarra 1 (KUH 5329)
IRQ
6
NT
+
.
.
.

SV084
I182
Karand 1 (KUH 5365)
IRN
2
NT
+
.
.
.

SV085
I304
Rewari
IND
6
5.0
+
.
.
.

SV086
I323
Charikar 2 (606 II)
AFG
6
3.3
+
C
.
.

SV087
I325
Iraq Barley 1
IRQ
6
3.5
+
.
.
.

SV088
I326
Katana 2 (183)
SAR
2
3.4
+
.
.
.

SV089
I327
Aleppo 2 (439)
SAR
2
3.1
+
.
.
.

SV090
I334
Damaneh 1 (165d)
IRN
6
3.3
+
.
.
.

SV091
I335
Ghazvin 1 (184)
IRN
2
3.0
+
.
.
.

SV092
I337
Firuzkuh 1 (277)
IRN
6
3.8
+
.
.
.

SV093
I339
Sarab 1 (347 I)
IRN
2
3.7
+
.
.
.

SV094
I341
Dunga Banse (N 5)
PKS
6
NT
+
C
.
.

SV095
I343
Happar 1 (N 14)
PKS
L
NT
+
.
.
.

SV096
I475
Baiji 2 (KUH 5333)
IRQ
2
NT
+
.
.
.

SV097
I607
Karad
IND
6
3.3
+
.
.
.

SV098
I617
Quetta 1 (14-1)
PKS
6
2.8
+
.
.
.

SV099
I618
Chaman 1 (47 II)
PKS
6
3.9
+
.
.
.

SV100
I622
H.E.S. 4 (Type 12)
AFG
6
2.0
+
.
.
.

SV101
I626
Katana 1 (182)
SAR
2
3.1
+
.
.
.

SV102
I639
Ardabil 1 (336 II)
IRN
6
3.9
+
C
.
.

SV103
I764
Baqubah 1 (KUH 5301)
IRQ
6
NT
+
.
.
.

SV104
I765
Khanaqin 1 (KUH 5304)
IRQ
2
NT
+
.
.
.

SV105
I766
Khanaqin 4 (KUH 5307)
IRQ
2
NT
+
.
.
.

SV106
I771
Sulaymaniyah 2 (KUH 5322)
IRQ
2
NT
+
.
.
.

SV107
I776
Sinjar 1 (KUH 5337)
IRQ
2
NT
+
.
.
.

SV108
J016
Gozen
JPN
6
2.9
+
.
.
.

SV109
J040
Hanbozu
JPN
6
1.7
+
.
.
.

SV110
J044
Hosomugi
JPN
6
3.7
+
.
.
.

SV111
J064
Hayakiso 2
JPN
6
2.1
+
.
.
.

SV112
J069
Yahazu
JPN
6
1.5
+
C
.
.

SV113
J075
Shishikui Zairai
JPN
6
3.6
+
.
.
.

SV114
J080
Irino Zairai
JPN
6
1.6
+
.
.
.

SV115
J087
Shimabara
JPN
6
1.3
+
.
.
.

SV116
J097
Sazanshu
JPN
6
4.1
+
.
.
.

SV117
J183
Yatomi Mochi
JPN
6
2.2
+
.
.
.

SV118
J326
Sekitori
JPN
6
1.4
+
.
.
.

SV119
J330
Suifu
JPN
6
1.6
+
.
.
.

SV120
J334
Honen
JPN
6
1.5
+
C
.
.

TABLE 5

Ear density

SV ID
OU ID
Variety name
Origin
Row-type
mm*
Flowering type
SNP1
SNP2
SNP3

SV121
J338
Chikurin
JPN
6
1.3
+
.
.
.

SV122
J366
Wase Bozu
JPN
6
2.3
+
.
.
.

SV123
J369
Kobinkatagi
JPN
6
1.4
+
C
.
.

SV124
J386
Hachikoku
JPN
6
1.8
+
.
.
.

SV125
J395
Tainan
TPE
6
3.3
+
.
.
.

SV126
J396
Zairai 1
TPE
6
4.4
+
.
.
.

SV127
J467
Bozu Mochi
JPN
6
2.0
+
.
.
.

SV128
J639
Shirochinko
JPN
6
1.6
+
C
.
.

SV129
J647
Akashinriki
JPN
6
1.7
+
C
.
.

SV130
J669
Shiroto
JPN
6
1.1
+
.
.
.

SV131
J672
Shikke Shirazu
JPN
6
1.7
+
.
.
.

SV132
J674
Wase Hadaka
JPN
6
2.0
+
.
.
.

SV133
J682
Hizahachi
JPN
6
1.4
+
.
.
.

SV134
J689
Hitokawa
JPN
6
1.5
+
.
.
.

SV135
J691
Hayatori Hadaka
JPN
6
2.3
+
.
.
.

SV136
J696
Zairai 2
TPE
6
4.4
+
.
.
.

SV137
J697
Taihoku A
TPE
6
3.0
+
.
.
.

SV138
K001
Goheung Covered 1
KOR
6
3.0
+
.
.
.

SV139
K002
Goheung Naked 2
KOR
6
1.4
+
.
.
.

SV140
K003
Yeongam Covered 2
KOR
6
2.7
+
.
.
.

SV141
K043
Masan Naked 1
KOR
6
2.5
+
.
.
.

SV142
K059
Waegwan Covered 1
KOR
6
2.6
+
.
.
.

SV143
K060
Yeongcheon Covered 2
KOR
6
1.6
+
.
.
.

SV144
K094
Anseong Covered 2
KOR
6
2.5
+
.
.
.

SV145
K095
Namyang Covered 2
KOR
6
2.5
+
.
.
.

SV146
K108
Gangneung Covered 3
KOR
6
1.7
+
.
.
.

SV147
K113
Hamjong Covered 1
KOR
6
3.8
+
.
.
.

SV148
K117
Hongweon Inuno-o
KOR
6
3.2
+
.
.
.

SV149
K304
Boseong Covered 3
KOR
6
1.6
+
.
.
.

SV150
K311
Gwangju Covered 4
KOR
6
1.8
+
.
.
.

SV151
K327
Buyong Oni Hadaka 2
KOR
6
1.5
+
.
.
.

SV152
K329
Dongsan Oni Hadaka 2
KOR
6
1.4
+
.
.
.

SV153
K342
Masan Covered 5
KOR
6
1.6
+
.
.
.

SV154
K374
Daecheon Covered 4
KOR
6
1.7
+
.
.
.

SV155
K377
Yesan Covered 2
KOR
6
1.9
+
.
.
.

SV156
K401
Baegcheon Covered 1
KOR
6
3.0
+
.
.
.

SV157
K419
Gyeongseong Rokkaku
KOR
6
1.7
+
.
.
.

SV158
K602
Jangheung Naked 2
KOR
6
1.4
+
.
.
.

SV159
K624
Sunchang Naked 4
KOR
6
1.7
+
.
.
.

SV160
K625
Mangyeong Naked 3
KOR
6
2.6
+
.
.
.

SV161
K638
Tongyeong Covered 1
KOR
6
1.5
+
.
.
.

SV162
K655
Gyeongju Covered 4
KOR
6
1.9
+
.
.
.

SV163
K672
Janghang Covered
KOR
6
1.8
+
.
.
.

SV164
K689
Yeongdong Seungmaeg 1
KOR
6
3.1
+
.
.
.

SV165
K692
Eumseong Covered 3
KOR
6
1.4
+
.
.
.

SV166
K702
Namcheon Covered
KOR
6
3.0
+
.
.
.

SV167
K706
Hongcheon Covered 1
KOR
6
2.3
+
.
.
.

SV168
N005
Sama 1 (1385)
NPL
6
2.2
+
.
.
.

SV169
N009
Tilman Camp 1 (1398)
NPL
6
2.6
+
C
.
.

SV170
N016
Pisang 1 (1427)
NPL
6
2.8
+
.
.
.

SV171
N017
Thangja 1 (1433)
NPL
6
2.6
+
C
.
.

SV172
N031
Birkna Camp 1 (1487)
NPL
6
2.5
+
.
.
.

SV173
N051
Kagbeni 1 (1616)
NPL
6
2.0
+
C
.
.

SV174
N055
Ulleri 1 (1633)
NPL
6
2.5
+
.
.
.

SV175
N077
Sipche 1
NPL
6
2.2
+
C
.
.

SV176
N308
Gho 1 (1392)
NPL
6
2.3
+
C
.
.

SV177
N319
Katmandu 2 (1438)
NPL
6
3.5
+
.
.
.

SV178
N333
Chame 1 (1493)
NPL
6
3.2
+
.
.
.

SV179
N340
Ngyak 1 (1524)
NPL
6
2.0
+
C
.
.

SV180
N344
Prok 1 (1537)
NPL
6
2.9
+
.
.
.

TABLE 6

Ear density

SV ID
OU ID
Variety name
Origin
Row-type
mm*
Flowering type
SNP1
SNP2
SNP3

SV181
N369
Lumley 1 (1674)
NPL
6
3.6
+
.
.
.

SV182
N615
Annapurna B.C. 1 (1422)
NPL
6
2.7
+
C
.
.

SV183
N622
Trisuli Bazar 3 (1449)
NPL
6
2.6
+
.
.
.

SV184
N628
Kakani Bangalow 3 (1477)
NPL
6
4.4
+
.
.
.

SV185
N630
Macha Khola 1 (1483)
NPL
6
2.5
+
.
.
.

SV186
N647
Dhumpu 1 (1596)
NPL
6
2.8
+
.
.
.

SV187
N653
Sikha2 (1626)
NPL
6
1.7
+
C
.
.

SV188
N661
Keronja 1 (1651)
NPL
6
2.3
+
.
.
.

SV189
T001
Turkey 1
TKY
6
3.8
+
.
.
.

SV190
T011
Turkey 31
TKY
2
3.2
+
.
.
.

SV191
T021
Turkey 61
TKY
2
3.2
+
.
.
.

SV192
T267
Bursa (918)
TKY
6
3.3
+
C
.
.

SV193
T268
Amasya (1208)
TKY
2
3.0
+
C
.
.

SV194
T304
Turkey 11
TKY
6
3.9
+
C
.
.

SV195
T314
Turkey 41
TKY
2
3.5
+
.
.
.

SV196
T324
Turkey 71
TKY
6
3.8
+
.
.
.

SV197
T334
Turkey 101
TKY
6
4.2
+
.
.
.

SV198
T566
Rerhauli 1 (454)
TKY
6
3.3
+
.
.
.

SV199
T567
Goenen (997)
TKY
6
3.2
+
C
.
.

SV200
T568
Ayas (1309)
TKY
2
2.9
+
.
.
.

SV201
T607
Turkey 21
TKY
6
4.1
+
.
.
.

SV202
T617
Turkey 51
TKY
2
3.8
+
.
.
.

SV203
T627
Turkey 81
TKY
2
3.7
+
.
.
.

SV204
T637
Turkey 111
TKY
2
3.6
+
.
.
.

SV205
T867
Istanbul (1024)
TKY
2
3.1
+
C
.
.

SV206
T868
Ankara (1369)
TKY
2
3.0
+
C
.
.

SV207
U005
Samaria 4 Zeilige
SPN
6
3.6
+
.
.
.

SV208
U009
Bolognes
ITL
6
4.1
+
C
.
.

SV209
U013
Orayio
ITL
6
2.1
+
.
.
.

SV210
U015
Bulgarian 447
BGA
6
3.4
+
C
.
.

SV211
U019
Kolnozni
YUG
6
3.3
+
C
.
.

SV212
U023
Darmatishe
YUG
6
2.2
+
C
.
.

SV213
U025
Balkan 2
BGA
6
2.4
+
.
.
.

SV214
U029
Rene
FRC
2
3.3
+
C
.
.

SV215
U030
Kleinwanz
GMN
6
3.1
+
.
.
.

SV216
U046
Adliker
SWL
2
4.1
+
.
.
.

SV217
U048
Michalovicky nahy
CSR
2
4.2
+
.
.
.

SV218
U049
Jubilee
CSR
2
3.6
+
.
.
.

SV219
U050
Prentice
UTK
2
3.2
+
.
.
.

SV220
U051
Archer
UTK
2
3.3
+
.
.
.

SV221
U053
Maja
DMK
2
3.4
+
.
.
.

SV222
U055
Erhart Frederickson
SWD
6
3.2
+
C
.
.

SV223
U059
Tsmmi
FIN
6
2.0
Cleistogamous
C
.
C

SV224
U089
Baku 1 (Cauc. 1)
AZR
6
3.5
+
.
.
.

SV225
U090
Erevan 1 (Cauc.15)
ARM
2
2.9
+
.
.
.

SV226
U094
Shemakha 1 (Cauc.37)
AZR
6
3.8
+
C
.
.

SV227
U095
Erevan 6 (Cauc.40)
ARM
2
2.8
+
.
.
.

SV228
U145
CSR 82
CSR
2
NT
+
.
.
.

SV229
U172
KUH 837
RMN
2
NT
+
.
.
.

SV230
U305
Badajoy
SPN
6
1.9
Cleistogamous
C
.
C

SV231
U316
Caveda
BGA
6
4.4
+
.
.
.

SV232
U317
Rumanian 19
RMN
6
3.1
+
.
.
.

SV233
U322
Urania
YUG
6
3.7
+
.
.
.

SV234
U325
Hungarian
HGY
D
2.7
+
.
.
.

SV235
U326
France 1
FRC
2
2.3
Cleistogamous
.
G
.

SV236
U327
Albert
FRC
6
3.8
+
.
.
.

SV237
U329
Cygne
FRC
2
2.5
Cleistogamous
.
G
.

SV238
U340
Oldenburger Landgerste
GMN
6
3.5
+
C
.
.

SV239
U341
Saalegerste
GMN
2
3.6
+
.
.
.

SV240
U347
Dometzkoer Paradies
CSR
2
4.0
+
.
.
.

TABLE 7

Ear density

SV ID
OU ID
Variety name
Origin
Row-type
mm*
Flowering type
SNP1
SNP2
SNP3

SV241
U351
Plumage
UTK
2
2.5
Cleistogamous
.
G
.

SV242
U352
Imperial
UTK
2
2.2
Cleistogamous
.
G
.

SV243
U353
Opal
DMK
2
3.2
+
.
.
.

SV244
U354
Drost
DMK
2
3.3
+
.
.
.

SV245
U355
Vega
SWD
6
3.6
+
.
.
.

SV246
U359
Olli
FIN
6
2.9
+
C
.
.

SV247
U388
Caucasus
SSU
2
3.3
+
.
.
.

SV248
U397
Geghard 1 (Cauc.44)
ARM
2
2.9
+
.
.
.

SV249
U400
Gori (Cauc.53)
GEO
6
3.3
+
C
.
.

SV250
U434
PLD 5
PLD
2
NT
+
.
.
.

SV251
U441
CSR 3
CSR
2
NT
+
.
.
.

SV252
U603
Ribofardo
SPN
6
3.9
+
.
.
.

SV253
U607
Valencia
SPN
6
1.9
Cleistogamous
C
.
C

SV254
U610
Tripoli
ITL
6
3.7
+
C
.
.

SV255
U613
Otello
ITL
6
1.8
Cleistogamous
C
.
C

SV256
U615
Bulgarian 347
BGA
6
3.6
+
C
.
.

SV257
U616
Moldavia
RMN
6
3.2
+
.
.
.

SV258
U628
Aurore
FRC
2
2.9
+
.
.
.

SV259
U633
Hanna
GMN
2
3.6
+
.
.
.

SV260
U640
Bavarian
GMN
2
2.9
+
.
.
.

SV261
U641
Bohemian
ATA
2
NT
+
.
.
.

SV262
U646
Tivannes
SWL
2
3.2
+
.
.
.

SV263
U647
Prokupkuynahy
CSR
2
3.4
+
C
.
.

SV264
U648
Tuxskynahy
CSR
6
3.6
+
C
.
.

SV265
U652
Binder
DMK
2
3.3
+
.
.
.

SV266
U658
Ymer
SWD
2
3.2
+
.
.
.

SV267
U659
Vankhuri
FIN
2
2.8
+
.
.
.

SV268
U692
Tibilisi 1 (Cauc.20)
GEO
6
3.6
+
.
.
.

SV269
U694
Baku 6 (Cauc.35)
AZR
6
3.1
+
.
.
.

SV270
U737
PLD 49
PLD
2
NT
+
C
.
.

SV271
U738
PLD 83c
PLD
2
NT
+
.
.
.

SV272
U740
PLD 139
PLD
2
NT
+
.
.
.

SV273
U771
KUH 836
RMN
6
NT
+
C
.
.

SV274
U773
KUH 842
RMN
2
NT
+
.
.
.

+ non-cleistogamous

L Labile;

D deficiens

*Takahashi et al. (1983), Catalogue of barley germplasm preserved in Okayama University (Kurashiki, Japan).

“.” indicates A (the same as SV001).

The sequence variation was present at the third base position of each codon, and hence did not bring about any variation in peptide sequence. A first variant “. . . C (A/C)G . . . ” was uncorrelated with cleistogamy, whereas second and third variants “. . . (A/G) TCATC (A/C) . . . ” were correlated. The fact that all the noncleistogamous types were of haplotype “ATCATCA” at the latter site suggested that this haplotype was necessary for the determination of noncleistogamy (FIG. 3B). The haplotype of the cleistogamous types was either “GTCATCA” or “ATCATCC” (FIG. 3B). The initial G was present in seven cleistogamous populations in addition to KNG. Hence, it was suggested that this change in a single base was sufficient for the change from noncleistogamy to cleistogamy. A second cly1 allele had the alternative haplotype “ATCATCC” (where a C replaces an A in comparison with the noncleistogamous type). This haplotype was present in four cleistogamous populations (FIG. 3B).

Example 5
Analysis of Cleavage of Cly1 mRNA with miR172

(1) RNAs were extracted from spikes at the awn primordium stage, and first strand cDNA synthesis was performed by use of SuperScipt II (Invitrogen). RT-PCR was conducted by use of a primer corresponding to one of the miR172 target sites (BF623536U514M060H23U540 “ACCAGCAGCAGCAACAGAGGC/SEQ ID NO: 12” and BF623536U514M060H23L919“GCTGGTAATGGCTGTGGGACG/SEQ ID NO: 13”) or one of the 3′UTRs (BF623536U514U794 “TCAAGAGCAGCCAGCCAAGAA/SEQ ID NO: 14” and BF623536U514M060H23L1053 “CCGCATCCGTCCTCCTCTCAA/SEQ ID NO: 15”). As a result, the gene expression pattern was essentially the same between an individual having the Cly1.a (AZ) allele and an individual having the cly1.b (KNG) allele (FIG. 5C). The expression level was slightly higher in KNG than AZ, but no significant change with time was identified by RT-PCR (FIG. 5C). The transcription level of gene fragment in the miR172 target site was similar to the transcription level of 3′UTR gene fragment.

(2) Modified 5′RACE was carried out to investigate the cleavage of Cly1 mRNA with miR172. An RNA ligase-mediated 5′RACE (Kasschau K D, et al. Dev Cell 4: 205-217, 2003) using the GeneRacer Kit (Invitrogen) was applied to total RNA extracted from whole spikes at the awn primordium stage. Dephosphorylation and decapping steps were omitted, so that only the 5′ends of the cleaved transcription products were able to be ligated to the GeneRacer RNA oligomer. A nested PCR employed a primer targeting the GeneRacer RNAoligomer, initially in combination with a gene specific reverse primer (BF623536U514M060H23L1053), and subsequently in combination with a primer (BF623536U514M060H23L1031“TCCATCTCTCGCTCTCACCCA/SEQ ID NO: 16”). PCR products were separated by agarose gel electrophoresis, and cloned into the TA vector(Invitrogen). Randomly selected clones without any prior size selection were used for DNA base sequencing.

As a result, the nested PCR targeting the miR172 target site produced an amplicon with 400 by or less from an individual having Cly1.a, but not from an individual having cly1.b (FIG. 5D). This suggests that the cleavage with miR172 occurred in the former, but not in the latter (FIG. 5D). Cleavage sites were present within the miR172 target sites of the majority (32/48) of sequences cloned from the Cly1.a RACE amplicon, and most of the cleavage sites were between the A and U nucleotides (FIG. 5E). However, most of the cly1.b amplicon clones were ribosomal RNAs or mRNAs of genes unrelated to Cly1, and only two of 48 clones contained sequence of Cly1 (FIG. 5E). Thus, it was conceivable that random mRNA breakage occurred in most of the cly1.b RACE products. Overall, it was shown that lodicule development and the resultant cleistogamy were brought about by a difference in cleavage of the Cly1 transcription product with miR172.

Note that since the miR172 target site was found in ESTs of not only barley, but also many other plants, it is conceivable that the cleavage of the transcription product with miR172 is present in wide varieties of plants (FIG. 6).

Example 6
Origin of Cleistogamous Barley

A phylogenetic analysis was conducted. ClustalW2 (http://www.ebi.ac.uk/Tools/clustalw2/) was used for amino acid alignment in this analysis. In addition, a phylogenetic tree was constructed by the neighbor joining method using PAUP4.0b10 (Swofford D PAUP*. Phylogenetic analysis using parsimony (*and other methods), ver.4. (Sinauer, Sunderland, Mass., USA) 1998).

Two distinct lineages of cleistogamy were found by the phylogenetic analysis (FIG. 7). The KNG haplotype (cly1.b) differed from the wild-type AZ sequence by only two base substitutions, one of which was at position 3084 within the miR712 target sequence, and the other of which was at position 626 within the first exon (FIG. 8). The KNG haplotype appears to be directly originated from the wild-type AZ haplotype (FIG. 7). The AZ haplotype may be originated from the SV012 haplotype, because G at position 2252 is shared with noncleistogamous cultivars and wild-type barley (FIG. 8). The origin of the second cleistogamous haplotype (cly1.c) is uncertain. However, the two cleistogamous haplotypes appear to represent independent mutation events (FIG. 7). The 3-kb Cly1 coding sequence was invariant across both cleistogamous haplotypes, which suggests that the origin of cleistogamous barley was probably relatively recent.

INDUSTRIAL APPLICABILITY

As described above, according to the present invention, a novel gene Cly1/cly1 controlling chasmogamy/cleistogamy of a plant was identified, and it is made possible to determine chasmogamy/cleistogamy of a plant and to produce or breed a cleistogamous plant by making use of the identified Cly1/cly1 gene. The determination of chasmogamy/cleistogamy in the present invention uses the gene controlling the chasmogamy/cleistogamy as a target, and besides can be carried out by use of individuals at an early stage of cultivation (for example, seeds or seedlings). For this reason, the use of the determination method of the present invention makes it possible to specifically and efficiently breed a cleistogamous variety.

A cleistogamous plant produced or bred by use of the cly1 gene has enhanced resistance to Fusarium ear blight. Accordingly, the present invention can contribute to reduction of damage due to Fusarium ear blight. Moreover, pollen dispersal can also be prevented by imparting a cleistogamous trait to a plant. Recently, it has been pointed out that genes artificially modified by genetic recombination or the like may be dispersed to the natural world, so that the ecosystem of the natural world may be threaten, and the conservation of wild species may be affected. The introduction of cleistogamy to a plant is also effective for prevention of the dispersal.

[Sequence Listing Free Text]

SEQ ID NO: 10

<223> microRNA

SEQ ID NO: 11

<223> microRNA target site

SEQ ID NOs: 12 to 16

<223> artificially synthesized primer sequences

GENE CONTROLLING CHASMOGAMY/CLEISTOGAMY OF PLANT AND USE THEREOF

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