NOVEL GENETIC LOCI ASSOCIATED WITH DISEASE RESISTANCE IN SOYBEANS

Information

  • Patent Application
  • 20210024950
  • Publication Number
    20210024950
  • Date Filed
    June 09, 2017
    7 years ago
  • Date Published
    January 28, 2021
    3 years ago
Abstract
The present invention relates to methods and compositions for identifying, selecting and/or producing a Disease resistant soybean plant or germplasm using markers, genes and chromosomal intervals derived from Glycine tomentella P1441001, P1441008, P1446958, P1509501, P1583970, or P1483224. A soybean plant or germplasm that has been identified, selected and/or produced by any of the methods of the present invention is also provided. Disease resistant soybean seeds, plants and germplasms are also provided.
Description
STATEMENT REGARDING ELECTRONIC FILING OF A SEQUENCE LISTING

A Sequence Listing in ASCII text format, is submitted, entitled 81045 SEQ LIST_ST25.txt and 6.90MB in size, generated on June 9, 2017 and an electronic sequence listing is filed in conjunction with this application. This Sequence Listing is hereby incorporated by reference into the specification for its disclosures.


FIELD OF THE INVENTION

The present invention relates to compositions and methods for identifying, selecting and producing enhanced disease and/or pathogen resistant soybean plants.


BACKGROUND

Plant pathogens are known to cause considerable damage to important crops, resulting in significant agricultural losses with widespread consequences for both the food supply and other industries that rely on plant materials. As such, there is a long felt need to reduce the incidence and/or impact of agricultural pathogens on crop production.


Several pathogens have been associated with damage to soybeans, which individually and collectively have the potential to cause significant yield losses in the United States and throughout the world. Exemplary pathogens include, but are not limited to fungi (e.g., genus Phytophthora and Asian Soybean rust Phakopsora pahyrhizi), nematodes (e.g., genus Meloidogyne, particularly, Meloidogyne javanica), and soybean stem canker. Given the significant threat to global food supplies that these pathogens present as well as the time and expense associated with treating soybean crops to prevent yield loss, new methods for producing pathogen resistant soybean cultivars are needed. What is needed is novel resistance genes (herein, “R-Genes”) that can be introduced into commercial soybean plants to control soybean pathogens


SUMMARY OF THE INVENTION

This summary lists several embodiments of the presently disclosed subject matter, and in many cases lists variations and permutations of these embodiments.


Thus, it is an object of the presently disclosed subject matter to provide methods for conveying pathogen resistance into non-resistant soybean germplasm or plant lines. Further the presently disclosed subject matter provides novel Glycine max lines comprising in its genome a chromosome interval, loci, and/or gene that is derived from Glycine tomentella and further confers Asian soybean rust resistance (herein, ‘ASR’) in said novel Glycine max line.


BRIEF DESCRIPTION OF THE SEQUENCE LISTING

SEQ ID NOs: 1 & 2 are chromosomal intervals derived from Glycine tomentella line accession PI441001 referred to herein as “Scaffold 46840” and “Scaffold 49652” respectively. Scaffold 49652 has been mapped to G. tomentella chromosome 5 and Scaffold 46840 has been mapped to G. tomentella chromosome 5. SEQ ID NO. 3 is a chromosomal interval derived from Glycine tomentella line accession PI 483224 referred to herein as “Scaffold 002687F”. Scaffold 002687F has been mapped to G. tomentella chromosome 5. SEQ ID NO. 4 is a chromosomal interval derived from Glycine tomentella line accession PI 583970 referred to herein as “Scaffold 001084F”. Scaffold 001084F has been mapped to G. tomentella chromosome 5. SEQ ID NO: 5 is a chromosomal interval derived from Glycine tomentella line accession PI583970 herein referred to “Scaffold 000819F”. Scaffold 000819F has been mapped to G. tomentella chromosome 5. Genetic population mapping studies for PI441001, PI483224 and PI 583970 indicate that Glycine tomentella Chromosome 5 contains chromosomal intervals highly associated with ASR resistance (e.g. as corresponding to SEQ ID NOs: 1-5). Tentative data, not to be limited by theory, also indicates that Glycine tomentella accessions PI446958 and/or PI483224 can be used as a source for said chromosomal intervals corresponding to SEQ ID NOs 1-5. These chromosomal intervals or portions thereof may be introduced (i.e. introgressed through use of embryo rescue & marker assisted breeding (MAB)) into Glycine max lines to create Glycine max lines resistant to various diseases such as ASR. Tables 1-5 indicate single nucleotide polymorphisms (SNP) within SEQ ID NOs 1-5 that are associated with ASR resistance. Table 1 displays SNP associations for SEQ ID NO: 1 (Scaffold 46840) and Table 2 displays SNP associations for SEQ ID NO: 2 (Scaffold 49652). Table 3 displays SNP associations for SEQ ID NO: 3 (Scaffold 002687F). Table 4 displays SNP association for SEQ ID NO. 4 (Scaffold 001084F). Table 5 displays SNP associations for SEQ ID NO: 5 (Scaffold 000819F). All alleles for the SNPs identified in Tables 1 -5 were determined to be significantly linked with resistance or susceptibility (p<0.05) to ASR.









TABLE 1







SNP Positions within SEQ ID NO: 1 that are


associated with increased resistance to ASR












Favorable
Unfavorable




Allele
Allele




(Rust
(Rust


SNP Name
Position
Resistant)
Susceptible)













scaffold46840_1828_SNP
1828
T
C


scaffold46840_3854_SNP
3854
A
T


scaffold46840_4596_SNP
4596
G
C


scaffold46840_7871_SNP
7871
G
T


scaffold46840_16578_SNP
16578
A
C


scaffold46840_19339_SNP
19339
T
A


scaffold46840_19702_SNP
19702
C
T


scaffold46840_19733_SNP
19733
A
G


scaffold46840_21388_SNP
21388
G
T


scaffold46840_21389_SNP
21389
G
A


scaffold46840_21402_SNP
21402
A
G


scaffold46840_21518_SNP
21518
A
G


scaffold46840_21519_SNP
21519
A
T


scaffold46840_23199_SNP
23199
T
C


scaffold46840_27734_SNP
27734
A
C


scaffold46840_28944_SNP
28944
C
A


scaffold46840_31424_SNP
31424
A
G


scaffold46840_33107_SNP
33107
G
A


scaffold46840_34009_SNP
34009
C
T


scaffold46840_53166_SNP
53166
C
T


scaffold46840_53469_SNP
53469
C
T


scaffold46840_53908_SNP
53908
A
C


scaffold46840_54203_SNP
54203
T
C


scaffold46840_56034_SNP
56034
T
G


scaffold46840_88414_SNP
88414
G
T


scaffold46840_98917_SNP
98917
T
G


scaffold46840_104913_SNP
104913
C
G


scaffold46840_106826_SNP
106826
T
C


scaffold46840_106962_SNP
106962
A
T


scaffold46840_107712_SNP
107712
T
A


scaffold46840_133407_SNP
133407
T
C


scaffold46840_135237_SNP
135237
A
T


scaffold46840_138711_SNP
138711
C
T


scaffold46840_143396_SNP
143396
G
A


scaffold46840_143399_SNP
143399
T
C


scaffold46840_144469_SNP
144469
A
G


scaffold46840_155153_SNP
155153
T
C


scaffold46840_156265_SNP
156265
C
T


scaffold46840_156445_SNP
156445
G
A


scaffold46840_157487_SNP
157487
A
G


scaffold46840_160570_SNP
160570
A
G


scaffold46840_173047_SNP
173047
C
T


scaffold46840_173086_SNP
173086
C
T


scaffold46840_175324_SNP
175324
T
C


scaffold46840_176807_SNP
176807
A
T


scaffold46840_183058_SNP
183058
G
A


scaffold46840_185660_SNP
185660
T
A


scaffold46840_187500_SNP
187500
A
G


scaffold46840_189638_SNP
189638
G
A


scaffold46840_193666_SNP
193666
A
G


scaffold46840_194620_SNP
194620
G
A


scaffold46840_195623_SNP
195623
A
G


scaffold46840_199643_SNP
199643
C
A


scaffold46840_203247_SNP
203247
T
C


scaffold46840_204613_SNP
204613
A
G


scaffold46840_205887_SNP
205887
C
T


scaffold46840_206645_SNP
206645
T
C


scaffold46840_206670_SNP
206670
A
T


scaffold46840_207999_SNP
207999
A
G


scaffold46840_208069_SNP
208069
T
G


scaffold46840_210361_SNP
210361
G
C


scaffold46840_210610_SNP
210610
T
C


scaffold46840_211145_SNP
211145
A
C


scaffold46840_213594_SNP
213594
A
G


scaffold46840_213644_SNP
213644
G
A


scaffold46840_228760_SNP
228760
T
G


scaffold46840_232915_SNP
232915
G
T


scaffold46840_244091_SNP
244091
T
A


scaffold46840_247995_SNP
247995
C
T


scaffold46840_252031_SNP
252031
A
G


scaffold46840_252294_SNP
252294
G
A


scaffold46840_265245_SNP
265245
C
G


scaffold46840_266739_SNP
266739
G
T


scaffold46840_292109_SNP
292109
C
T


scaffold46840_301218_SNP
301218
T
A


scaffold46840_305019_SNP
305019
A
G


scaffold46840_305252_SNP
305252
A
G


scaffold46840_306327_SNP
306327
T
C


scaffold46840_306369_SNP
306369
C
T


scaffold46840_308096_SNP
308096
T
C


scaffold46840_309679_SNP
309679
A
T


scaffold46840_310247_SNP
310247
C
A


scaffold46840_310792_SNP
310792
A
T


scaffold46840_312460_SNP
312460
C
A


scaffold46840_313406_SNP
313406
A
C


scaffold46840_329689_SNP
329689
G
A


scaffold46840_330435_SNP
330435
G
C


scaffold46840_331328_SNP
331328
G
A


scaffold46840_337919_SNP
337919
C
A


scaffold46840_350957_SNP
350957
A
T


scaffold46840_354267_SNP
354267
A
G


scaffold46840_355661_SNP
355661
T
C


scaffold46840_356478_SNP
356478
T
C


scaffold46840_358994_SNP
358994
T
C


scaffold46840_363408_SNP
363408
A
G


scaffold46840_367504_SNP
367504
G
C


scaffold46840_368441_SNP
368441
A
T


scaffold46840_371665_SNP
371665
C
T


scaffold46840_372390_SNP
372390
C
A


scaffold46840_372415_SNP
372415
T
A


scaffold46840_380899_SNP
380899
C
T


scaffold46840_381701_SNP
381701
T
G


scaffold46840_382539_SNP
382539
A
G


scaffold46840_384909_SNP
384909
A
T


scaffold46840_386383_SNP
386383
G
A


scaffold46840_386883_SNP
386883
G
C


scaffold46840_387699_SNP
387699
A
G


scaffold46840_388192_SNP
388192
C
G


scaffold46840_401306_SNP
401306
G
C


scaffold46840_402205_SNP
402205
C
T


scaffold46840_419063_SNP
419063
A
C


scaffold46840_419121_SNP
419121
C
T


scaffold46840_419259_SNP
419259
G
A


scaffold46840_420963_SNP
420963
C
G


scaffold46840_421037_SNP
421037
C
T


scaffold46840_421906_SNP
421906
T
C


scaffold46840_424476_SNP
424476
C
T


scaffold46840_426504_SNP
426504
T
C


scaffold46840_426550_SNP
426550
C
T


scaffold46840_433738_SNP
433738
C
A


scaffold46840_435442_SNP
435442
C
T


scaffold46840_435446_SNP
435446
T
C


scaffold46840_435456_SNP
435456
G
A


scaffold46840_436445_SNP
436445
G
T


scaffold46840_436844_SNP
436844
T
G


scaffold46840_437526_SNP
437526
G
T


scaffold46840_438692_SNP
438692
C
A


scaffold46840_440329_SNP
440329
G
A


scaffold46840_441638_SNP
441638
T
C


scaffold46840_442882_SNP
442882
C
T


scaffold46840_444624_SNP
444624
C
T


scaffold46840_444829_SNP
444829
G
T


scaffold46840_444833_SNP
444833
C
T


scaffold46840_445506_SNP
445506
T
C


scaffold46840_451845_SNP
451845
A
G


scaffold46840_455083_SNP
455083
G
A


scaffold46840_455349_SNP
455349
G
C


scaffold46840_456838_SNP
456838
C
T


scaffold46840_456840_SNP
456840
C
T


scaffold46840_456888_SNP
456888
G
A


scaffold46840_457510_SNP
457510
G
A


scaffold46840_459924_SNP
459924
A
T


scaffold46840_493769_SNP
493769
G
A


scaffold46840_493863_SNP
493863
T
C


scaffold46840_495644_SNP
495644
G
A


scaffold46840_498269_SNP
498269
G
C


scaffold46840_500187_SNP
500187
C
T


scaffold46840_524750_SNP
524750
G
A


scaffold46840_531774_SNP
531774
G
C


scaffold46840_532217_SNP
532217
A
G


scaffold46840_532460_SNP
532460
C
A


scaffold46840_532849_SNP
532849
C
T


scaffold46840_533165_SNP
533165
T
G


scaffold46840_534674_SNP
534674
A
G


scaffold46840_534815_SNP
534815
T
C


scaffold46840_541100_SNP
541100
T
C


scaffold46840_547800_SNP
547800
A
G


scaffold46840_548096_SNP
548096
A
T


scaffold46840_548651_SNP
548651
A
G


scaffold46840_548909_SNP
548909
C
A


scaffold46840_550359_SNP
550359
A
G


scaffold46840_554136_SNP
554136
T
C


scaffold46840_557231_SNP
557231
G
C


scaffold46840_557476_SNP
557476
T
C


scaffold46840_559239_SNP
559239
G
T


scaffold46840_566877_SNP
566877
G
T


scaffold46840_573263_SNP
573263
C
G


scaffold46840_576344_SNP
576344
G
A


scaffold46840_576937_SNP
576937
T
A


scaffold46840_581793_SNP
581793
T
C


scaffold46840_631321_SNP
631321
T
A


scaffold46840_632437_SNP
632437
T
C


scaffold46840_644135_SNP
644135
G
A


scaffold46840_646516_SNP
646516
A
C


scaffold46840_646661_SNP
646661
C
T


scaffold46840_650395_SNP
650395
C
G


scaffold46840_650533_SNP
650533
T
G


scaffold46840_650883_SNP
650883
T
C


scaffold46840_680820_SNP
680820
T
C


scaffold46840_700296_SNP
700296
G
T


scaffold46840_709091_SNP
709091
T
C


scaffold46840_717250_SNP
717250
A
G


scaffold46840_717919_SNP
717919
C
T


scaffold46840_723204_SNP
723204
A
G


scaffold46840_737847_SNP
737847
A
C


scaffold46840_742854_SNP
742854
G
C


scaffold46840_761047_SNP
761047
C
T


scaffold46840_763626_SNP
763626
G
A


scaffold46840_767022_SNP
767022
A
T


scaffold46840_773124_SNP
773124
G
A


scaffold46840_795852_SNP
795852
G
A


scaffold46840_844662_SNP
844662
A
T


scaffold46840_856241_SNP
856241
C
T


scaffold46840_864819_SNP
864819
A
C


scaffold46840_868404_SNP
868404
T
A


scaffold46840_881483_SNP
881483
G
A


scaffold46840_881687_SNP
881687
G
A


scaffold46840_948734_SNP
948734
C
G


scaffold46840_951580_SNP
951580
C
A


scaffold46840_979277_SNP
979277
C
A


scaffold46840_984144_SNP
984144
A
G


scaffold46840_985119_SNP
985119
A
G


scaffold46840_990969_SNP
990969
T
G


scaffold46840_991246_SNP
991246
G
A


scaffold46840_996069_SNP
996069
A
T


scaffold46840_996617_SNP
996617
T
C


scaffold46840_1005071_SNP
1005071
G
T


scaffold46840_1012711_SNP
1012711
C
A


scaffold46840_1013144_SNP
1013144
A
T


scaffold46840_1013502_SNP
1013502
C
T


scaffold46840_1013853_SNP
1013853
G
T


scaffold46840_1014491_SNP
1014491
A
G


scaffold46840_1017387_SNP
1017387
T
G


scaffold46840_1017454_SNP
1017454
C
T


scaffold46840_1017456_SNP
1017456
A
G


scaffold46840_1017513_SNP
1017513
G
A


scaffold46840_1017562_SNP
1017562
G
A


scaffold46840_1017580_SNP
1017580
A
G


scaffold46840_1018041_SNP
1018041
G
C


scaffold46840_1018803_SNP
1018803
A
G


scaffold46840_1018807_SNP
1018807
A
T


scaffold46840_1018808_SNP
1018808
A
T


scaffold46840_1018809_SNP
1018809
A
T


scaffold46840_1019830_SNP
1019830
T
A


scaffold46840_1019879_SNP
1019879
C
T


scaffold46840_1023021_SNP
1023021
A
G


scaffold46840_1025444_SNP
1025444
T
C


scaffold46840_1027183_SNP
1027183
T
C


scaffold46840_1027185_SNP
1027185
T
C


scaffold46840_1027206_SNP
1027206
C
T


scaffold46840_1028386_SNP
1028386
T
A


scaffold46840_1035663_SNP
1035663
T
G


scaffold46840_1050796_SNP
1050796
A
T


scaffold46840_1092407_SNP
1092407
C
T


scaffold46840_1092836_SNP
1092836
A
T


scaffold46840_1097462_SNP
1097462
G
T


scaffold46840_1100700_SNP
1100700
C
A


scaffold46840_1107270_SNP
1107270
C
G


scaffold46840_1108688_SNP
1108688
T
C


scaffold46840_1110411_SNP
1110411
G
A


scaffold46840_1110578_SNP
1110578
G
A


scaffold46840_1113083_SNP
1113083
C
A


scaffold46840_1128638_SNP
1128638
A
G


scaffold46840_1132152_SNP
1132152
A
T


scaffold46840_1145964_SNP
1145964
T
G


scaffold46840_1151108_SNP
1151108
T
C


scaffold46840_1152027_SNP
1152027
T
C


scaffold46840_1164739_SNP
1164739
A
C


scaffold46840_1179177_SNP
1179177
A
G


scaffold46840_1196044_SNP
1196044
T
C


scaffold46840_1208547_SNP
1208547
T
A


scaffold46840_1222050_SNP
1222050
T
C


scaffold46840_1236321_SNP
1236321
C
A


scaffold46840_1238462_SNP
1238462
A
T


scaffold46840_1245039_SNP
1245039
A
T
















TABLE 2







SNP Positions within SEQ ID NO: 2 that are


associated with increased resistance to ASR












Favorable
Unfavorable




Allele
Allele




(Rust
(Rust


SNP Name
Position
Resistant)
Susceptible)













scaffold49652_5217_SNP
5217
T
C


scaffold49652_17452_SNP
17452
T
C


scaffold49652_17508_SNP
17508
T
C


scaffold49652_18133_SNP
18133
G
A


scaffold49652_23299_SNP
23299
T
G


scaffold49652_23932_SNP
23932
T
A


scaffold49652_25316_SNP
25316
C
T


scaffold49652_27493_SNP
27493
C
T


scaffold49652_31604_SNP
31604
A
C


scaffold49652_33717_SNP
33717
T
C


scaffold49652_33754_SNP
33754
G
A


scaffold49652_33815_SNP
33815
C
T


scaffold49652_35579_SNP
35579
A
G


scaffold49652_42441_SNP
42441
C
T


scaffold49652_45742_SNP
45742
A
G


scaffold49652_47403_SNP
47403
G
T


scaffold49652_50271_SNP
50271
C
G


scaffold49652_50273_SNP
50273
A
C


scaffold49652_52163_SNP
52163
A
G


scaffold49652_53843_SNP
53843
T
C


scaffold49652_53867_SNP
53867
T
C


scaffold49652_57089_SNP
57089
A
G


scaffold49652_60723_SNP
60723
C
T


scaffold49652_62132_SNP
62132
T
C


scaffold49652_64164_SNP
64164
T
A


scaffold49652_65402_SNP
65402
G
A


scaffold49652_67001_SNP
67001
G
T


scaffold49652_68551_SNP
68551
G
A


scaffold49652_88556_SNP
88556
A
G


scaffold49652_90063_SNP
90063
T
C


scaffold49652_95177_SNP
95177
A
G


scaffold49652_95604_SNP
95604
C
T


scaffold49652_98488_SNP
98488
G
A


scaffold49652_112122_SNP
112122
G
T


scaffold49652_119068_SNP
119068
T
C


scaffold49652_129424_SNP
129424
G
A


scaffold49652_130808_SNP
130808
A
G


scaffold49652_136261_SNP
136261
C
A


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T
C


scaffold49652_2075781_SNP
2075781
C
T


scaffold49652_2076365_SNP
2076365
C
T


scaffold49652_2076469_SNP
2076469
T
C


scaffold49652_2092527_SNP
2092527
T
C


scaffold49652_2092549_SNP
2092549
T
C


scaffold49652_2092809_SNP
2092809
C
G


scaffold49652_2094093_SNP
2094093
C
A


scaffold49652_2105568_SNP
2105568
A
G


scaffold49652_2115691_SNP
2115691
T
A


scaffold49652_2125447_SNP
2125447
C
T


scaffold49652_2126155_SNP
2126155
G
A


scaffold49652_2133188_SNP
2133188
T
C


scaffold49652_2138716_SNP
2138716
T
C


scaffold49652_2138774_SNP
2138774
T
C


scaffold49652_2156405_SNP
2156405
G
C


scaffold49652_2161240_SNP
2161240
C
T


scaffold49652_2178581_SNP
2178581
C
G


scaffold49652_2185469_SNP
2185469
A
T


scaffold49652_2187968_SNP
2187968
T
C


scaffold49652_2188098_SNP
2188098
T
C


scaffold49652_2188172_SNP
2188172
C
T


scaffold49652_2188805_SNP
2188805
G
C


scaffold49652_2198605_SNP
2198605
G
A


scaffold49652_2201366_SNP
2201366
A
C


scaffold49652_2216007_SNP
2216007
C
T


scaffold49652_2216622_SNP
2216622
G
A


scaffold49652_2227103_SNP
2227103
T
G


scaffold49652_2252002_SNP
2252002
A
C


scaffold49652_2267719_SNP
2267719
G
T


scaffold49652_2267778_SNP
2267778
G
C


scaffold49652_2275369_SNP
2275369
A
T


scaffold49652_2278763_SNP
2278763
A
G


scaffold49652_2284434_SNP
2284434
G
T


scaffold49652_2289155_SNP
2289155
G
A


scaffold49652_2293585_SNP
2293585
G
A


scaffold49652_2295350_SNP
2295350
A
G


scaffold49652_2319323_SNP
2319323
A
T


scaffold49652_2319892_SNP
2319892
A
G


scaffold49652_2340651_SNP
2340651
G
C


scaffold49652_2342022_SNP
2342022
G
T


scaffold49652_2350721_SNP
2350721
C
A


scaffold49652_2353391_SNP
2353391
T
G


scaffold49652_2368805_SNP
2368805
A
G


scaffold49652_2380689_SNP
2380689
T
C


scaffold49652_2380714_SNP
2380714
A
C


scaffold49652_2382130_SNP
2382130
T
C


scaffold49652_2383282_SNP
2383282
C
T


scaffold49652_2383554_SNP
2383554
T
C


scaffold49652_2384963_SNP
2384963
C
T


scaffold49652_2387325_SNP
2387325
C
T


scaffold49652_2387645_SNP
2387645
G
A


scaffold49652_2388437_SNP
2388437
A
C


scaffold49652_2400554_SNP
2400554
T
G


scaffold49652_2402164_SNP
2402164
T
C


scaffold49652_2405435_SNP
2405435
A
G


scaffold49652_2409799_SNP
2409799
C
T


scaffold49652_2410701_SNP
2410701
C
T


scaffold49652_2415748_SNP
2415748
A
G


scaffold49652_2415764_SNP
2415764
T
C


scaffold49652_2422192_SNP
2422192
T
G


scaffold49652_2442690_SNP
2442690
A
G


scaffold49652_2444153_SNP
2444153
A
C


scaffold49652_2458358_SNP
2458358
G
T


scaffold49652_2460701_SNP
2460701
G
C


scaffold49652_2471976_SNP
2471976
T
A


scaffold49652_2475982_SNP
2475982
G
C


scaffold49652_2476211_SNP
2476211
A
C


scaffold49652_2483904_SNP
2483904
C
A


scaffold49652_2492670_SNP
2492670
G
T


scaffold49652_2492681_SNP
2492681
C
T


scaffold49652_2503387_SNP
2503387
A
G


scaffold49652_2512568_SNP
2512568
C
A


scaffold49652_2513576_SNP
2513576
C
A
















TABLE 3







SNP Positions within SEQ ID NO: 3 that are


associated with increased resistance to ASR












Favorable
Unfavorable




Allele (Rust
Allele (Rust


SNP Name
Position
Resistant)
Susceptible)













002687F_347209_SNP||S_164680479
347209
C
T


002687F_205199_SNP||S_164660488
205199
A
C


002687F_219471_SNP||S_164662254
219471
A
T


002687F_219766_SNP||S_164662304
219766
A
C


002687F_342670_SNP||S_164679830
342670
T
A


002687F_347216_SNP||S_164680481
347216
C
T


002687F_214317_SNP||S_164661625
214317
G
T


002687F_214627_SNP||S_164661653
214627
T
A


002687F_214883_SNP||S_164661676
214883
T
C


002687F_223183_SNP||S_164662750
223183
C
T


002687F_224184_SNP||S_164662864
224184
T
G


002687F_224879_SNP||S_164662947
224879
T
C


002687F_347638_SNP||S_164680535
347638
G
A


002687F_213909_SNP||S_164661595
213909
C
A


002687F_342685_SNP||S_164679832
342685
A
C


002687F_355543_SNP||S_164681678
355543
G
A


002687F_220657_SNP||S_164662418
220657
A
G


002687F_208869_SNP||S_164661018
208869
G
A


002687F_220760_SNP||S_164662425
220760
C
A


002687F_221002_SNP||S_164662446
221002
G
A


002687F_279573_SNP||S_164670418
279573
C
G


002687F_215594_SNP||S_164661771
215594
T
C


002687F_236335_SNP||S_164664304
236335
T
C


002687F_213017_SNP||S_164661504
213017
T
G


002687F_220051_SNP||S_164662335
220051
A
T


002687F_4944_SNP||S_164619728
4944
T
C


002687F_343869_SNP||S_164679986
343869
T
A


002687F_227603_SNP||S_164663273
227603
A
G


002687F_200922_SNP||S_164659943
200922
C
T


002687F_202410_SNP||S_164660103
202410
T
C


002687F_257232_SNP||S_164667413
257232
C
T


002687F_258539_SNP||S_164667602
258539
A
C


002687F_264907_SNP||S_164668587
264907
T
A


002687F_265651_SNP||S_164668676
265651
C
T


002687F_271932_SNP||S_164669551
271932
T
C


002687F_283205_SNP||S_164670839
283205
C
T


002687F_204093_SNP||S_164660340
204093
C
T


002687F_210615_SNP
210615
T
C


002687F_237462_SNP||S_164664507
237462
T
A


002687F_244322_SNP||S_164665473
244322
G
C


002687F_262053_SNP||S_164668143
262053
C
T


002687F_236247_SNP||S_164664292
236247
C
T


002687F_236323_SNP||S_164664301
236323
T
C


002687F_154489_SNP||S_164653160
154489
A
G


002687F_233977_SNP||S_164664019
233977
A
G


002687F_257999_SNP||S_164667512
257999
G
A


002687F_279277_SNP||S_164670387
279277
A
G


002687F_282755_SNP||S_164670788
282755
G
A


002687F_283768_SNP||S_164670937
283768
T
C


002687F_302554_SNP||S_164673590
302554
A
G


002687F_164869_SNP||S_164655174
164869
T
G


002687F_288304_SNP||S_164671605
288304
T
G


002687F_294526_SNP||S_164672282
294526
T
G


002687F_309973_SNP||S_164674519
309973
G
T


002687F_337382_SNP||S_164679163
337382
G
A


002687F_211731_SNP||S_164661365
211731
C
T


002687F_220577_SNP||S_164662407
220577
G
A


002687F_237097_SNP||S_164664465
237097
T
C


002687F_266479_SNP||S_164668817
266479
C
A


002687F_271386_SNP||S_164669455
271386
T
G


002687F_273756_SNP||S_164669758
273756
C
T


002687F_273817_SNP||S_164669764
273817
T
C


002687F_276363_SNP||S_164670071
276363
G
A


002687F_298340_SNP||S_164672831
298340
G
A


002687F_238876_SNP||S_164664664
238876
T
A


002687F_239424_SNP||S_164664741
239424
A
G


002687F_256831_SNP||S_164667336
256831
G
A


002687F_259186_SNP||S_164667703
259186
A
G


002687F_275640_SNP||S_164669976
275640
G
A


002687F_277720_SNP||S_164670211
277720
T
C


002687F_279232_SNP||S_164670381
279232
C
T


002687F_263744_SNP||S_164668442
263744
T
A


002687F_304142_SNP||S_164673806
304142
A
G


002687F_281179_SNP||S_164670589
281179
G
A


002687F_236591_SNP||S_164664403
236591
G
A


002687F_297512_SNP||S_164672702
297512
A
T


002687F_305090_SNP||S_164673953
305090
T
A


002687F_224674_SNP||S_164662923
224674
A
G


002687F_275330_SNP||S_164669940
275330
A
G


002687F_304685_SNP
304685
T
G


002687F_319681_SNP
319681
T
C


002687F_353495_SNP
353495
C
T


002687F_52497_SNP||S_164627583
52497
T
C


002687F_268767_SNP
268767
G
C


002687F_278674_SNP
278674
A
G


002687F_302719_SNP
302719
T
C


002687F_343777_SNP
343777
T
C


002687F_168567_SNP||S_164655687
168567
A
T


002687F_325074_SNP||S_164677221
325074
T
G


002687F_325106_SNP||S_164677230
325106
T
C


002687F_333863_SNP
333863
A
G


002687F_195487_SNP
195487
A
T


002687F_228040_SNP||S_164663308
228040
T
A


002687F_244345_SNP
244345
T
A


002687F_278494_SNP||S_164670290
278494
A
G


002687F_349619_SNP
349619
C
T


002687F_198468_SNP
198468
G
T


002687F_224844_SNP
224844
A
G


002687F_224922_SNP
224922
A
G


002687F_275515_SNP
275515
T
A


002687F_292027_SNP
292027
T
A


002687F_346308_SNP
346308
T
C


002687F_362288_SNP
362288
A
C


002687F_185377_SNP
185377
G
A


002687F_220542_SNP
220542
G
A


002687F_223788_SNP
223788
A
T


002687F_343709_SNP
343709
T
C


002687F_343862_SNP
343862
A
G


002687F_201858_SNP
201858
T
G


002687F_333763_SNP
333763
A
G


002687F_347210_SNP
347210
A
G


002687F_160730_SNP
160730
A
G


002687F_161496_SNP
161496
A
G


002687F_189663_SNP
189663
C
T


002687F_341508_SNP
341508
A
T


002687F_346605_SNP
346605
A
G


002687F_362101_SNP
362101
G
A
















TABLE 4







SNP Positions within SEQ ID NO: 4 that are


associated with increased resistance to ASR












Favorable
Unfavorable




Allele (Rust
Allele (Rust


SNP Name
Position
Resistant)
Susceptible)













001084F-001-01_1285_SNP||S_96261695
1285
T
A


001084F-001-01_1521_SNP||S_96261716
1521
C
A


001084F-001-01_2588_SNP||S_96261833
2588
A
G


001084F-001-01_2699_SNP||S_96261849
2699
G
A


001084F-001-01_7021_SNP||S_96262358
7021
T
C


001084F-001-01_8184_SNP||S_96262509
8184
G
A


001084F-001-01_9147_SNP||S_96262590
9147
G
T


001084F-001-01_10435_SNP||S_96262737
10435
G
C


001084F-001-01_13118_SNP||S_96263136
13118
C
T


001084F_27070_SNP||S_96182069
27070
T
C


001084F_28184_SNP||S_96182234
28184
G
T


001084F_31379_SNP||S_96182641
31379
C
G


001084F_32184_SNP||S_96182765
32184
C
T


001084F_42660_SNP||S_96183942
42660
T
A


001084F_52001_SNP||S_96185095
52001
C
T


001084F_52023_SNP
52023
A
G


001084F_57467_SNP||S_96185758
57467
A
C


001084F_57737_SNP||S_96185798
57737
C
G


001084F_58089_SNP||S_96185849
58089
G
A


001084F_63976_SNP||S_96186652
63976
G
A


001084F_65903_SNP||S_96186876
65903
A
G


001084F_82007_SNP||S_96188830
82007
G
T


001084F-001-01_82274_SNP||S_96272178
82274
T
G


001084F_84479_SNP||S_96189187
84479
T
G


001084F_85287_SNP||S_96189334
85287
A
C


001084F_85888_SNP||S_96189417
85888
A
T


001084F_86201_SNP||S_96189465
86201
C
T


001084F-001-01_86502_SNP||S_96272667
86502
A
G


001084F_87914_SNP||S_96189697
87914
G
A


001084F_88555_SNP||S_96189801
88555
T
A


001084F_93651_SNP||S_96190428
93651
G
A


001084F_95283_SNP||S_96190621
95283
G
C


001084F-001-01_97554_SNP||S_96274217
97554
A
C


001084F_98814_SNP||S_96191018
98814
C
A


001084F_103767_SNP||S_96191744
103767
T
A


001084F_106721_SNP||S_96192163
106721
G
T


001084F_110421_SNP||S_96192646
110421
C
G


001084F_111143_SNP||S_96192765
111143
C
T


001084F_111365_SNP||S_96192803
111365
A
G


001084F_113202_SNP||S_96193055
113202
A
T


001084F_114276_SNP
114276
G
T


001084F_114340_SNP||S_96193207
114340
A
G


001084F_114450_SNP||S_96193224
114450
T
C


001084F_114536_SNP||S_96193238
114536
G
A


001084F_115661_SNP||S_96193442
115661
T
C


001084F_121396_SNP||S_96194243
121396
A
T


001084F_122184_SNP||S_96194326
122184
A
G


001084F_123018_SNP||S_96194413
123018
T
C


001084F_123034_SNP||S_96194416
123034
A
T


001084F_124257_SNP||S_96194591
124257
A
C


001084F_124583_SNP||S_96194626
124583
G
A


001084F_125117_SNP||S_96194736
125117
C
A


001084F_125329_SNP||S_96194763
125329
C
G


001084F_125691_SNP||S_96194803
125691
T
C


001084F_126047_SNP||S_96194860
126047
A
T


001084F_126132_SNP||S_96194877
126132
G
A


001084F_126350_SNP
126350
A
G


001084F_126379_SNP||S_96194890
126379
G
A


001084F_126664_SNP||S_96194933
126664
A
G


001084F_126712_SNP||S_96194939
126712
G
C


001084F-001-01_127911_SNP||S_96278033
127911
C
T


001084F_129197_SNP||S_96195328
129197
A
G


001084F_129484_SNP||S_96195378
129484
T
C


001084F_130167_SNP||S_96195529
130167
C
T


001084F_130305_SNP||S_96195546
130305
A
G


001084F_130497_SNP||S_96195566
130497
C
A


001084F_130604_SNP
130604
A
C


001084F_132646_SNP||S_96195748
132646
A
C


001084F_132795_SNP||S_96195769
132795
A
C


001084F_133258_SNP||S_96195812
133258
A
C


001084F_133487_SNP||S_96195836
133487
T
A


001084F_139504_SNP||S_96195994
139504
T
C


001084F_140393_SNP||S_96196060
140393
G
A


001084F_140734_SNP||S_96196116
140734
G
A


001084F_140889_SNP||S_96196121
140889
G
A


001084F_140943_SNP||S_96196125
140943
C
G


001084F_140956_SNP||S_96196127
140956
T
C


001084F_141136_SNP||S_96196151
141136
C
T


001084F_141999_SNP||S_96196230
141999
A
T


001084F_142002_SNP||S_96196231
142002
T
C


001084F_142266_SNP||S_96196269
142266
G
A


001084F_142328_SNP||S_96196272
142328
A
G


001084F_142364_SNP||S_96196276
142364
A
T


001084F_142627_SNP
142627
T
C


001084F_142993_SNP||S_96196324
142993
A
C


001084F_143091_SNP||S_96196333
143091
A
T


001084F_143145_SNP||S_96196341
143145
T
C


001084F_143227_SNP||S_96196350
143227
A
C


001084F_143257_SNP||S_96196353
143257
A
G


001084F_144001_SNP||S_96196414
144001
A
C


001084F_144670_SNP||S_96196479
144670
A
G


001084F_144689_SNP||S_96196480
144689
G
A


001084F_144794_SNP||S_96196492
144794
A
C


001084F_145076_SNP
145076
C
T


001084F_147040_SNP||S_96196783
147040
G
T


001084F_148598_SNP||S_96196947
148598
G
A


001084F_150856_SNP||S_96197142
150856
G
A


001084F_150890_SNP||S_96197144
150890
C
T


001084F_150946_SNP||S_96197148
150946
C
G


001084F_151501_SNP||S_96197186
151501
C
T


001084F_151988_SNP||S_96197248
151988
G
T


001084F_152716_SNP||S_96197335
152716
A
C


001084F_152718_SNP||S_96197336
152718
G
A


001084F_153080_SNP||S_96197385
153080
G
T


001084F_154824_SNP||S_96197620
154824
T
A


001084F_155266_SNP||S_96197675
155266
A
T


001084F_156572_SNP||S_96197878
156572
G
A


001084F_157730_SNP||S_96198007
157730
T
C


001084F_158682_SNP||S_96198187
158682
T
C


001084F_158723_SNP||S_96198192
158723
T
G


001084F_158742_SNP||S_96198194
158742
G
A


001084F_159166_SNP||S_96198257
159166
A
T


001084F_159313_SNP||S_96198276
159313
A
G


001084F_159442_SNP||S_96198291
159442
C
T


001084F_159587_SNP||S_96198308
159587
T
C


001084F_160320_SNP||S_96198404
160320
A
C


001084F_160645_SNP||S_96198429
160645
T
C


001084F_161095_SNP||S_96198508
161095
C
T


001084F_161709_SNP||S_96198644
161709
C
T


001084F_162179_SNP||S_96198670
162179
C
G


001084F_162814_SNP||S_96198732
162814
A
T


001084F_163017_SNP||S_96198749
163017
C
A


001084F_163383_SNP||S_96198774
163383
G
T


001084F_163680_SNP||S_96198808
163680
G
A


001084F_164905_SNP||S_96198896
164905
C
A


001084F_167287_SNP||S_96199111
167287
G
T


001084F_167515_SNP||S_96199122
167515
G
C


001084F_167652_SNP||S_96199135
167652
T
C


001084F_167962_SNP||S_96199157
167962
A
T


001084F_168247_SNP||S_96199187
168247
T
A


001084F_168725_SNP||S_96199246
168725
A
G


001084F_168757_SNP||S_96199252
168757
C
T


001084F_169076_SNP||S_96199300
169076
A
G


001084F_169079_SNP||S_96199301
169079
C
T


001084F_169225_SNP||S_96199313
169225
T
C


001084F_169491_SNP||S_96199351
169491
A
G


001084F_169747_SNP||S_96199380
169747
G
T


001084F_170170_SNP||S_96199415
170170
A
G


001084F_170426_SNP||S_96199442
170426
A
T


001084F_170606_SNP||S_96199460
170606
A
C


001084F_170818_SNP||S_96199484
170818
T
G


001084F_171563_SNP||S_96199521
171563
A
G


001084F_172571_SNP||S_96199666
172571
G
T


001084F_172598_SNP||S_96199673
172598
G
C


001084F_172978_SNP||S_96199717
172978
A
G


001084F_173956_SNP||S_96199838
173956
C
T


001084F_174469_SNP||S_96199929
174469
T
G


001084F_174541_SNP||S_96199946
174541
G
C


001084F_174758_SNP||S_96199978
174758
C
T


001084F_174810_SNP||S_96199982
174810
C
G


001084F_175992_SNP||S_96200176
175992
A
T


001084F_176004_SNP||S_96200178
176004
G
A


001084F_176028_SNP||S_96200179
176028
A
G


001084F_176079_SNP||S_96200184
176079
G
A


001084F_176112_SNP||S_96200191
176112
T
C


001084F_176675_SNP||S_96200247
176675
C
T


001084F_176780_SNP||S_96200251
176780
A
G


001084F_176983_SNP||S_96200275
176983
A
T


001084F_177786_SNP||S_96200387
177786
C
A


001084F_177903_SNP||S_96200440
177903
G
A


001084F_177935_SNP||S_96200455
177935
G
A


001084F_178018_SNP||S_96200464
178018
A
T


001084F_178034_SNP||S_96200468
178034
C
A


001084F_178300_SNP||S_96200512
178300
C
G


001084F_178555_SNP||S_96200539
178555
A
G


001084F_178630_SNP||S_96200546
178630
G
A


001084F_179301_SNP||S_96200625
179301
A
T


001084F_179344_SNP||S_96200632
179344
C
T


001084F_179983_SNP||S_96200681
179983
C
T


001084F_179991_SNP||S_96200682
179991
C
T


001084F_179996_SNP||S_96200683
179996
C
A


001084F_180047_SNP||S_96200686
180047
C
G


001084F_180211_SNP
180211
A
T


001084F_180253_SNP||S_96200700
180253
A
G


001084F_180363_SNP||S_96200718
180363
A
G


001084F_181550_SNP||S_96200860
181550
A
C


001084F_184764_SNP||S_96201129
184764
C
A


001084F_185504_SNP||S_96201216
185504
G
A


001084F_185881_SNP||S_96201245
185881
T
C


001084F_185892_SNP||S_96201246
185892
A
T


001084F_186629_SNP||S_96201304
186629
A
G


001084F_188635_SNP||S_96201526
188635
A
G


001084F_190570_SNP||S_96201789
190570
T
C


001084F_198311_SNP||S_96202837
198311
A
T


001084F_199171_SNP||S_96202922
199171
G
A


001084F_202466_SNP||S_96203367
202466
T
C


001084F_205193_SNP||S_96203796
205193
T
A


001084F_211317_SNP||S_96204657
211317
A
T


001084F_213117_SNP||S_96204953
213117
T
C


001084F_213481_SNP||S_96205009
213481
T
C


001084F_213587_SNP||S_96205028
213587
G
T


001084F_218631_SNP||S_96205568
218631
G
A


001084F_226564_SNP||S_96206645
226564
C
T


001084F_227857_SNP||S_96206816
227857
G
A


001084F_237891_SNP||S_96208029
237891
A
C


001084F_239017_SNP||S_96208161
239017
C
T


001084F_239368_SNP||S_96208190
239368
T
G


001084F_239536_SNP||S_96208211
239536
C
T


001084F_239682_SNP||S_96208242
239682
T
A


001084F_245799_SNP||S_96209112
245799
A
T


001084F_246318_SNP||S_96209151
246318
C
T


001084F_246386_SNP||S_96209159
246386
A
T


001084F_249008_SNP||S_96209600
249008
A
G


001084F_250639_SNP
250639
T
C


001084F_250641_SNP
250641
C
T


001084F_251193_SNP||S_96209831
251193
T
C


001084F_251515_SNP||S_96209892
251515
A
G


001084F_252366_SNP||S_96209966
252366
T
C


001084F_252578_SNP||S_96209979
252578
C
G


001084F_253950_SNP||S_96210134
253950
C
G


001084F_253956_SNP||S_96210135
253956
G
A


001084F_254157_SNP||S_96210146
254157
T
G


001084F_254286_SNP||S_96210168
254286
G
T


001084F_254514_SNP||S_96210191
254514
A
G


001084F_254545_SNP||S_96210194
254545
A
G


001084F_255300_SNP||S_96210279
255300
G
C


001084F_255476_SNP||S_96210306
255476
C
T


001084F_255933_SNP||S_96210349
255933
C
T


001084F_255992_SNP||S_96210355
255992
G
A


001084F_256289_SNP||S_96210412
256289
C
T


001084F_256296_SNP||S_96210413
256296
A
G


001084F_256670_SNP||S_96210467
256670
T
A


001084F_256861_SNP||S_96210477
256861
T
C


001084F_256888_SNP||S_96210478
256888
T
G


001084F_256929_SNP||S_96210482
256929
G
A


001084F_257126_SNP||S_96210501
257126
C
T


001084F_257133_SNP||S_96210503
257133
T
C


001084F_257136_SNP||S_96210504
257136
T
C


001084F_257289_SNP||S_96210519
257289
T
C


001084F_257327_SNP||S_96210520
257327
A
G


001084F_257534_SNP||S_96210589
257534
G
C


001084F_257676_SNP||S_96210618
257676
C
T


001084F_257874_SNP||S_96210661
257874
C
G


001084F_257934_SNP||S_96210667
257934
G
A


001084F_258230_SNP||S_96210699
258230
C
G


001084F_258395_SNP||S_96210734
258395
C
G


001084F_258418_SNP||S_96210739
258418
G
T


001084F_258653_SNP||S_96210766
258653
A
G


001084F_259060_SNP||S_96210844
259060
C
A


001084F_259168_SNP
259168
G
T


001084F_259273_SNP||S_96210882
259273
A
G


001084F_259443_SNP||S_96210898
259443
C
G


001084F_260067_SNP||S_96210964
260067
C
T


001084F_260664_SNP||S_96211072
260664
T
C


001084F_261242_SNP||S_96211105
261242
G
A


001084F_262054_SNP||S_96211201
262054
G
A


001084F_262740_SNP||S_96211245
262740
C
A


001084F_263131_SNP||S_96211295
263131
C
T


001084F_263585_SNP||S_96211367
263585
A
C


001084F_263650_SNP||S_96211378
263650
G
A


001084F_263970_SNP||S_96211410
263970
T
C


001084F_264720_SNP||S_96211554
264720
A
T


001084F_265298_SNP||S_96211619
265298
A
C


001084F_265844_SNP||S_96211678
265844
C
T


001084F_265895_SNP||S_96211683
265895
A
G


001084F_268195_SNP||S_96211902
268195
T
G


001084F_270197_SNP||S_96212223
270197
G
A


001084F_271842_SNP||S_96212410
271842
A
G


001084F_272342_SNP||S_96212494
272342
T
C


001084F_272520_SNP||S_96212517
272520
C
T


001084F_273104_SNP||S_96212595
273104
C
A


001084F_273591_SNP||S_96212652
273591
T
C


001084F_273652_SNP||S_96212656
273652
A
C


001084F_275546_SNP||S_96212833
275546
T
C


001084F_275658_SNP||S_96212859
275658
T
A


001084F_278078_SNP||S_96213204
278078
G
A


001084F_279158_SNP||S_96213320
279158
A
C


001084F_279575_SNP||S_96213380
279575
A
G


001084F_279729_SNP||S_96213387
279729
C
G


001084F_279954_SNP||S_96213419
279954
C
T


001084F_281389_SNP||S_96213625
281389
C
T


001084F_281513_SNP||S_96213642
281513
C
T


001084F_281542_SNP||S_96213648
281542
C
T


001084F_285388_SNP||S_96214072
285388
C
T


001084F_285487_SNP||S_96214096
285487
C
T


001084F_285683_SNP||S_96214122
285683
C
T


001084F_285771_SNP||S_96214134
285771
G
T


001084F_286094_SNP||S_96214209
286094
A
G


001084F_286116_SNP||S_96214211
286116
A
G


001084F_288436_SNP||S_96214424
288436
A
T


001084F_292939_SNP||S_96215141
292939
G
C


001084F_293422_SNP||S_96215191
293422
C
T


001084F_293810_SNP||S_96215229
293810
A
G


001084F_295524_SNP||S_96215424
295524
A
G


001084F_299778_SNP||S_96215969
299778
A
G


001084F_299821_SNP||S_96215974
299821
G
T


001084F_300075_SNP||S_96215990
300075
G
A


001084F_300887_SNP||S_96216153
300887
A
G


001084F_301156_SNP||S_96216230
301156
G
A


001084F_301165_SNP||S_96216235
301165
T
C


001084F_301641_SNP||S_96216305
301641
A
G


001084F_301793_SNP||S_96216321
301793
A
C


001084F_301853_SNP||S_96216333
301853
C
T


001084F_302997_SNP
302997
C
T


001084F_303003_SNP
303003
C
T


001084F_304597_SNP||S_96216721
304597
G
A


001084F_304622_SNP||S_96216723
304622
T
C


001084F_304909_SNP||S_96216751
304909
T
C


001084F_305891_SNP||S_96216891
305891
G
A


001084F_306716_SNP||S_96217046
306716
G
A


001084F_307693_SNP
307693
G
A


001084F_310749_SNP||S_96217542
310749
C
T


001084F_313646_SNP||S_96217955
313646
A
T


001084F_313895_SNP||S_96217991
313895
A
G


001084F_314482_SNP||S_96218079
314482
G
T


001084F_315263_SNP||S_96218215
315263
G
A


001084F_315605_SNP||S_96218253
315605
C
A


001084F_316003_SNP||S_96218288
316003
C
A


001084F_325995_SNP||S_96219601
325995
T
G


001084F_326011_SNP||S_96219606
326011
A
G


001084F_326714_SNP||S_96219700
326714
C
T


001084F_327975_SNP||S_96219824
327975
T
A


001084F_333039_SNP||S_96220391
333039
T
C


001084F_335872_SNP||S_96220742
335872
A
G


001084F_336344_SNP||S_96220819
336344
G
T


001084F_337412_SNP||S_96220956
337412
C
T


001084F_344980_SNP||S_96221826
344980
A
C


001084F_345034_SNP||S_96221832
345034
T
G


001084F_346595_SNP
346595
T
G


001084F_346779_SNP
346779
T
C


001084F_366657_SNP||S_96224390
366657
C
A


001084F_368696_SNP||S_96224623
368696
A
G


001084F_370079_SNP||S_96224756
370079
A
G


001084F_370253_SNP||S_96224774
370253
T
C


001084F_380989_SNP||S_96226270
380989
A
G


001084F_382368_SNP||S_96226437
382368
C
T


001084F_386547_SNP||S_96226875
386547
C
T


001084F_392211_SNP||S_96227525
392211
C
T


001084F_392954_SNP
392954
G
C


001084F_393013_SNP||S_96227637
393013
T
C


001084F_393748_SNP||S_96227753
393748
T
C


001084F_394557_SNP||S_96227856
394557
G
A


001084F_395656_SNP||S_96228004
395656
A
G


001084F_395876_SNP||S_96228023
395876
T
A


001084F_397385_SNP||S_96228189
397385
G
T


001084F_398551_SNP||S_96228339
398551
C
T


001084F_404731_SNP||S_96229018
404731
A
G


001084F_404792_SNP||S_96229021
404792
T
A


001084F_405196_SNP||S_96229072
405196
C
T


001084F_405197_SNP||S_96229073
405197
A
C


001084F_405198_SNP||S_96229074
405198
T
A


001084F_405731_SNP||S_96229143
405731
C
G


001084F_407194_SNP||S_96229325
407194
A
G


001084F_409622_SNP||S_96229641
409622
A
T


001084F_410452_SNP||S_96229734
410452
C
T


001084F_412571_SNP||S_96229970
412571
T
C


001084F_412785_SNP||S_96230001
412785
A
G


001084F_413752_SNP||S_96230139
413752
G
A


001084F_416185_SNP||S_96230412
416185
G
T


001084F_416395_SNP||S_96230427
416395
C
A


001084F_416591_SNP||S_96230446
416591
T
G


001084F_416593_SNP||S_96230447
416593
G
C


001084F_417106_SNP||S_96230492
417106
G
C


001084F_419325_SNP||S_96230786
419325
A
G


001084F_419460_SNP||S_96230801
419460
C
A


001084F_420529_SNP||S_96230939
420529
C
T


001084F_420584_SNP||S_96230944
420584
A
G


001084F_421121_SNP||S_96231014
421121
T
C


001084F_427016_SNP||S_96231729
427016
G
C


001084F_432148_SNP||S_96232338
432148
A
G


001084F_432700_SNP||S_96232398
432700
A
G


001084F_432798_SNP||S_96232404
432798
A
G


001084F_433511_SNP||S_96232528
433511
C
T


001084F_433994_SNP||S_96232606
433994
T
A


001084F_434231_SNP||S_96232644
434231
G
T


001084F_436588_SNP||S_96232887
436588
A
G


001084F_437273_SNP||S_96232934
437273
T
C


001084F_439876_SNP||S_96233294
439876
T
G


001084F_446565_SNP||S_96234158
446565
C
A


001084F_446712_SNP||S_96234176
446712
A
G


001084F_446950_SNP||S_96234212
446950
C
T


001084F_448070_SNP||S_96234319
448070
T
C


001084F_448364_SNP||S_96234350
448364
C
T


001084F_449012_SNP
449012
A
G


001084F_449590_SNP||S_96234450
449590
C
T


001084F_451682_SNP||S_96234684
451682
T
C


001084F_453264_SNP
453264
A
G


001084F_454594_SNP||S_96235135
454594
G
A


001084F_457770_SNP||S_96235545
457770
T
C


001084F_458788_SNP||S_96235648
458788
A
G


001084F_459147_SNP||S_96235687
459147
C
T


001084F_461166_SNP||S_96236019
461166
A
G


001084F_461247_SNP||S_96236039
461247
G
A


001084F_461752_SNP||S_96236125
461752
C
T


001084F_466437_SNP||S_96236630
466437
T
G


001084F_466805_SNP||S_96236678
466805
T
C


001084F_467644_SNP||S_96236780
467644
A
C


001084F_468704_SNP||S_96236898
468704
T
A


001084F_471659_SNP||S_96237333
471659
T
A


001084F_471667_SNP||S_96237334
471667
G
T


001084F_471959_SNP||S_96237354
471959
T
G


001084F_474765_SNP||S_96237787
474765
T
C


001084F_475731_SNP||S_96237878
475731
A
T


001084F_476014_SNP||S_96237900
476014
A
T


001084F_481574_SNP||S_96238618
481574
C
T


001084F_481748_SNP||S_96238640
481748
A
T


001084F_481949_SNP||S_96238661
481949
T
A


001084F_483822_SNP||S_96238932
483822
C
T


001084F_483922_SNP||S_96238940
483922
A
C


001084F_491255_SNP||S_96239840
491255
T
C


001084F_491264_SNP||S_96239843
491264
C
T


001084F_491333_SNP||S_96239854
491333
A
G


001084F_491388_SNP||S_96239874
491388
C
T


001084F_491438_SNP||S_96239884
491438
C
A


001084F_491456_SNP||S_96239888
491456
T
C


001084F_491474_SNP||S_96239891
491474
A
G


001084F_492676_SNP||S_96240013
492676
C
G


001084F_492681_SNP||S_96240014
492681
C
T


001084F_493223_SNP||S_96240071
493223
G
A


001084F_493257_SNP||S_96240074
493257
C
T


001084F_495167_SNP||S_96240310
495167
G
T


001084F_495237_SNP||S_96240320
495237
A
G


001084F_496103_SNP
496103
C
A


001084F_511172_SNP||S_96242515
511172
T
C


001084F_575347_SNP||S_96250573
575347
A
G


001084F_577730_SNP||S_96251010
577730
G
A


001084F_578149_SNP||S_96251054
578149
G
A


001084F_579372_SNP||S_96251212
579372
A
G


001084F_586316_SNP||S_96252046
586316
A
G


001084F_589859_SNP||S_96252610
589859
T
C


001084F_589957_SNP||S_96252616
589957
T
C


001084F_589968_SNP||S_96252619
589968
T
C


001084F_590712_SNP||S_96252758
590712
T
C


001084F_591010_SNP||S_96252775
591010
T
A


001084F_591944_SNP||S_96252903
591944
C
A


001084F_592110_SNP||S_96252917
592110
C
T


001084F_592173_SNP||S_96252923
592173
G
A


001084F_594029_SNP||S_96253180
594029
A
G


001084F_594234_SNP||S_96253198
594234
T
C


001084F_594408_SNP||S_96253219
594408
C
T


001084F_594539_SNP||S_96253244
594539
G
A


001084F_595688_SNP||S_96253403
595688
C
T


001084F_595748_SNP||S_96253409
595748
A
G


001084F_596093_SNP||S_96253455
596093
A
C


001084F_598845_SNP||S_96253843
598845
G
A


001084F_599340_SNP||S_96253911
599340
A
C


001084F_600996_SNP||S_96254147
600996
A
G


001084F_601300_SNP||S_96254185
601300
T
C


001084F_601957_SNP||S_96254250
601957
G
A


001084F_602486_SNP
602486
C
T


001084F_606403_SNP||S_96254906
606403
C
G


001084F_607071_SNP||S_96254986
607071
G
T


001084F_610092_SNP||S_96255394
610092
T
C


001084F_610896_SNP||S_96255567
610896
A
G


001084F_611678_SNP||S_96255725
611678
C
T


001084F_612116_SNP||S_96255826
612116
C
T


001084F_613144_SNP||S_96256025
613144
A
G


001084F_614025_SNP
614025
G
A


001084F_616919_SNP||S_96256727
616919
T
G


001084F_617682_SNP||S_96256806
617682
A
T


001084F_617849_SNP||S_96256827
617849
A
G


001084F_618353_SNP
618353
T
C


001084F_621278_SNP||S_96257215
621278
G
T


001084F_621394_SNP||S_96257226
621394
T
C


001084F_623147_SNP||S_96257479
623147
A
G


001084F_624529_SNP
624529
T
A


001084F_627999_SNP||S_96258130
627999
T
G


001084F_628120_SNP||S_96258147
628120
C
T


001084F_628359_SNP||S_96258172
628359
T
G


001084F_628992_SNP||S_96258268
628992
T
C


001084F_629050_SNP||S_96258285
629050
A
G


001084F_629328_SNP||S_96258334
629328
C
T


001084F_630582_SNP||S_96258523
630582
G
C


001084F_631413_SNP||S_96258645
631413
T
G


001084F_633048_SNP||S_96258882
633048
A
T


001084F_643660_SNP||S_96261113
643660
A
G
















TABLE 5







SNP Positions within SEQ ID NO: 5 that are


associated with increased resistance to ASR












Favorable
Unfavorable




Allele (Rust
Allele (Rust


SNP Name
Position
Resistant)
Susceptible)













000819F/G_tomentella_PI_583970_v1
114599
G
C


000819F/G_tomentella_PI_583970_v1
149238
C
T


000819F/G_tomentella_PI_583970_v1
149288
C
T


000819F/G_tomentella_PI_583970_v1
150032
T
C


000819F/G_tomentella_PI_583970_v1
151944
C
T


000819F/G_tomentella_PI_583970_v1
152479
A
T


000819F/G_tomentella_PI_583970_v1
155540
G
A


000819F/G_tomentella_PI_583970_v1
162204
A
C


000819F/G_tomentella_PI_583970_v1
163754
G
A


000819F/G_tomentella_PI_583970_v1
165362
A
C


000819F/G_tomentella_PI_583970_v1
165535
A
T


000819F/G_tomentella_PI_583970_v1
165577
G
C


000819F/G_tomentella_PI_583970_v1
167131
T
C


000819F/G_tomentella_PI_583970_v1
171396
A
G


000819F/G_tomentella_PI_583970_v1
172021
T
C


000819F/G_tomentella_PI_583970_v1
172471
G
C


000819F/G_tomentella_PI_583970_v1
177992
A
C


000819F/G_tomentella_PI_583970_v1
180263
A
C


000819F/G_tomentella_PI_583970_v1
181800
C
T


000819F/G_tomentella_PI_583970_v1
193762
C
T


000819F/G_tomentella_PI_583970_v1
194604
T
A


000819F/G_tomentella_PI_583970_v1
205989
T
A


000819F/G_tomentella_PI_583970_v1
212017
A
G


000819F/G_tomentella_PI_583970_v1
213446
C
T


000819F/G_tomentella_PI_583970_v1
232768
A
T


000819F/G_tomentella_PI_583970_v1
245161
G
A


000819F/G_tomentella_PI_583970_v1
245854
T
A


000819F/G_tomentella_PI_583970_v1
246180
C
A


000819F/G_tomentella_PI_583970_v1
246738
C
T


000819F/G_tomentella_PI_583970_v1
246919
G
A


000819F/G_tomentella_PI_583970_v1
248321
G
A


000819F/G_tomentella_PI_583970_v1
252345
A
G


000819F/G_tomentella_PI_583970_v1
252360
A
T


000819F/G_tomentella_PI_583970_v1
265534
A
G


000819F/G_tomentella_PI_583970_v1
266733
T
C


000819F/G_tomentella_PI_583970_v1
266773
T
C


000819F/G_tomentella_PI_583970_v1
266963
G
A


000819F/G_tomentella_PI_583970_v1
267269
A
T


000819F/G_tomentella_PI_583970_v1
267342
G
A


000819F/G_tomentella_PI_583970_v1
267921
C
T


000819F/G_tomentella_PI_583970_v1
267929
A
G


000819F/G_tomentella_PI_583970_v1
275462
G
A


000819F/G_tomentella_PI_583970_v1
275759
T
C


000819F/G_tomentella_PI_583970_v1
276045
T
C


000819F/G_tomentella_PI_583970_v1
276067
G
A


000819F/G_tomentella_PI_583970_v1
278203
C
T


000819F/G_tomentella_PI_583970_v1
278888
A
T


000819F/G_tomentella_PI_583970_v1
283800
G
A


000819F/G_tomentella_PI_583970_v1
284053
T
A


000819F/G_tomentella_PI_583970_v1
284831
G
C


000819F/G_tomentella_PI_583970_v1
287570
G
C


000819F/G_tomentella_PI_583970_v1
288787
A
T


000819F/G_tomentella_PI_583970_v1
289782
A
T


000819F/G_tomentella_PI_583970_v1
290827
T
C


000819F/G_tomentella_PI_583970_v1
291200
T
C


000819F/G_tomentella_PI_583970_v1
291213
G
A


000819F/G_tomentella_PI_583970_v1
293207
G
A


000819F/G_tomentella_PI_583970_v1
293867
C
T


000819F/G_tomentella_PI_583970_v1
297410
T
G


000819F/G_tomentella_PI_583970_v1
297431
T
C


000819F/G_tomentella_PI_583970_v1
297475
T
C


000819F/G_tomentella_PI_583970_v1
298295
G
T


000819F/G_tomentella_PI_583970_v1
298437
A
G


000819F/G_tomentella_PI_583970_v1
298979
G
C


000819F/G_tomentella_PI_583970_v1
303692
A
G


000819F/G_tomentella_PI_583970_v1
304046
T
A


000819F/G_tomentella_PI_583970_v1
304512
C
T


000819F/G_tomentella_PI_583970_v1
304764
C
A


000819F/G_tomentella_PI_583970_v1
305269
T
C


000819F/G_tomentella_PI_583970_v1
305624
T
C


000819F/G_tomentella_PI_583970_v1
306037
T
A


000819F/G_tomentella_PI_583970_v1
306171
G
A


000819F/G_tomentella_PI_583970_v1
318002
C
T


000819F/G_tomentella_PI_583970_v1
328015
G
A


000819F/G_tomentella_PI_583970_v1
333209
A
G


000819F/G_tomentella_PI_583970_v1
341293
C
T


000819F/G_tomentella_PI_583970_v1
344251
C
T


000819F/G_tomentella_PI_583970_v1
346694
T
C


000819F/G_tomentella_PI_583970_v1
347362
A
C


000819F/G_tomentella_PI_583970_v1
347867
A
G


000819F/G_tomentella_PI_583970_v1
369651
C
A


000819F/G_tomentella_PI_583970_v1
380730
C
T


000819F/G_tomentella_PI_583970_v1
381546
C
T


000819F/G_tomentella_PI_583970_v1
385059
A
G


000819F/G_tomentella_PI_583970_v1
386671
A
T


000819F/G_tomentella_PI_583970_v1
387021
C
T


000819F/G_tomentella_PI_583970_v1
387788
T
A


000819F/G_tomentella_PI_583970_v1
388859
T
C


000819F/G_tomentella_PI_583970_v1
401614
G
C


000819F/G_tomentella_PI_583970_v1
420350
C
G


000819F/G_tomentella_PI_583970_v1
427998
G
A


000819F/G_tomentella_PI_583970_v1
428798
T
C


000819F/G_tomentella_PI_583970_v1
450156
C
T


000819F/G_tomentella_PI_583970_v1
453725
C
T


000819F/G_tomentella_PI_583970_v1
466651
A
G


000819F/G_tomentella_PI_583970_v1
467520
T
C


000819F/G_tomentella_PI_583970_v1
501821
G
A


000819F/G_tomentella_PI_583970_v1
510702
G
C


000819F/G_tomentella_PI_583970_v1
533134
T
G


000819F/G_tomentella_PI_583970_v1
586465
G
A


000819F/G_tomentella_PI_583970_v1
704705
C
G


000819F/G_tomentella_PI_583970_v1
704714
A
G









Oligonucleotide primers (herein, ‘primers’) can be developed and used to identify plants carrying any one of the chromosomal intervals depicted in SEQ ID NOs 1, 2, 3, 4 and/or 5 found to be highly associated with ASR resistance. Specifically, one having ordinary skill in the art can develop primers to detect any single nucleotide polymorphism (herein ‘SNP’) as identified in any one of Tables 1-5 in respect to identifying or producing soybean lines having any one of or a portion of the chromosome intervals depicted in SEQ ID NOs: 1, 2, 3, 4 or 5 that are associated with ASR resistance. A TAQMAN® assay (e.g. generally a two-step allelic discrimination assay or similar), a KASP™ assay (generally a one-step allelic discrimination assay defined below or similar), or both can be employed to identify the SNPs that associate with increased ASR resistance as disclosed herein (e.g. favorable alleles as depicted in Tables 1-5). In an exemplary two-step assay, a forward primer, a reverse primer, and two assay probes (or hybridization oligos) are employed. The forward and reverse primers are employed to amplify genetic loci that comprise SNPs that are associated with ASR resistance loci (for example, any of the favorable alleles as shown in Tables 1-5). The particular nucleotides that are present at the SNP positions are then assayed using the assay primers (which in some embodiments are differentially labeled with, for example, fluorophores to permit distinguishing between the two assay probes in a single reaction), which in each pair differ from each other with respect to the nucleotides that are present at the SNP position (although it is noted that in any given pair, the probes can differ in their 5′ or 3′ ends without impacting their abilities to differentiate between nucleotides present at the corresponding SNP positions). In some embodiments, the assay primers and the reaction conditions are designed such that an assay primer will only hybridize to the reverse complement of a 100% perfectly matched sequence, thereby permitting identification of which allele(s) that are present based upon detection of hybridizations.


Compositions and methods for identifying, selecting and producing Glycine plants (including wild Glycines (e.g. Glycine tomentella) and Glycine max lines) with enhanced disease resistance are provided. Disease resistant soybean plants and germplasms are also provided.


In some embodiments, methods of identifying a disease resistant soybean plant or germplasm are provided. Such methods may comprise detecting, in the soybean plant or germplasm, a genetic loci or molecular marker (e.g. SNP or a Quantitative Trait Loci (QTL)) associated with enhanced disease resistance, in particular ASR resistance. In some embodiments the genetic loci or molecular marker associates with the presence of a chromosomal interval comprising the nucleotide sequence or a portion thereof of SEQ ID NOs 1, 2, 3, 4 or 5, wherein the portion thereof associates with ASR resistance.


In some embodiments, methods of producing a disease resistant soybean plant are provided. Such methods may comprise detecting, in a soybean plant or germplasm, the presence of a genetic loci and/or a genetic marker associated with enhanced pathogen resistance (e.g. ASR) and producing a progeny plant from said soybean germplasm.


In some embodiments, methods of selecting a disease resistant soybean plant or germplasm are provided. Such methods may comprise crossing a first soybean plant or germplasm with a second soybean plant or germplasm, wherein the first soybean plant or germplasm comprises a genetic loci derived from any one of plant accessions PI441001, PI441008, PI446958, PI509501, PI583970, PI483224,or a progeny plant thereof comprising any one of SEQ ID NOs 1, 2, 3, 4 or 5 or a portion thereof associated with enhanced disease and/or ASR resistance, and/or tolerance, and selecting a progeny plant or germplasm that possesses the genetic loci.


In some embodiments, methods of introgressing a genetic loci derived from soybean accession numbers PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 associated with enhanced pathogen resistance into a soybean plant or germplasm are provided. Such methods may comprise crossing a first soybean plant or germplasm comprising a chromosomal interval (e.g. SEQ ID Nos: 1, 2, 3, 4 or 5) derived from soybean accession number PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 associated with enhanced pathogen resistance with a second soybean plant or germplasm that lacks said genetic loci and optionally repeatedly backcrossing progeny plants comprising said genetic allele with the second soybean plant or germplasm to produce an soybean plant (e.g. Glycine max) or germplasm with enhanced pathogen resistance comprising the chromosomal interval derived from soybean accession number PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 associated with enhanced ASR resistance. Progeny comprising the chromosomal interval associated with enhanced pathogen resistance may be identified by detecting, in their genomes, the presence of a marker associated with or genetically linked to said chromosomal interval derived from soybean accession number PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval comprises SEQ ID NOs 1, 2, 3, 4 or 5 or a portion thereof and the marker can be any of the favorable alleles as described in Tables 1-5. R-Genes from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 can be introgressed into a Glycine max line through the use of embryo rescue methods known by those skilled in the art for example as is disclosed in U.S. Pat. No. 7,842,850 herein incorporated by reference and through methods as described in the working Examples herein, describing a alternative method of embryo rescue.


Soybean plants and/or germplasms identified, produced or selected by the methods of this invention are also provided, as are any progeny and/or seeds derived from a soybean plant or germplasm identified, produced or selected by these methods. In one embodiment molecular markers associating with the presence of a chromosomal intervals depicted in any one of SEQ ID NOs 1, 2, 3, 4 or 5 may be used to identify or select for plant lines resistant to ASR. Further said molecular markers may be located within 20 cM, 10 cM, ScM, 4 cM, 3 cM, 2 cM, and 1 cM of said chromosomal interval or from any respective favorable allele associated with ASR resistance as depicted in any one of Tables 1-5. In another embodiment, said molecular marker may be located within 20 cM, 10 cM, ScM, 4 cM, 3 cM, 2 cM, 1 cM of any SNP markers associated with ASR as described in any one of Tables 1-5.


Non-naturally occurring soybean seeds, plants and/or germplasms comprising one or genetic loci derived from plant accession number PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 (herein, TI441001′, TI441008′, TI446958′, PI509501″, TI583970′, or TI483224′) associated with enhanced pathogen resistance (e.g. ASR, Cyst Nematode, Phytopthora, etc.) are also provided. In specific embodiments said genetic loci comprise SEQ ID NOs 1, 2, 3, 4 or 5 and/or any favorable alleles as depicted in Tables 1-5.


A marker associated with enhanced pathogen resistance, more specifically ASR, may comprise, consist essentially of or consist of a single allele or a combination of alleles at one or more genetic loci derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 that associate with enhanced pathogen (ASR) resistance. In one embodiment the marker is within a chromosomal interval as described by SEQ ID NOs 1, 2, 3, 4 or 5. In another embodiment the marker is any one of the favorable alleles as depicted in Tables 1-5.


The foregoing and other objects and aspects of the present invention are explained in detail in the drawings and specification set forth below.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 shows a depiction of Glycine tomentella SNPs associated with ASR resistance on Glycine tomentella genomic scaffolding located on chromosome 5.



FIG. 2 shows a mapping interval 0.023-1.16Mb on Scaffold 49652 associated with ASR resistance.



FIG. 3 shows a mapping interval 0.02-1.19Mb on Scaffold 46840 associated with ASR resistance.



FIG. 4 is a marker association map for Glycine tomentella (PI441001) where bands indicate regions/intervals of respective chromosomes associated with ASR resistance.



FIG. 5 illustrates the rust rating scale used to measure plant phenotype.



FIG. 6 shows chromosome mapping for ASR resistance QTL for Glycine tomentella PI583970.



FIG. 7 is a marker association map for Glycine tomentella (PI583970) where bands indicate regions/intervals of respective chromosomes associated with ASR resistance.



FIG. 8 shows a mapping interval on scaffold 000819F associated with ASR resistance.



FIG. 9 shows chromosome mapping for ASR resistance QTL for Glycine tomentella PI483224.



FIG. 10 is a marker association map for Glycine tomentella (PI483224) where bands indicate regions/intervals of respective chromosomes associated with ASR resistance.



FIG. 11 shows a mapping interval on scaffold 002687F associated with ASR resistance.





DETAILED DESCRIPTION OF THE INVENTION

The presently disclosed subject matter relates at least in part to the identification of a genomic region (i.e. chromosomal interval(s) on Glycine tomentella Chromosome 5) derived from Glycine tomentella accession lines PI441001, PI441008, PI446958, PI509501, PI583970, PI483224, PI441008 or progeny thereof associated with enhanced ASR resistance. As such, said chromosomal interval from PI441001, PI441008, PI446958, PI509501, PI583970, PI483224, PI441008 or progeny thereof, may be introgressed into Glycine max lines via somatic embryo rescue (see for example U.S. Patent Publication 2007/0261139 and examples herein describing a alternative method of embryo rescue) or through the use of a Glycine max donor line having introgressed into its genome the genetic region from PI441001, PI441008, PI583970, or PI483224, , wherein the region comprises any one of SEQ ID NO: 1-5 or a portion thereof wherein presence of said genetic region is associated with increased or enhanced disease resistance to, for example, ASR, SCN, Stem termination, Stem Canker, Bacterial pustule, root knot nematode, brown stem rot, Frogeye leaf spot, or phytopthora. In another embodiment a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 is introduced into a Glycine max line not comprising said chromosomal interval wherein said introduction confers in the Glycine max line or its progeny increased resistances to disease (e.g. ASR) wherein the said chromosome interval is derived from chromosome 5 of Glycine tomentella and further wherein said chromosomal interval comprises at least one allele that associates with the trait of increased disease resistance, such as ASR, wherein said allele is any one of the alleles respectively selected from any one as depicted in Tables 1-5.


This description is not intended to be a detailed catalog of all the different ways in which the invention may be implemented, or all the features that may be added to the instant invention. For example, features illustrated with respect to one embodiment may be incorporated into other embodiments, and features illustrated with respect to a particular embodiment may be deleted from that embodiment. Thus, the invention contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted. In addition, numerous variations and additions to the various embodiments suggested herein will be apparent to those skilled in the art in light of the instant disclosure, which do not depart from the instant invention. Hence, the following descriptions are intended to illustrate some particular embodiments of the invention, and not to exhaustively specify all permutations, combinations and variations thereof.


All references listed below, as well as all references cited in the instant disclosure, including but not limited to all patents, patent applications and publications thereof, scientific journal articles, and database entries (e.g., GENBANK® database entries and all annotations available therein) are incorporated herein by reference in their entireties to the extent that they supplement, explain, provide a background for, or teach methodology, techniques, and/or compositions employed herein.


Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which the presently disclosed subject matter belongs.


Although the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate understanding of the presently disclosed subject matter.


As used herein, the terms “a” or “an” or “the” may refer to one or more than one. For example, “a” marker can mean one marker or a plurality of markers.


As used herein, the term “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).


As used herein, the term “about,” when used in reference to a measurable value such as an amount of mass, dose, time, temperature, and the like, is meant to encompass variations of up to 10% of the specified amount.


The term “consists essentially of” (and grammatical variants thereof), as applied to a polynucleotide sequence of this invention, means a polynucleotide sequence that consists of both the recited sequence (e.g., SEQ ID NO) and a total of ten or less (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) additional nucleotides on the 5′ and/or 3′ ends of the recited sequence such that the function of the polynucleotide is not materially altered. The total of ten or less additional nucleotides includes the total number of additional nucleotides on both ends added together. The term “materially altered,” as applied to polynucleotides of the invention, refers to an increase or decrease in ability to express the polynucleotide sequence of at least about 50% or more as compared to the expression level of a polynucleotide sequence consisting of the recited sequence.


The term “introduced” as used herein, in connection to a plant, means accomplished by any manner including but not limited to; introgression, transgenic, Clustered Regularly Interspaced Short Palindromic Repeats modification (CRISPR), Transcription activator-like effector nucleases (TALENs) (Feng et al. 2013, Joung & Sander 2013), meganucleases, or zinc finger nucleases (ZFNs).


As used herein, the term “wild glycine” refers to a perennial Glycine plant, for example any one of G. canescens, G. argyrea, G. clandestine, G. latrobeana, G. albicans, G. aphyonota, G. arenaria, G. curvata, G. cyrtoloba, G. dolichocarpa, G. falcate, G. gracei, G. hirticaulis, G. lactovirens, G. latifolia, G. microphylla, G. montis-douglas, G. peratosa, G. pescadrensis, G. pindanica, G. pullenii, G. rubiginosa, G. stenophita, G. syndetika, orG. tomentella.


As used herein, the term “allele” refers to one of two or more different nucleotides or nucleotide sequences that occur at a specific locus.


A marker is “associated with” a trait when it is linked to it and when the presence of the marker is an indicator of whether and/or to what extent the desired trait or trait form will occur in a plant/germplasm comprising the marker. Similarly, a marker is “associated with” an allele when it is linked to it and when the presence of the marker is an indicator of whether the allele is present in a plant/germplasm comprising the marker. For example, “a marker associated with enhanced pathogen resistance” refers to a marker whose presence or absence can be used to predict whether and/or to what extent a plant will display a pathogen resistant phenotype (e.g. any favorable SNP allele as described in Tables 1-5 are “associated with” ASR resistance in a soybean plant).


As used herein, the terms “backcross” and “backcrossing” refer to the process whereby a progeny plant is repeatedly crossed back to one of its parents. In a backcros sing scheme, the “donor” parent refers to the parental plant with the desired gene or locus to be introgressed. The “recipient” parent (used one or more times) or “recurrent” parent (used two or more times) refers to the parental plant into which the gene or locus is being introgressed. For example, see Ragot, M. et al. Marker-assisted Backcrossing: A Practical Example, in TECHNIQUES ET UTILISATIONS DES MARQUEURS MOLECULAIRES LES COLLOQUES, Vol. 72, pp. 45-56 (1995); and Openshaw et al., Marker-assisted Selection in Backcross Breeding, in PROCEEDINGS OF THE SYMPOSIUM “ANALYSIS OF MOLECULAR MARKER DATA,” pp. 41-53 (1994). The initial cross gives rise to the F1 generation. The term “BC1” refers to the second use of the recurrent parent, “BC2” refers to the third use of the recurrent parent, and so on.


A centimorgan (“cM”) is a unit of measure of recombination frequency. One cM is equal to a 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation.


As used herein, the term “chromosomal interval defined by and including,” used in reference to particular loci and/or alleles, refers to a chromosomal interval delimited by and encompassing the stated loci/alleles.


As used herein, the terms “cross” or “crossed” refer to the fusion of gametes via pollination to produce progeny (e.g., cells, seeds or plants). The term encompasses both sexual crosses (the pollination of one plant by another) and selfing (self-pollination, e.g., when the pollen and ovule are from the same plant). The term “crossing” refers to the act of fusing gametes via pollination to produce progeny.


As used herein, the terms “cultivar” and “variety” refer to a group of similar plants that by structural or genetic features and/or performance can be distinguished from other varieties within the same species.


As used herein, the terms “desired allele”, “favorable allele” and “allele of interest” are used interchangeably to refer to an allele associated with a desired trait (e.g. ASR resistance).


As used herein, the terms “enhanced pathogen resistance” or “enhanced disease resistance” refers to an improvement, enhancement, or increase in a plant's ability to endure and/or thrive despite being infected with a disease (e.g. Asian soybean rust) as compared to one or more control plants (e.g., one or both of the parents, or a plant lacking a marker associated with enhanced pathogen resistance to respective pathogen/disease). Enhanced disease resistance includes any mechanism (other than whole-plant immunity or resistance) that reduces the expression of symptoms indicative of infection for a respective disease such as Asian soybean rust, soybean cyst nematode, Pytophthora, etc.


An “elite line” or “elite strain” is an agronomically superior line that has resulted from many cycles of breeding and selection for superior agronomic performance. Numerous elite lines are available and known to those of skill in the art of soybean breeding. An “elite population” is an assortment of elite individuals or lines that can be used to represent the state of the art in terms of agronomically superior genotypes of a given crop species, such as soybean. Similarly, an “elite germplasm” or elite strain of germplasm is an agronomically superior germplasm, typically derived from and/or capable of giving rise to a plant with superior agronomic performance, such as an existing or newly developed elite line of soybean.


An “elite” plant is any plant from an elite line, such that an elite plant is a representative plant from an elite variety. Non-limiting examples of elite soybean varieties that are commercially available to farmers or soybean breeders include: AG00802, A0868, AG0902, A1923, AG2403, A2824, A3704, A4324, A5404, AG5903, AG6202 AG0934; AG1435; AG2031; AG2035; AG2433; AG2733; AG2933; AG3334; AG3832; AG4135; AG4632; AG4934; AG5831; AG6534; and AG7231 (Asgrow Seeds, Des Moines, Iowa, USA); BPRO144RR, BPR 4077NRR and BPR 4390NRR (Bio Plant Research, Camp Point, Ill., USA); DKB17-51 and DKB37-51 (DeKalb Genetics, DeKalb, Ill., USA); DP 4546 RR, and DP 7870 RR (Delta & Pine Land Company, Lubbock, Tex., USA); JG 03R501, JG 32R606C ADD and JG 55R503C (JGL Inc., Greencastle, Ind., USA); NKS 13-K2 (NK Division of Syngenta Seeds, Golden Valley, Minn., USA); 90M01, 91M30, 92M33, 93M11, 94M30, 95M30, 97B52, P008T22R2; P16T17R2; P22T69R; P25T51R; P34T07R2; P35T58R; P39T67R; P47T36R; P46T21R; and P56T03R2 (Pioneer Hi-Bred International, Johnston, Iowa, USA); SG4771NRR and SG5161NRR/STS (Soygenetics, LLC, Lafayette, Ind., USA); S00-K5, S11-L2, S28-Y2, S43-B1, S53-Al, S76-L9, S78-G6, 50009-M2; 5007-Y4; 504-D3; S14-A6; S20-T6; S21-M7; S26-P3; S28-N6; S30-V6; S35-C3; S36-Y6; S39-C4; S47-K5; S48-D9; S52-Y2; S58-Z4; S67-R6; S73-S8; and S78-G6 (Syngenta Seeds, Henderson, Ky., USA); Richer (Northstar Seed Ltd. Alberta, Calif.); 14RD62 (Stine Seed Co. Iowa., USA); or Armor 4744 (Armor Seed, LLC, Ark., USA).


The terms “agronomically elite” as used herein, means a genotype that has a culmination of many distinguishable traits such as emergence, vigor, vegetative vigor, disease resistance, seed set, standability, yield and threshability which allows a producer to harvest a product of commercial significance.


As used herein, the term “commercially significant yield” or “agronomically acceptable yield” refers to a grain yield of at least 100% of a commercial check variety such as AG2703 or DKB23-51.


As used herein, the terms “exotic,” “exotic line” and “exotic germplasm” refer to any plant, line or germplasm that is not elite. In general, exotic plants/germplasms are not derived from any known elite plant or germplasm, but rather are selected to introduce one or more desired genetic elements into a breeding program (e.g., to introduce novel alleles into a breeding program).


A “genetic map” is a description of genetic linkage relationships among loci on one or more chromosomes within a given species, generally depicted in a diagrammatic or tabular form. For each genetic map, distances between loci are measured by the recombination frequencies between them. Recombinations between loci can be detected using a variety of markers. A genetic map is a product of the mapping population, types of markers used, and the polymorphic potential of each marker between different populations. The order and genetic distances between loci can differ from one genetic map to another.


As used herein, the term “genotype” refers to the genetic constitution of an individual (or group of individuals) at one or more genetic loci, as contrasted with the observable and/or detectable and/or manifested trait (the phenotype). Genotype is defined by the allele(s) of one or more known loci that the individual has inherited from its parents. The term genotype can be used to refer to an individual's genetic constitution at a single locus, at multiple loci, or more generally, the term genotype can be used to refer to an individual's genetic make-up for all the genes in its genome. Genotypes can be indirectly characterized, e.g., using markers and/or directly characterized by nucleic acid sequencing.


As used herein, the term “germplasm” refers to genetic material of or from an individual (e.g., a plant), a group of individuals (e.g., a plant line, variety or family), or a clone derived from a line, variety, species, or culture. The germplasm can be part of an organism or cell, or can be separate from the organism or cell. In general, germplasm provides genetic material with a specific molecular makeup that provides a physical foundation for some or all of the hereditary qualities of an organism or cell culture. As used herein, germplasm may refer to seeds, cells (including protoplasts and calli) or tissues from which new plants may be grown, as well as plant parts that can be cultured into a whole plant (e.g., stems, buds, roots, leaves, etc.).


A “haplotype” is the genotype of an individual at a plurality of genetic loci, i.e., a combination of alleles. Typically, the genetic loci that define a haplotype are physically and genetically linked, i.e., on the same chromosome segment. The term “haplotype” can refer to polymorphisms at a particular locus, such as a single marker locus, or polymorphisms at multiple loci along a chromosomal segment.


As used herein, the term “heterozygous” refers to a genetic status wherein different alleles reside at corresponding loci on homologous chromosomes.


As used herein, the term “homozygous” refers to a genetic status wherein identical alleles reside at corresponding loci on homologous chromosomes.


As used herein, the term “hybrid” refers to a seed and/or plant produced when at least two genetically dissimilar parents are crossed.


As used herein, the term “inbred” refers to a substantially homozygous plant or variety. The term may refer to a plant or variety that is substantially homozygous throughout the entire genome or that is substantially homozygous with respect to a portion of the genome that is of particular interest.


As used herein, the term “indel” refers to an insertion or deletion in a pair of nucleotide sequences, wherein a first sequence may be referred to as having an insertion relative to a second sequence or the second sequence may be referred to as having a deletion relative to the first sequence.


As used herein, the terms “introgression,” “introgressing” and “introgressed” refer to both the natural and artificial transmission of a desired allele or combination of desired alleles of a genetic locus or genetic loci from one genetic background to another. For example, a desired allele at a specified locus can be transmitted to at least one progeny via a sexual cross between two parents of the same species, where at least one of the parents has the desired allele in its genome. Alternatively, for example, transmission of an allele can occur by recombination between two donor genomes, e.g., in a fused protoplast, where at least one of the donor protoplasts has the desired allele in its genome. The desired allele may be a selected allele of a marker, a QTL, a transgene, or the like. Offspring comprising the desired allele can be repeatedly backcrossed to a line having a desired genetic background and selected for the desired allele, with the result being that the desired allele becomes fixed in the desired genetic background. For example, a marker associated with enhanced ASR tolerance may be introgressed from a donor into a recurrent parent that is not disease resistant. The resulting offspring could then be repeatedly backcrossed and selected until the progeny possess the ASR tolerance allele(s) in the recurrent parent background.


As used herein, the term “linkage” refers to the degree with which one marker locus is associated with another marker locus or some other locus (for example, an ASR tolerance locus). The linkage relationship between a molecular marker and a phenotype may be given as a “probability” or “adjusted probability.” Linkage can be expressed as a desired limit or range. For example, in some embodiments, any marker is linked (genetically and physically) to any other marker when the markers are separated by less than about 50, 40, 30, 25, 20, or 15 map units (or cM). For example, embodiments of the invention herein, provide for marker loci closely linked to ASR resistant chromosomal intervals comprising a nucleotide sequence of any one of SEQ ID NOs 1-5.


In some aspects of the present invention, it is advantageous to define a bracketed range of linkage, for example, from about 10 cM and about 20 cM, from about 10 cM and about 30 cM, or from about 10 cM and about 40 cM. The more closely a marker is linked to a second locus, the better an indicator for the second locus that marker becomes. Thus, “closely linked loci” such as a marker locus and a second locus display an inter-locus recombination frequency of about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, or 2% or less. In some embodiments, the relevant loci display a recombination frequency of about 1% or less, e.g., about 0.75%, 0.5%, 0.25% or less. Two loci that are localized to the same chromosome, and at such a distance that recombination between the two loci occurs at a frequency of less than about 10% (e.g., about 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25%, or less) may also be said to be “proximal to” each other. Since one cM is the distance between two markers that show a 1% recombination frequency, any marker is closely linked (genetically and physically) to any other marker that is in close proximity, e.g., at or less than about 10 cM distant. Two closely linked markers on the same chromosome may be positioned about 9, 8, 7, 6, 5, 4, 3, 2, 1, 0.75, 0.5 or 0.25 cM or less from each other.


As used herein, the term “linkage disequilibrium” refers to a non-random segregation of genetic loci or traits (or both). In either case, linkage disequilibrium implies that the relevant loci are within sufficient physical proximity along a length of a chromosome so that they segregate together with greater than random (i.e., non-random) frequency (in the case of co-segregating traits, the loci that underlie the traits are in sufficient proximity to each other). Markers that show linkage disequilibrium are considered linked. Linked loci co-segregate more than 50% of the time, e.g., from about 51% to about 100% of the time. In other words, two markers that co-segregate have a recombination frequency of less than 50% (and, by definition, are separated by less than 50 cM on the same chromosome). As used herein, linkage can be between two markers, or alternatively between a marker and a phenotype. A marker locus can be “associated with” (linked to) a trait, e.g., Asian Soybean Rust. The degree of linkage of a molecular marker to a phenotypic trait is measured, e.g., as a statistical probability of co-segregation of that molecular marker with the phenotype.


Linkage disequilibrium is most commonly assessed using the measure r2, which is calculated using the formula described by Hill and Robertson, Theor. Appl. Genet. 38:226 (1968). When r2=1, complete linkage disequilibrium exists between the two marker loci, meaning that the markers have not been separated by recombination and have the same allele frequency. Values for r2 above 1/3 indicate sufficiently strong linkage disequilibrium to be useful for mapping. Ardlie et al., Nature Reviews Genetics 3:299 (2002). Hence, alleles are in linkage disequilibrium when r2 values between pairwise marker loci are greater than or equal to about 0.33, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1.0.


As used herein, the term “linkage equilibrium” describes a situation where two markers independently segregate, i.e., sort among progeny randomly. Markers that show linkage equilibrium are considered unlinked (whether or not they lie on the same chromosome).


A “locus” is a position on a chromosome where a gene or marker or allele is located. In some embodiments, a locus may encompass one or more nucleotides.


As used herein, the terms “marker” and “genetic marker” are used interchangeably to refer to a nucleotide and/or a nucleotide sequence that has been associated with a phenotype, trait or trait form. In some embodiments, a marker may be associated with an allele or alleles of interest and may be indicative of the presence or absence of the allele or alleles of interest in a cell or organism. A marker may be, but is not limited to, an allele, a gene, a haplotype, a restriction fragment length polymorphism (RFLP), a simple sequence repeat (SSR), random amplified polymorphic DNA (RAPD), cleaved amplified polymorphic sequences (CAPS) (Rafalski and Tingey, Trends in Genetics 9:275 (1993)), an amplified fragment length polymorphism (AFLP) (Vos et al., Nucleic Acids Res. 23:4407 (1995)), a single nucleotide polymorphism (SNP) (Brookes, Gene 234:177 (1993)), a sequence-characterized amplified region (SCAR) (Paran and Michelmore, Theor. Appl. Genet. 85:985 (1993)), a sequence-tagged site (STS) (Onozaki et al., Euphytica 138:255 (2004)), a single-stranded conformation polymorphism (SSCP) (Orita et al., Proc. Natl. Acad. Sci. USA 86:2766 (1989)), an inter-simple sequence repeat (ISSR) (Blair et al., Theor. Appl. Genet. 98:780 (1999)), an inter-retrotransposon amplified polymorphism (IRAP), a retrotransposon-microsatellite amplified polymorphism (REMAP) (Kalendar et al., Theor. Appl. Genet. 98:704 (1999)), a chromosome interval, or an RNA cleavage product (such as a Lynx tag). A marker may be present in genomic or expressed nucleic acids (e.g., ESTs). The term marker may also refer to nucleic acids used as probes or primers (e.g., primer pairs) for use in amplifying, hybridizing to and/or detecting nucleic acid molecules according to methods well known in the art. A large number of soybean molecular markers are known in the art, and are published or available from various sources, such as the SoyBase internet resource.


Markers corresponding to genetic polymorphisms between members of a population can be detected by methods well-established in the art. These include, e.g., nucleic acid sequencing, hybridization methods, amplification methods (e.g., PCR-based sequence specific amplification methods), detection of restriction fragment length polymorphisms (RFLP), detection of isozyme markers, detection of polynucleotide polymorphisms by allele specific hybridization (ASH), detection of amplified variable sequences of the plant genome, detection of self-sustained sequence replication, detection of simple sequence repeats (SSRs), detection of single nucleotide polymorphisms (SNPs), and/or detection of amplified fragment length polymorphisms (AFLPs). Well established methods are also known for the detection of expressed sequence tags (ESTs) and SSR markers derived from EST sequences and randomly amplified polymorphic DNA (RAPD).


A “marker allele,” also described as an “allele of a marker locus,” can refer to one of a plurality of polymorphic nucleotide sequences found at a marker locus in a population that is polymorphic for the marker locus.


“Marker-assisted selection” (MAS) is a process by which phenotypes are selected based on marker genotypes. In some embodiments, marker genotypes are used to identify plants that will be selected for a breeding program or for planting. In some embodiments, marker genotypes are used to identify plants that will not be selected for a breeding program or for planting (i.e., counter-selected plants), allowing them to be removed from the breeding/planting population.


As used herein, the terms “marker locus” and “marker loci” refer to a specific chromosome location or locations in the genome of an organism where a specific marker or markers can be found. A marker locus can be used to track the presence of a second linked locus, e.g., a linked locus that encodes or contributes to expression of a phenotypic trait. For example, a marker locus can be used to monitor segregation of alleles at a locus, such as a QTL or single gene, that are genetically or physically linked to the marker locus.


As used herein, the terms “marker probe” and “probe” refer to a nucleotide sequence or nucleic acid molecule that can be used to detect the presence of one or more particular alleles within a marker locus (e.g., a nucleic acid probe that is complementary to all of or a portion of the marker or marker locus, through nucleic acid hybridization). Marker probes comprising about 8, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more contiguous nucleotides may be used for nucleic acid hybridization. Alternatively, in some aspects, a marker probe refers to a probe of any type that is able to distinguish (i.e., genotype) the particular allele that is present at a marker locus.


As used herein, the terms “molecular marker” or “genetic marker” may be used to refer to a genetic marker, as defined above, or an encoded product thereof (e.g., a protein) used as a point of reference when identifying a linked locus. A molecular marker can be derived from genomic nucleotide sequences or from expressed nucleotide sequences (e.g., from a spliced RNA, a cDNA, etc.). The term also refers to nucleotide sequences complementary to or flanking the marker sequences, such as nucleotide sequences used as probes and/or primers capable of amplifying the marker sequence. Nucleotide sequences are “complementary” when they specifically hybridize in solution, e.g., according to Watson-Crick base pairing rules. Some of the markers described herein are also referred to as hybridization markers when located on an indel region. This is because the insertion region is, by definition, a polymorphism vis-ã-vis a plant without the insertion. Thus, the marker need only indicate whether the indel region is present or absent. Any suitable marker detection technology may be used to identify such a hybridization marker, e.g., SNP technology is used in the examples provided herein.


A “non-naturally occurring variety of soybean” is any variety of soybean that does not naturally exist in nature. A “non-naturally occurring variety of soybean” may be produced by any method known in the art, including, but not limited to, transforming a soybean plant or germplasm, transfecting a soybean plant or germplasm and crossing a naturally occurring variety of soybean with a non-naturally occurring variety of soybean. In some embodiments, a “non-naturally occurring variety of soybean” may comprise one of more heterologous nucleotide sequences. In some embodiments, a “non-naturally occurring variety of soybean” may comprise one or more non-naturally occurring copies of a naturally occurring nucleotide sequence (i.e., extraneous copies of a gene that naturally occurs in soybean). In some embodiments, a “non-naturally occurring variety of soybean” may comprise a non-natural combination of two or more naturally occurring nucleotide sequences (i.e., two or more naturally occurring genes that do not naturally occur in the same soybean, for instance genes not found in Glycine max lines).


As used herein, the term “primer” refers to an oligonucleotide which is capable of annealing to a nucleic acid target and serving as a point of initiation of DNA synthesis when placed under conditions in which synthesis of a primer extension product is induced (e.g., in the presence of nucleotides and an agent for polymerization such as DNA polymerase and at a suitable temperature and pH). A primer (in some embodiments an extension primer and in some embodiments an amplification primer) is in some embodiments single stranded for maximum efficiency in extension and/or amplification. In some embodiments, the primer is an oligodeoxyribonucleotide. A primer is typically sufficiently long to prime the synthesis of extension and/or amplification products in the presence of the agent for polymerization. The minimum length of the primer can depend on many factors, including, but not limited to temperature and composition (A/T vs. G/C content) of the primer. In the context of amplification primers, these are typically provided as a pair of bi-directional primers consisting of one forward and one reverse primer or provided as a pair of forward primers as commonly used in the art of DNA amplification such as in PCR amplification. As such, it will be understood that the term “primer,” as used herein, can refer to more than one primer, particularly in the case where there is some ambiguity in the information regarding the terminal sequence(s) of the target region to be amplified. Hence, a “primer” can include a collection of primer oligonucleotides containing sequences representing the possible variations in the sequence or includes nucleotides which allow a typical base pairing. Primers can be prepared by any suitable method known in the art. Methods for preparing oligonucleotides of specific sequence are known in the art, and include, for example, cloning and restriction of appropriate sequences and direct chemical synthesis. Chemical synthesis methods can include, for example, the phospho di- or tri-ester method, the diethylphosphoramidate method and the solid support method disclosed in U.S. Pat. No. 4,458,066. Primers can be labeled, if desired, by incorporating detectable moieties by for instance spectroscopic, fluorescence, photochemical, biochemical, immunochemical, or chemical moieties. Primers diagnostic (i.e. able to identify or select based on presence of ASR resistant alleles) for ASR resistance can be created to any favorable SNP as described in any one of Tables 1-5. The PCR method is well described in handbooks and known to the skilled person. After amplification by PCR, target polynucleotides can be detected by hybridization with a probe polynucleotide, which forms a stable hybrid with the target sequence under stringent to moderately stringent hybridization and wash conditions. If it is expected that the probes are essentially completely complementary (i.e., about 99% or greater) to the target sequence, stringent conditions can be used. If some mismatching is expected, for example if variant strains are expected with the result that the probe will not be completely complementary, the stringency of hybridization can be reduced. In some embodiments, conditions are chosen to rule out non-specific/adventitious binding. Conditions that affect hybridization, and that select against non-specific binding are known in the art, and are described in, for example, Sambrook & Russell (2001). Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., United States of America. Generally, lower salt concentration and higher temperature hybridization and/or washes increase the stringency of hybridization conditions.


As used herein, the terms “phenotype,” “phenotypic trait” or “trait” refer to one or more traits and/or manifestations of an organism. The phenotype can be a manifestation that is observable to the naked eye, or by any other means of evaluation known in the art, e.g., microscopy, biochemical analysis, or an electromechanical assay. In some cases, a phenotype or trait is directly controlled by a single gene or genetic locus, i.e., a “single gene trait.” In other cases, a phenotype or trait is the result of several genes. It is noted that, as used herein, the term “disease resistant phenotype” takes into account environmental conditions that might affect the respective disease such that the effect is real and reproducible.


As used herein, the term “plant” may refer to a whole plant, any part thereof, or a cell or tissue culture derived from a plant. Thus, the term “plant” can refer to any of: whole plants, plant components or organs (e.g., roots, stems, leaves, buds, flowers, pods, etc.), plant tissues, seeds and/or plant cells. A plant cell is a cell of a plant, taken from a plant, or derived through culture from a cell taken from a plant. Thus, the term “soybean plant” may refer to a whole soybean plant, one or more parts of a soybean plant (e.g., roots, root tips, stems, leaves, buds, flowers, pods, seeds, cotyledons, etc.), soybean plant cells, soybean plant protoplasts and/or soybean plant calli.


As used herein, the term “plant part” includes but is not limited to embryos, pollen, seeds, leaves, flowers (including but not limited to anthers, ovules and the like), fruit, stems or branches, roots, root tips, cells including cells that are intact in plants and/or parts of plants, protoplasts, plant cell tissue cultures, plant calli, plant clumps, and the like. Thus, a plant part includes soybean tissue culture from which soybean plants can be regenerated. Further, as used herein, “plant cell” refers to a structural and physiological unit of the plant, which comprises a cell wall and also may refer to a protoplast. A plant cell of the present invention can be in the form of an isolated single cell or can be a cultured cell or can be a part of a higher-organized unit such as, for example, a plant tissue or a plant organ.


As used herein, the term “polymorphism” refers to a variation in the nucleotide sequence at a locus, where said variation is too common to be due merely to a spontaneous mutation. A polymorphism can be a single nucleotide polymorphism (SNP) or an insertion/deletion polymorphism, also referred to herein as an “indel.” Additionally, the variation can be in a transcriptional profile or a methylation pattern. The polymorphic site or sites of a nucleotide sequence can be determined by comparing the nucleotide sequences at one or more loci in two or more germplasm entries.


As used herein, the terms “closely linked” refers to linked markers displaying a cross over frequency with a given marker of about 10% or less (e.g. the given marker is within about 10 cM of a closely linked ASR marker). Put another way, closely linked loci co-segregate at least about 90% of the time. With regard to physical position on a chromosome, closely linked markers can be separated, for example, by about 1 megabase (Mb; 1 million nucleotides), about 500 kilobases (Kb; 1000 nucleotides), about 400 Kb, about 300 Kb, about 200 Kb, about 100 Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb, about 4 Kb, about 3 Kb, about 2 Kb, about 1 Kb, about 500 nucleotides, about 250 nucleotides, or less.


As used herein, the term “population” refers to a genetically heterogeneous collection of plants sharing a common genetic derivation.


As used herein, the terms “progeny” and “progeny plant” refer to a plant generated from a vegetative or sexual reproduction from one or more parent plants. A progeny plant may be obtained by cloning or selfing a single parent plant, or by crossing two parental plants.


As used herein, the term “reference sequence” refers to a defined nucleotide sequence used as a basis for nucleotide sequence comparison. The reference sequence for a marker, for example, is obtained by genotyping a number of lines at the locus or loci of interest, aligning the nucleotide sequences in a sequence alignment program, and then obtaining the consensus sequence of the alignment. Hence, a reference sequence identifies the polymorphisms in alleles at a locus. A reference sequence may not be a copy of an actual nucleic acid sequence from any particular organism; however, it is useful for designing primers and probes for actual polymorphisms in the locus or loci.


As used herein, the terms “disease tolerance” and “disease resistant” refer to a plant's ability to endure and/or thrive despite being infected with a respective disease. When used in reference to germplasm, the terms refer to the ability of a plant that arises from that germplasm to endure and/or thrive despite being infected with a respective disease. In some embodiments, infected Disease resistant soybean plants may yield as well (or nearly as well) as uninfected soybean plants. In general, a plant or germplasm is labeled as “Disease resistant” if it displays “enhanced pathogen resistance.”


An “unfavorable allele” of a marker is a marker allele that segregates with the unfavorable plant phenotype, therefore providing the benefit of identifying plants that can be removed from a breeding program or planting. For instance, one could eliminate from a plant breeding program plant lines carrying unfavorable alleles for ASR resistance.


“PI441001, PI441008, PI583970, or PI483224,” refers to Glycine tomentella plant accession number PI441001, PI441008, PI583970, or PI483224.


Genetic Mapping

Genetic loci correlating with particular phenotypes, such as disease resistance, can be mapped in an organism's genome. By identifying a marker or cluster of markers that co-segregate with a trait of interest, the breeder is able to rapidly select a desired phenotype by selecting for the proper marker (a process called marker-assisted selection, or “MAS”). Such markers may also be used by breeders to design genotypes in silico and to practice whole genome selection.


The present invention provides markers associated with enhanced disease resistance. Detection of these markers and/or other linked markers can be used to identify, select and/or produce disease resistant, more specifically ASR resistant, plants and/or to eliminate plants that are not disease resistant from breeding programs or planting.


Glycine Tomentella Genetic Loci Associated with Enhanced Disease Resistance


Markers associated with enhanced disease resistance are identified herein (see Tables 1-5 indicating favorable markers associated with enhanced ASR resistance). A marker of the present invention may comprise a single allele or a combination of alleles at one or more genetic loci (for example, any combination of a favorable markers from Tables 1- 5). For example, the marker may comprise one or more marker alleles located within a first chromosomal interval (e.g. SEQ ID NO: 1) and one or more marker alleles located within a second chromosomal interval (e.g. SEQ ID NO: 2).


Marker-Assisted Selection

Markers can be used in a variety of plant breeding applications. See, e.g., Staub et al., Hortscience 31: 729 (1996); Tanksley, Plant Molecular Biology Reporter 1: 3 (1983). One of the main areas of interest is to increase the efficiency of backcros sing and introgressing genes using marker-assisted selection (MAS). In general, MAS takes advantage of genetic markers that have been identified as having a significant likelihood of co-segregation with a desired trait. Such markers are presumed to be in/near the gene(s) that give rise to the desired phenotype, and their presence indicates that the plant will possess the desired trait. Plants which possess the marker are expected to transfer the desired phenotype to their progeny.


A marker that demonstrates linkage with a locus affecting a desired phenotypic trait provides a useful tool for the selection of the trait in a plant population. This is particularly true where the phenotype is hard to assay or occurs at a late stage in plant development. Since DNA marker assays are less laborious and take up less physical space than field phenotyping, much larger populations can be assayed, increasing the chances of finding a recombinant with the target segment from the donor line moved to the recipient line. The closer the linkage, the more useful the marker, as recombination is less likely to occur between the marker and the gene causing or imparting the trait. Having flanking markers decreases the chances that false positive selection will occur. The ideal situation is to have a marker within the causative gene itself, so that recombination cannot occur between the marker and the gene. Such a marker is called a “perfect marker”.


When a gene is introgressed by MAS, it is not only the gene that is introduced but also the flanking regions. Gepts, Crop Sci 42:1780 (2002). This is referred to as “linkage drag.” In the case where the donor plant is highly unrelated to the recipient plant, these flanking regions carry additional genes that may code for agronomically undesirable traits. This “linkage drag” may also result in reduced yield or other negative agronomic characteristics even after multiple cycles of backcrossing into the elite soybean line. This is also sometimes referred to as “yield drag.” The size of the flanking region can be decreased by additional backcrossing, although this is not always successful, as breeders do not have control over the size of the region or the recombination breakpoints. Young et al., Genetics 120:579 (1998). In classical breeding, it is usually only by chance that recombinations that contribute to a reduction in the size of the donor segment are selected. Tanksley et al., Biotechnology 7: 257 (1989). Even after 20 backcrosses, one might find a sizeable piece of the donor chromosome still linked to the gene being selected. With markers, however, it is possible to select those rare individuals that have experienced recombination near the gene of interest. In 150 backcross plants, there is a 95% chance that at least one plant will have experienced a crossover within 1 cM of the gene, based on a single meiosis map distance. Markers allow for unequivocal identification of those individuals. With one additional backcross of 300 plants, there would be a 95% chance of a crossover within 1 cM single meiosis map distance of the other side of the gene, generating a segment around the target gene of less than 2 cM based on a single meiosis map distance. This can be accomplished in two generations with markers, while it would have required on average 100 generations without markers. See Tanksley et al., supra. When the exact location of a gene is known, flanking markers surrounding the gene can be utilized to select for recombinations in different population sizes. For example, in smaller population sizes, recombinations may be expected further away from the gene, so more distal flanking markers would be required to detect the recombination.


The availability of integrated linkage maps of the soybean genome containing increasing densities of public soybean markers has facilitated soybean genetic mapping and MAS.


Of all the molecular marker types, SNPs are the most abundant and have the potential to provide the highest genetic map resolution. Bhattramakki et al., Plant Molec. Biol. 48:539 (2002). SNPs can be assayed in a so-called “ultra-high-throughput” fashion because they do not require large amounts of nucleic acid and automation of the assay is straight-forward. SNPs also have the benefit of being relatively low-cost systems. These three factors together make SNPs highly attractive for use in MAS. Several methods are available for SNP genotyping, including but not limited to, hybridization, primer extension, oligonucleotide ligation, nuclease cleavage, minisequencing and coded spheres. Such methods have been reviewed in various publications: Gut, Hum. Mutat. 17:475 (2001); Shi, Clin. Chem. 47:164 (2001); Kwok, Pharmacogenomics 1:95 (2000); Bhattramakki and Rafalski, Discovery and Application of Single Nucleotide Polymorphism Markers in Plants, in PLANT GENOTYPING: THE DNA FINGERPRINTING OF PLANTS, CABI Publishing, Wallingford (2001). A wide range of commercially available technologies utilize these and other methods to interrogate SNPs, including Masscode™ (Qiagen, Germantown, Md.), Invader® (Hologic, Madison, Wis.), SnapShot® (Applied Biosystems, Foster City, Calif.), Taqman® (Applied Biosystems, Foster City, Calif.) and Beadarrays™ (Illumina, San Diego, Calif.).


A number of SNP alleles together within a sequence, or across linked sequences, can be used to describe a haplotype for any particular genotype. Ching et al., BMC Genet. 3:19 (2002); Gupta et al., (2001), Rafalski, Plant Sci. 162:329 (2002b). Haplotypes can be more informative than single SNPs and can be more descriptive of any particular genotype. For example, a single SNP may be allele “T” for a specific Disease resistant line or variety, but the allele “T” might also occur in the soybean breeding population being utilized for recurrent parents. In this case, a combination of alleles at linked SNPs may be more informative. Once a unique haplotype has been assigned to a donor chromosomal region, that haplotype can be used in that population or any subset thereof to determine whether an individual has a particular gene. The use of automated high throughput marker detection platforms known to those of ordinary skill in the art makes this process highly efficient and effective.


The markers of the present invention can be used in marker-assisted selection protocols to identify and/or select progeny with enhanced Asian soybean rust resistance. Such methods can comprise, consist essentially of or consist of crossing a first soybean plant or germplasm with a second soybean plant or germplasm, wherein the first soybean plant or germplasm comprises a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1 or wherein the chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2, and selecting a progeny plant that possesses the marker. Either of the first and second soybean plants, or both, may be of a non-naturally occurring variety of soybean. In some embodiments, the second soybean plant or germplasm is of an elite variety of soybean. In some embodiments, the genome of the second soybean plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean. In another embodiment, the first soybean plant comprises the chromosomal interval a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1 or wherein the chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2 wherein the chromosome interval further comprises at least one allele as depicted in any of Tables 1-5


Methods for identifying and/or selecting a disease resistant soybean plant or germplasm may comprise, consist essentially of or consist of detecting the presence of a marker associated with enhanced ASR tolerance. The marker may be detected in any sample taken from the plant or germplasm, including, but not limited to, the whole plant or germplasm, a portion of said plant or germplasm (e.g., a seed chip, a leaf punch disk or a cell from said plant or germplasm) or a nucleotide sequence from said plant or germplasm. Such a sample may be taken from the plant or germplasm using any present or future method known in the art, including, but not limited to, automated methods of removing a portion of endosperm with a sharp blade, drilling a small hole in the seed and collecting the resultant powder, cutting the seed with a laser and punching a leaf disk. The soybean plant may be of a non-naturally occurring variety of soybean. In some embodiments, the genome of the soybean plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.


In some embodiments, the marker detected in the sample may comprise, consist essentially of or consist of one or more marker alleles located within a chromosomal interval selected from the group consisting of:

    • 1) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or
    • 2) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.; or
    • 3) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or
    • 4) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;
    • 5) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5; or
    • 6) A chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any favorable SNP marker displayed in Tables 1-5.


Methods for producing an disease resistant soybean plant may comprise, consist essentially of or consist of detecting, in a germplasm, a marker associated with enhanced disease resistance (e.g. ASR) wherein said marker is selected from Tables 1-5 or wherein marker is a closely linked loci of any marker described in any one of Tables 1-5 and producing a soybean plant from said germplasm. The marker may be detected in any sample taken from the germplasm, including, but not limited to, a portion of said germplasm (e.g., a seed chip or a cell from said germplasm) or a nucleotide sequence from said germplasm. Such a sample may be taken from the germplasm using any present or future method known in the art, including, but not limited to, automated methods of removing a portion of endosperm with a sharp blade, drilling a small hole in the seed and collecting the resultant powder, cutting the seed with a laser and punching a leaf disk. The germplasm may be of a non-naturally occurring variety of soybean. In some embodiments, the genome of the germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean. A disease resistant soybean plant is then produced from the germplasm identified as having the marker associated with enhanced disease resistance (e.g. ASR) according to methods well known in the art for breeding and producing plants from germplasm.


In some embodiments, the marker detected in the germplasm may comprise, consist essentially of or consist of one or more marker alleles located within a chromosomal interval selected from the group consisting of:


1) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or

    • 2) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.; or
    • 3) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or
    • 4) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;
    • 5) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5;or
    • 6) A chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any favorable SNP marker displayed in Tables 1-5.


In some embodiments, the marker detected in the germplasm may comprise, consist essentially of or consist of one or more marker alleles selected from any of Tables 1-5.


Methods for producing and/or selecting an Asian soy rust resistant/tolerant soybean plant or germplasm may comprise crossing a first soybean plant or germplasm with a second soybean plant or germplasm, wherein said first soybean plant or germplasm comprises a chromosomal interval selected from the group consisting of:

    • 1) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or
    • 2) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.; or
    • 3) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or
    • 4) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.; or
    • 5) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5; or
    • 6) A chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5; and crossing with a second soybean plant not comprising the chromosome interval then producing a progeny plant with increased ASR resistance. Either the first or second soybean plant or germplasm, or both, may be of a non-naturally occurring variety of soybean. In some embodiments, the second soybean plant or germplasm is of an elite variety of soybean. In some embodiments, the genome of the second soybean plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.


Also provided herein is a method of introgres sing an allele associated with enhanced Disease (e.g. ASR, SCN, SDS, RKN, Phytopthora, etc.) resistance / tolerance into a soybean plant. Such methods for introgressing an allele associated with enhanced Disease (e.g. ASR, SCN, SDS, RKN, Phytopthora, etc.) resistance / tolerance into a soybean plant or germplasm may comprise, consist essentially of or consist of crossing a first soybean plant or germplasm comprising said allele (the donor) wherein said allele is selected from any allele listed in Table 1 or Table 2 or a maker in “close proximity” to a marker listed in Tables 1-5 with a second soybean plant or germplasm that lacks said allele (the recurrent parent) and repeatedly backcrossing progeny comprising said allele with the recurrent parent. Progeny comprising said allele may be identified by detecting, in their genomes, the presence of a marker associated with enhanced Disease (e.g. ASR, SCN, SDS, RKN, Phytopthora, etc.) resistance/tolerance. The marker may be detected in any sample taken from the progeny, including, but not limited to, a portion of said progeny (e.g., a seed chip, a leaf punch disk or a cell from said plant or germplasm) or a nucleotide sequence from said progeny. Such a sample may be taken from the progeny using any present or future method known in the art, including, but not limited to, automated methods of removing a portion of endosperm with a sharp blade, drilling a small hole in the seed and collecting the resultant powder, cutting the seed with a laser and punching a leaf disk. Either the donor or the recurrent parent, or both, may be of a non-naturally occurring variety of soybean. In some embodiments, the recurrent parent is of an elite variety of soybean. In some embodiments, the genome of the recurrent parent is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.


In some embodiments, the marker used to identify progeny comprising an allele associated with enhanced Disease (e.g. ASR, SCN, SDS, RKN, Phytopthora, etc.) resistance / tolerance may comprise, consist essentially of or consist of one or more marker alleles located within a chromosomal interval selected from the group consisting of:


1) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or


2) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.;


3) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or 4) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;


5) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5; or


6) a chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5 or any closely linked markers in close proximity to said intervals 1)-5).


In some embodiments, the marker may comprise, consist essentially of or consist of marker alleles located in at least two different chromosomal intervals. For example, the marker may comprise one or more alleles located in the chromosomal interval defined by and including any two markers in Table 1, any two markers located in Table 2 any two markers in Table 3 or any two markers in Tables 4 and/or 5.

  • The following are all embodiments contemplated and encompassed within the invention:
    • 1. An elite Glycine max plant having in its genome a chromosomal interval from a wild


Glycine plant wherein the chromosomal interval comprises any one of SEQ ID NOs: 1-5 or a functional portion thereof that confers ASR resistance in said plant; in some instances the wild Glycine plant is Glycine tomentella and in further instances the wild Glycine plant is selected from any one of plant accessions PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 , wherein said chromosomal interval confers increased Asian soy rust (ASR) resistance as compared to a control plant not comprising said chromosomal interval; Further in a variation of embodiment 1 said elite Glycine max plant is produced by a) performing a non-natural cross between a Glycine max plant and a Glycine tomentella plant wherein “non-natural cross” means a cross between two species that will not produce viable offspring without further intervention (e.g. embryo rescue such as described in Example 3) such as; a) performing embryo rescue as essentially described in Example 3 to create a amphidiploid plant; b) backcros sing the amphidiploid plant of b) with a Glycine max plant for at least 1 backcross generation (preferably BC4) resulting in the generation of an elite Glycine max

    • plant having introgressed in its genome said chromosome interval(s); further the said elite Glycine max plant may have 20 chromosome pairs or could maintain a chromosome pair from Glycine tomentella and inheriting said intervals to confer ASR resistance in said elite Glycine max plant.
    • 2. The plant of embodiment 1, wherein the chromosomal interval comprises SEQ ID NOs: 1, 2, 3, 4, 5 or a portion of any thereof wherein said portion confers ASR resistance to elite Glycine max plant.
    • 3. The plant of embodiments 1-2, wherein the chromosomal interval comprises a SNP marker associated with increased ASR resistance wherein said SNP marker corresponds with any one of the favorable SNP markers as listed in Tables 1-5; or in another variation a haplotype comprising at least 2 SNP markers associated with ASR resistance and further wherein the at least 2 SNP markers are selected from any favorable SNP markers as listed in Tables 1-5.
    • 4. The plant of embodiments 1-3, wherein the chromosomal interval is derived from Glycine tomentella chromosome 5 at an approximate mapping interval of 0.02-1.19 Mb.
    • 5. The plant of embodiments 1-5, wherein the chromosomal interval corresponds to a position within the wild Glycine and/or Glycine tomentella genome that comprises SEQ ID NOs: 1-5 or a portion thereof wherein said portion confers increased ASR resistance in said elite Glycine max plant.
    • 6. The plant of embodiments 1-5, wherein the elite Glycine max plant further shows resistance to any one of the stresses selected from: diseases (such as powdery mildew, Pythium ultimum, Phytophthora root rot, leaf spot, blast, brown spot, root-knot nematode, soybean cyst nematode, soybean vein necrosis virus, soybean stem canker, soybean sudden death syndrome, leaf and neck blast, rust, frogeye leaf spot, brown stem rot, Fusarium, or sheath blight); insect pests (such as whitefly, aphid, grey field slug, sugarcane borer, green bug, or aphid); abiotic stress (such as drought tolerance, flooding, high level of salinity, heavy metal, aluminum, manganese, cadmium, zinc, UV-B, boron, iron deficiency chlorosis or cold tolerance (i.e. extreme temperatures)) and further wherein said resistance to stress is conferred from said chromosomal interval.
    • 7. The plant of embodiments 1-6, wherein at least one parental line of said plant was selected or identified through molecular marker selection, wherein said parental line is selected or identified based on a molecular marker located within or closely associated with said chromosome interval corresponding to any one of SEQ ID NOs: 1-5.
    • 8. The plant of embodiment 7, wherein the molecular marker is a single nucleotide polymorphism (SNP), a quantitative trait locus (QTL), a amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), a restriction fragment length polymorphism (RFLP) or a microsatellite.
    • 9. The plant of embodiments 7-8, wherein the molecular marker is a SNP marker and the molecular marker is any favorable marker as shown in Tables 1-5.
    • 10. The plant of any of embodiments 1-9, wherein the plant is a agronomically elite Glycine max plant having a commercially significant yield as well as commercially susceptible: vigor, seed set, standability or threshability.
    • 11. The plant of any of embodiments 1-10, wherein said interval is introduced into said plant genome by a “non-natural” wide cross between a Glycine max and Glycine tomentella line followed by subsequent embryo rescue (e.g. as described in Example 3) and then resultant plant backcrossed at least once and more preferably at least four backcrosses (BC4) with Glycine max line (i.e. in some instances a recurrent Glycine max line) to produce an elite or agronomically elite Glycine max line.
    • 12. The plant of any of embodiments 1-10, wherein said interval is introduced into said plant genome by transgenic expression or genome editing of sequences corresponding to and comprising any one of SEQ ID NOS: 1-5 or a portion thereof wherein said portion retains ASR resistance when introduced into a susceptible line.
    • 13. The plant of embodiment 12, wherein the interval is introduced by genome editing of a Glycine max genomic region homologous to, or a ortholog of any of the intervals corresponding to SEQ ID NOs: 1-5 and further making at least one genetic edit to said Glycine max genomic region to include at least 1 allele change corresponding to any favorable allele as described in any of Tables 1-5 wherein said Glycine max genomic region did not comprise said allele change before genome edit and said genome edit confers in plant increased ASR resistance as compared to a control plant.
    • 14. The plant of embodiment 13, wherein the genetic edit is accomplished through CRISPR, TALEN, meganucleases or through modification of genomic nucleic acids.
    • 15. The plant of embodiments 1-14 wherein the chromosomal interval comprises any one of or a portion thereof (where said portion retains ASR resistance) of nucleotide base pair positions: 1-1251375 of SEQ ID NO: 1; 1-2515428 of SEQ ID NO: 2; 1-365842 of SEQ ID NO: 3; 1-646429 of SEQ ID NO: 4, or 1-750080 of SEQ ID NO: 5.
    • 16. A ASR resistant agronomically elite Glycine max plant having commercially significant yield, wherein said plant comprises an introgression of a chromosomal interval from a wild Glycine plant wherein said chromosome interval corresponds to and/or comprises any one of SEQ ID NOs: 1-5; in some instances said wild Glycine plant is Glycine tomentella, in further instances the wild Glycine plant is any one of accessions PI441001, PI441008, PI446958, PI509501, PI583970, PI483224 or progeny thereof, wherein the introgression comprises a ASR resistance conferring QTL linked to at least one marker located on the chromosome equivalent to Glycine tomentella chromosome 5.
    • 17. The ASR resistant elite Glycine max plant of embodiment 16, wherein said QTL is homozygous.
    • 18. The plant of embodiments 16-17, wherein the parental plant of said ASR resistant agronomically elite Glycine max plant is a wide cross between Glycine max and Glycine tomentella parental lines; in one variation the parental line is a amphidiploid hybrid between Glycine max and Glycine tomentella parental lines (herein, “amphidiploid hybrid”).
    • 19. An agronomically elite Glycine max plant having commercially significant yield comprising an ASR resistant allele which confers increased resistance to ASR, and wherein the ASR allele comprises at least one single nucleotide polymorphism (SNP) selected from the group of favorable SNPs described in any one of Tables 1-5 and further wherein said plant comprises in its genome a chromosomal interval (i.e. such as any one of SEQ ID NOs: 1-5) from Glycine tomentella or a progeny there of (e.g. a amphidiploid hybrid).
    • 20. An agronomically elite soybean having commercially significant yield comprising a chromosomal interval from Glycine tomentella chromosome 5 comprising at least one favorable SNP marker selected from any one of Tables 1-5; in one variation the chromosome interval is any one of SEQ ID NOs: 1-5.
    • 21. The plant of embodiment 20, wherein said chromosomal interval from Glycine tomentella chromosome 5 is derived from any one of plant accessions PI441001, PI441008, PI446958, PI509501, PI583970, PI483224 or progeny thereof (e.g. such as a amphidiploid hybrid).
    • 22. The plant of embodiments 20-21, wherein the chromosomal interval comprises SEQ ID


NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5 or a portion thereof wherein said chromosomal interval confers increased ASR resistance in said plant as compared to a control plant not comprising said chromosomal interval.

    • 23. A plant cell or plant part derived from the plant or seed of embodiments 1-22; in some instances the plant cell or plant part cannot be used to regenerate a plant (e.g. thus a plant cell or plant part unable to be used to regenerate a plant from the plant or seed of embodiments 1-22).
    • 24. A progeny plant or seed from any of the plants of embodiments 1-22.
    • 25. A Glycine max plant of embodiments 1-22, wherein said plant has 20 chromosome pairs and/or 40 paired chromosomes or in some instances said plant maintains a chromosomal pair derived from a wild glycine line.
    • 26. A Glycine max plant of embodiments 1-25, wherein there is no yield drag or negative agronomic effects as compared to a control plant.
    • 27. A method of producing a soybean plant (in some instances a “amphidiploid hybrid”) having increased resistance to Asian soybean rust (ASR), the method comprising the steps of:
      • a. crossing a Glycine max plant with a ASR resistant wild Glycine plant, in some instances a Glycine tomentella plant;
      • b. generating soybean pods from the cross of a);
      • c. isolating embryos from the pods of b) and placing said embryos onto embryo rescue medium (in some instances the embryo rescue medium comprises or has a composition essentially equivalent to: 3.1g B5 basal salt, Gamborg's, lml B5 vitamins 1000×, 40 g sucrose [C12H220O11], 0.25 g casein hydrolysate, 0.25 mg BAP, 0.75g MgCl2*6H20, 20 ml glutamine 25 mg/ml, 0.1 g serine [C3H7NO3], 4ml Asparagine 25 mg/ml, 0.05ml of IBA 1 mg/ml, and 2.0 g Gelzan); or Murashige and Skoog Medium (MS) or Gamborg's B-5 media (Bridgen, 1994)) wherein there is no callus induction caused or initiated in this step c);
      • d. transferring the embryos of c) onto germination medium or elongation medium (in some instances the germination medium comprises or has a composition essentially equivalent to: 3.2 g Schenk and Hilderbrandt Basal salt mixture, 1 g Myo-inositol [C6 H12O6], 5ml Thiamine 1mg/ml, 0.5ml pyridoxine 1 mg/ml, lOg sucrose [C12H12O11], and 7.5 g purified agar) or elongation medium comprising or has a composition essentially equivalent to: 4.3 g MS Basal salt Mixture [MSP01], 5ml MS iron 200×, 30 g Sucrose [C12H22O11], 1 g MES [C6H13NO4S], 8g purified agar, lml B5 vitamins 100×, 2 ml glutamine 25 mg/ml, 0.50 ml zeatin riboside, trans isomers 1 mg/ml, 0.1 ml IAA 1 mg/ml, 0.2 ml GA3); and collecting shoots from said embryos;
      • e. growing the collected shoots of d) on germination or elongation medium; and
      • f. transferring established shoots of e) to soil, thereby producing a soybean plant having increased resistance to ASR (in a preferred instance the shoots are rooted on elongation or germination medium to form plantlets and subsequently hardened.)
    • 28. The method of embodiment 27, wherein the wild Glycine plant or Glycine tomentella plant of step a) comprises in its genome a chromosomal interval corresponding to and defined by (herein, “a chromosomal defined by” means the interval is the span of nucleotide bases from the first nucleotide to final nucleotide of the respective SEQ ID NO:) any one of SEQ ID NOs: 1-5 or a portion thereof where said portion confers increased ASR resistance in a plant.
    • 29. The method of embodiments 27-28, wherein the Glycine tomentella plant comprises in its genome an allele associated with ASR resistance wherein said allele corresponds to any of the favorable alleles listed in Tables 1-5 or is a allele or SNP within any one of chromosome intervals comprising any one of SEQ ID NOs: 1-5 wherein said allele or SNP is associated with or closely linked to ASR resistance in a plant.
    • 30. The method of embodiments 27-29, wherein the wild Glycine or Glycine tomentella plant is any one of P1441001, P1441008, P1446958, P1509501, P1583970, P1483224 or progeny thereof (in some instances the progeny is a amphidiploid hybrid).
    • 31. The method of embodiment 30, wherein the progeny plant is a wide cross between Glycine max and Glycine tomentella parental lines.
    • 32. The method of embodiments 27-31, further comprising the step of molecular marker selection where an isolated genomic nucleic acid from any one of: the parent plants of a), the embryo of c) or the shoot or resultant plant of f) is isolated and analyzed (e.g. genotyped) for the presence of a allele that associates with increased ASR resistance and further wherein said allele is closely linked with the chromosome intervals corresponding to and defined by SEQ ID NOs: 1-5 (e.g. any of the favorable alleles as described in any one of Tables 1-5).
    • 33. The method of embodiment 32, wherein the allele corresponds to any of the favorable alleles listed in Tables 1-5.
    • 34. The method of embodiments 27-33, wherein the Glycine max plant of a) has a relative maturity of 3.7 to 4.8. or in other variations the Glycine max plant may be selected from soybean maturity groups 000 the X
    • 35. The method of embodiments 27-34, wherein the Glycine max plant of a) is used as a female plant and said wild Glycine or Glycine tomentella plant is the pollen donor; alternatively in some instances the Glycine max plant of a) can be uses as the male pollen donor plant and Wild Glycine or Glycine tomentella plant is used as a female plant.
    • 36. The method of embodiments 27-35, wherein the pods of b) are treated with a hormone mixture comprising GA3, NAA and Kinetin (in some embodiments 100 mg GA3, 25mg NAA and 5 mg kinetin /L and further, in some instances, wherein said hormone treatment is sprayed on pods daily until harvest).
    • 37. The method of embodiments 27-36, wherein the pods are collected prior to 19 days after pollination.
    • 38. The method of embodiments 27-37, wherein the embryos and/or shoots are treated with a chromosome doubling agent in any one of steps e)-h) to create amphidiploid plants (or amphidiploid hybrid) capable of being backcrossed with a domestic annual Glycine cultivar to produce at least one backcross generation in some instances a BC4 generation, further wherein the amphidiploid plant further comprises in its genome a favorable agronomic trait, such as ASR resistance that was inherited from the wild Glycine or Glycine tomentella parent; in other instances the amphidiploid plants are backcrossed with a recurrent Glycine max parental line followed by embryo rescue (e.g. as described in embodiments 65-83) to create a BC1 and repeated multiple times to produce a BC4 generation wherein said BC4 generation is fertile (i.e. no need for embryo rescue to generate plants) and capable of producing ASR resistant Glycine max progeny plants.
    • 39. The method of embodiment 38, wherein the chromosome doubling agent is either colchicine or trifluralin; further contemplated chromosome doubling agents that may be used in embodiment 38 may comprise oryzalin.
    • 40. The method of embodiments 27-39, wherein the embryos of c) remains on embryo rescue medium for at least about 20 days at about 24° C.
    • 41. The method of embodiments 27-39, wherein the embryos of d) remain on germination or elongation medium for at least about 20 days at about 24° C.
    • 42. The method of embodiment 41, wherein the embryo rescue medium is Soy ER1-1 wherein Soy ER1-1 comprises the following: 3.1g B5 basal salt, Gamborg's, 1 ml B5 vitamins 1000×, 40g sucrose [C12H22O11], 0.25g casein hydrolysate, 0.25ml BAP, 0.75 g MgCl2*6H20, 20 ml glutamine 25 mg/ml, 0.1 g serine [C3H7NO3], 4 ml Asparagine 25 mg/ml and 0.05 ml of IBA 1 mg/ml (herein, “Soy ER1-1”).
    • 43. A method of producing a Glycine max plant having increased resistance to Asian soybean rust (ASR), the method comprising the steps of:
      • a. providing a first Glycine max plant comprising in its genome a chromosomal interval corresponding to any one of SEQ ID NOs: 1-5 wherein said first Glycine max plant has increased resistance to ASR;
      • b. crossing the Glycine max plant of a) with a second Glycine max plant not comprising said chromosomal interval;
      • c. (in some embodiments this step is omitted) selecting a progeny plant from the cross of b) by isolating a nucleic acid from said progeny plant and detecting within said nucleic acid an allele that associates with increased ASR resistance and further wherein said allele is closely linked with the chromosome intervals corresponding to SEQ ID NOs: 1-5,
      • d. thereby, producing a Glycine max plant having increased resistance to ASR.
    • 44. The method of embodiment 43, wherein the allele in c) corresponds to any of the favorable alleles as depicted in any one of Tables 1-5.
    • 45. The method of embodiments 43-44, wherein either first or second Glycine max plant is an elite Glycine max plant; further the first or second Glycine max plant could also be an elite Glycine max plant having commercially significant yield and in further embodiments be a agronomically elite Glycine max plant.
    • 46. The method of embodiments 43-45, wherein the progeny plant is backcrossed by one or more generations, in some instances at least four (BC4) backcrosses; in further instances the BC1, BC2, BC3 generation is followed by embryo rescue as described in Example 3 or in embodiments 65-82 below.
    • 47. The method of embodiments 27-46, wherein the chromosome interval corresponds to a Glycine tomentella chromosome interval located on Glycine tomentella chromosome 5 at an approximate mapping interval of 0.02-1.19 Mb and additionally comprises any one of SEQ ID NOS: 1-5 or a portion thereof wherein portion confers ASR resistance or is associated with ASR resistance.
    • 48. The method of embodiment 47, wherein the Glycine tomentella chromosome interval is derived from any one of plant accessions: P1441001, P1441008, P1446958, P1509501, PI1583970, P1483224 or a progeny thereof, in some instances the progeny comprises a amphidiploid hybrid plant.
    • 49. The method of embodiment 48, wherein the progeny plant is a wide cross between Glycine max and Glycine tomentella parental lines.
    • 50. A method of producing a Glycine max plant with increased ASR resistance, the method comprising the steps of:
      • a) isolating a nucleic acid from a Glycine max plant;
      • b) detecting in the nucleic acid of a) at least one molecular marker associated with increased ASR wherein said molecular marker is located within 20 cM, 10 cM, ScM, 1 cM 0.5 cM, or closely linked with a chromosomal interval corresponding to a genomic region from a wild Glycine plant or Glycine tomentella plant comprising any one of SEQ ID NOs: 1-5, or a portion thereof;
      • c) selecting a plant based on the presence of the molecular marker detected in b) additionally crossing the selected plant with a second plant (e.g. Glycine max plant) not comprising said chromosomal interval; and
      • d) producing a Glycine max progeny plant from the plant of c) identified as having said allele associated with increased ASR resistance and/or crossed with a second plant.
    • 51. The method of embodiment 50, wherein the molecular marker is closely linked with or corresponds to any one of the favorable alleles as depicted in Tables 1-5 and/or said molecular marker is within a chromosomal interval from Glycine tomentella corresponding to and/or defined by SEQ ID NOs: 1-5.
    • 52. A method of identifying and/or selecting a plant (in some embodiments either a Glycine max or a Glycine tomentella plant) having a ASR resistance, the method comprising the steps of
      • a. isolating a nucleic acid from a soybean plant or plant part;
      • b. detecting in the nucleic acid the presence of a molecular marker that associates with increased ASR resistance wherein the molecular marker is located within 20 cM, 10 cM, ScM, 1 cM, 0.5 cM of a marker as described in any one of Tables 1-5 or in another embodiment the molecular marker is closely linked with, in close proximity to, closely associated with or within a chromosomal interval corresponding to and/or comprising any one of SEQ ID NOs: 1-5 ; and
      • c. identifying or selecting a soybean plant having increased ASR resistance on the basis of the molecular marker detected in b), thereby identifying and/or selecting a plant, having ASR resistance.
    • 53. The method of embodiment 52, wherein the molecular marker detected in b) consists of any favorable marker as described in any one of Tables 1-5 or a allele or molecular marker associated with ASR wherein the allele or molecular marker is located within a chromosomal interval comprising and defined by any one of SEQ ID NOs: 1-5.
    • 54. The method of embodiments 50-53, wherein the molecular marker is a single nucleotide polymorphism (SNP), a quantitative trait locus (QTL), an amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), a restriction fragment length polymorphism (RFLP) or a microsatellite.
    • 55. The method of any one of embodiments 50-54, wherein the detecting comprises amplifying a marker locus or a portion of the marker locus and detecting the resulting amplified marker amplicon (in some embodiments the amplicon comprises a nucleotide sequence as shown in any one of SEQ ID NOs 1-5; further, in another embodiment, a primer able to anneal to said marker locus and amplify said locus allowing for the detection of the resulting amplified marker amplicon.)
    • 56. The method of embodiment 55, wherein the amplifying comprises: a) admixing an amplification primer or amplification primer pair with a nucleic acid isolated from the first soybean plant or germplasm, wherein the primer or primer pair is complementary or partially complementary to at least a portion of the marker locus, and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and, b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon; further embodiments, include the primer pair used in said DNA polymerization reaction and/or a composition comprising said primer pair.
    • 57. The method of embodiments 32-56, wherein the nucleic acid is selected from DNA or RNA, in some embodiments isolated genomic DNA and/or RNA.
    • 58. The method of embodiments 55-57, wherein the amplifying comprises employing a polymerase chain reaction (PCR) or ligase chain reaction (LCR) using a nucleic acid isolated from a soybean plant or germplasm as a template in the PCR or LCR, further embodiments wherein said soybean plant is either Glycine max or Glycine tomentella
    • 59. A primer diagnostic for ASR resistance wherein said primer can be used in a PCR reaction to indicate the presence of an allele associated with ASR resistance, wherein said allele is any favorable allele as described in Tables 1-5 and/or said primer comprises a nucleotide sequence including any of SEQ ID NOs: 1-5 wherein primer is used in a PCR reaction to generate a amplicon diagnostic for at least one allele that is associated with ASR resistance; further a composition comprising said primer.
    • 60. The method of embodiments 27-58, wherein the plant produced or identified by said methods, further confers increased resistance to any one of soy cyst nematode, bacterial pustule, IDC, root knot nematode, frog eye leaf spot, phytopthora, brown stem rot, nematode, rust, smut, Golovinomyces cichoracearum, Erysiphe cichoracearum, Blumeria graminis, Podosphaera xanthii, Sphaerotheca fuliginea, Pythium ultimum, Uncinula necator, Mycosphaerella pinodes, Magnaporthe grisea, Bipolaris oryzae, Magnaporthe grisea, Rhizoctonia solani, Phytophthora sojae, Schizaphis graminum, Bemisia tabaci, Rhopalosiphum maidis, Deroceras reticulatum, Diatraea saccharalis, Schizaphis graminum and Myzus persicae; or a combination thereof.
    • 61. A plant, seed or plant part produced by the methods of embodiments 27-58 or 60.
    • 62. The plant of claim 61, wherein the plant is an elite Glycine max plant, in some embodiments the plant is an elite Glycine max plant having commercially significant yield.
    • 63. The plant of embodiment 62, wherein the plant is an agronomically elite Glycine max plant and in some instances the agronomically elite Glycine max plant shows commercially significant yield.
    • 64. The plant of embodiments 61-63, wherein said plant displays no yield drag or negative agronomic effects as compared to a control and/or check plant; or in other instances has susceptible commercial performance as compared to a commercial check.
    • 65. A method for producing at least one hybrid between a first parent plant of a wild perennial Glycine species and a second parent plant that is a domestic annual Glycine cultivar, wherein said Glycine cultivar is capable of being backcrossed with a domestic annual Glycine cultivar to produce at least one plant of a first backcross generation, or fertile progeny thereof, said method comprising the steps of:
      • a. providing at least one wild glycine plant (wg) and at least one domestic annual Glycine parental plant (dg);
      • b. allowing parental plants to flower;
      • c. crossing said wg plant with dg plant (In most embodiments this cross is a “non-natural cross” thus not able to produce viable/fertile offspring);
      • d. generating pods from the cross of c);
      • e. isolating embryos from the pods of d) and placing said embryos onto embryo rescue medium, wherein there is no callus induction;
      • f. transferring the embryos of e) onto germination medium or elongation medium and collecting shoots from said embryos;
      • g. growing the collected shoots of f) on germination or elongation medium; and
      • h. transferring established shoots of e) to soil, thereby producing a hybrid between a first parent plant of a wild perennial Glycine species and a second parent plant that is a domestic annual Glycine; in some embodiments this hybrid is a amphidiploid hybrid capable of being backcrossed with a Glycine max plant for at least 1 generation.
    • 66. The method of embodiment 65 wherein said wild Glycine line is selected from the group consisting of G. canescens, G. argyrea, G. clandestine, G. latrobeana, G. albicans, G. aphyonota, G. arenaria, G. curvata, G. cyrtoloba, G. dolichocarpa, G. falcate, G. gracei, G. hirticaulis, G. lactovirens, G. latifolia, G. microphylla, G. montis-douglas, G. peratosa, G. pescadrensis, G. pindanica, G. pullenii, G. rubiginosa, G. stenophita, G. syndetika, and G. tomentella.
    • 67. The method of embodiments 65-66, wherein the wild Glycine parental plant is Glycine tomentella.
    • 68. The method of embodiments 65-66, wherein the wild perennial Glycine carries a desirable agronomic trait such as disease resistance (e.g. ASR) and/or abiotic stress resistance (e.g. drought resistance) and/or insect resistance (e.g. Aphid resistance) and/or higher yield.
    • 69. The method of embodiment 68, wherein the desirable trait is selected from the group consisting of: disease resistance including but not limited to, resistance to: soy cyst nematode, bacterial pustule, root knot nematode, frog eye leaf spot, phytopthora, brown stem rot, nematode, rust, smut, Golovinomyces cichoracearum, Erysiphe cichoracearum, Blumeria graminis, Podosphaera xanthii, Sphaerotheca fuliginea, Pythium ultimum, Uncinula necator, Mycosphaerella pinodes, Magnaporthe grisea, Bipolaris oryzae, Magnaporthe grisea, Rhizoctonia solani, Phytophthora sojae, Schizaphis graminum, Bemisia tabaci, Rhopalosiphum maidis, Deroceras reticulatum, Diatraea saccharalis, Schizaphis graminum or Myzus persicae; increased yield, increased resistance or tolerance to iron deficiency chlorosis, and increased drought or heat tolerance.
    • 70. The method of embodiments 65-69, wherein the domestic annual Glycine is Glycine max.
    • 71. The method of embodiments 65-70, wherein the dg plant is used as a female plant and said wg plant is the pollen donor or alternatively the dg plant can be used as a pollen donor (i.e. male line) and wg used as the female line.
    • 72. The method of embodiments 65-71, wherein the pods of d) are treated with a hormone mixture comprising GA3, NAA and Kinetin (in some embodiments 100 mg GA3, 25 mg NAA and 5 mg kinetin /L and further, in some instances, wherein said hormone treatment is sprayed on pods daily until harvest.
    • 73. The method of embodiments 65-72, wherein the pods are collected prior to 19 days after pollination.
    • 74. The method of embodiments 65-73, wherein the embryos and/or shoots are treated with a chromosome doubling agent in any one of steps e)-h) to create amphidiploid plants capable of being backcrossed with a domestic annual Glycine cultivar to produce at least one backcross generation.
    • 75. The method of embodiment 74, wherein the chromosome doubling agent is either colchicine, oryzalin or trifluralin.
    • 76. The method of embodiments 65-75, wherein the embryos of e) remain on embryo rescue medium for at least about 20 days at about 24° C.
    • 77. The method of embodiments 65-76, wherein the embryos of f) remain on germination or elongation medium for at least about 20 days at about 24° C.
    • 78. The method of embodiment 76, wherein the embryo rescue medium is Soy ER1-1.
    • 79. The method of embodiments 65-78, wherein the cross of c) does not require the emasculation of flowers.
    • 80. The method of embodiments 65-79, wherein the cross of c) is a non-natural cross wherein no viable and/or fertile offspring would be produced without further intervention such as, for example, steps d)-h).
    • 81. The method of embodiments 65-80, wherein the method further comprises a step i) wherein the hybrid plant of h) is backcrossed at least once with a Glycine max plant in most embodiments the backcross retains a favorable inherited agronomic trait from said wg, for example, the favorable agronomic trait could be disease resistance (e.g. ASR) and/or abiotic stress resistance (e.g. drought resistance) and/or insect resistance (e.g. Aphid resistance) and/or higher yield; In further instances the backcross is carried out for four generations (BC4) resulting in a fertile dg progeny plant comprising said favorable inherited agronomic trait wherein the backcross progression follows a wide cross between wg and dg plant followed by embryo rescue as in embodiment 65 thus generating a backcrossed plant which is repeated for BC2, BC3, and in preferred instances BC4 to produce fertile progeny plants comprising said favorable inherited agronomic trait.
    • 82. The method of embodiments 65-81, wherein the method further comprises step j) wherein the hybrid plant of h) is backcrossed multiple times and further wherein each back crossed (BC) generation is selected based on a favorable agronomic trait derived from said wg line; in some instances each backcross is followed by (a-h) for four generations (BC4) thus producing fertile hybrid offspring/progeny plants.
    • 83. The method of embodiments 65-82, wherein the method further comprises step k) counting the number of chromosomes in at least one BC generation and selecting those that have 40 paired chromosomes, 20 chromosome pairs or lines not comprising unpaired chromosomes, or in some instances the plant has more than 20 chromosome pairs.
    • 84. The method of embodiments 65-82, wherein the method further comprises step k) counting the number of chromosomes in at least one BC generation and selecting for lines that have no unpaired chromosomes and carrying these lines forward for further breeding.
    • 85. A amphidiploid plant produced by the method of embodiments 65-85.
    • 86. A domestic annual Glycine plant derived from the plant of embodiment 86.
    • 87. A domestic annual Glycine plant of embodiment 87, wherein the Glycine plant has inherited a desirable agronomic trait from perennial wild Glycine parent for example, the desirable agronomic trait could be disease resistance (e.g. ASR) and/or abiotic stress resistance (e.g. drought resistance) and/or insect resistance (e.g. Aphid resistance) and/or higher yield.
    • 88. The domestic annual Glycine plant of embodiment 88, wherein the desirable agronomic trait is increased disease resistance to any one of: soy cyst nematode, bacterial pustule, root knot nematode, frog eye leaf spot, phytopthora, brown stem rot, nematode, rust, smut, Golovinomyces cichoracearum, Erysiphe cichoracearum, Blumeria graminis, Podosphaera xanthii, Sphaerotheca fuliginea, Pythium ultimum, Uncinula necator, Mycosphaerella pinodes, Magnaporthe grisea, Bipolaris oryzae, Magnaporthe grisea, Rhizoctonia solani, Phytophthora sojae, Schizaphis graminum, Bemisia tabaci, Rhopalosiphum maidis, Deroceras reticulatum, Diatraea saccharalis, Schizaphis graminum or Myzus persicae.
    • 89. The domestic annual Glycine plant of embodiments 88-89, wherein the desirable agronomic traits is better field or commercial performance in regards to any one of the following: increased yield, lodging, plant height, field emergence, resistance or tolerance to herbicides, bacteria, fungi, viruses and nematodes, drought tolerance, heat tolerance, chilling or freezing tolerance, excessing moisture, salt stress, oxidative stress, food content and makeup, physical appearance, male sterility, dry down, standability, prolificacy, sugar properties, biomass, oil quality or production, protein quality and overall quality.
    • 90. A plant cell, plant part from any of the plants of embodiments 85-90; in some embodiments said plant cell is incapable of producing a plant.
    • 91. A method of controlling ASR in a field comprising the step of planting the seed from any of the plants described in embodiments 1-21; 24-26; 61-64 or 85-89.


Disease resistant Soybean Plants and Germplasms

The present invention provides disease resistant soybean plants and germplasms. As discussed above, the methods of the present invention may be utilized to identify, produce and/or select a disease resistant soybean plant or germplasm (for example a soybean plant resistant or having increased tolerance to Asian Soybean Rust). In addition, to the methods described above, an Disease resistant soybean plant or germplasm may be produced by any method whereby a marker associated with enhanced disease tolerance is introduced into the soybean plant or germplasm, including, but not limited to, transformation, protoplast transformation or fusion, a double haploid technique, embryo rescue, gene editing and/or by any other nucleic acid transfer system.


In some embodiments, the soybean plant or germplasm comprises a non-naturally occurring variety of soybean. In some embodiments, the soybean plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.


The disease resistant soybean plant or germplasm may be the progeny of a cross between an elite variety of soybean and a variety of soybean that comprises an allele associated with enhanced Disease tolerance (e.g. ASR) wherein the allele is within a chromosomal interval selected from the group consisting of:


1) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or


2) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.;


3) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or


4) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;


5) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5.; or


6) a chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM or in close proximity from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5


The disease resistant soybean plant or germplasm may be the progeny of an introgression wherein the recurrent parent is an elite variety of soybean and the donor comprises an allele associated with enhanced disease tolerance and/or resistance wherein the donor carries a chromosomal interval or a portion thereof comprising any one of SEQ ID NOs: 1-4 and wherein the chromosome interval comprises at least one allele selected respectively from Tables 1-5.


The disease resistant soybean plant or germplasm may be the progeny of a cross between a first elite variety of soybean (e.g., a tester line) and the progeny of a cross between a second elite variety of soybean (e.g., a recurrent parent) and a variety of soybean that comprises an allele associated with enhanced ASR tolerance (e.g., a donor).


The disease resistant soybean plant or germplasm may be the progeny of a cross between a first elite variety of soybean and the progeny of an introgression wherein the recurrent parent is a second elite variety of soybean and the donor comprises an allele associated with enhanced ASR tolerance.


A disease resistant soybean plant and germplasm of the present invention may comprise one or more markers of the present invention (e.g. any marker described in Tables 1-5; or any marker in close proximity to any marker as described in Tables 1-5).


In some embodiments, the disease resistant soybean plant or germplasm may comprise within its genome, a marker associated with enhanced ASR tolerance, wherein said marker is located within a chromosomal interval selected from the group consisting of:


1) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or


2) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.;


3) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or


4) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;


5) 5) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5.; or


6) a chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM or in close proximity from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5.


In some embodiments, the disease resistant soybean plant or germplasm may comprise within its genome a marker that comprises, consists essentially of or consists of marker alleles located in at least two different chromosomal intervals. For example, the marker may comprise one or more alleles located in the chromosomal interval defined by and including any combination of two markers in Table 1 and one or more alleles located in the chromosomal interval defined by and including any combination of two markers in Table 2.


Disease Resistant Soybean Seeds

The present invention provides disease resistant soybean seeds. As discussed above, the methods of the present invention may be utilized to identify, produce and/or select a disease resistant soybean seed. In addition to the methods described above, a disease resistant soybean seed may be produced by any method whereby a marker associated with enhanced ASR tolerance is introduced into the soybean seed, including, but not limited to, transformation, protoplast transformation or fusion, a double haploid technique, embryo rescue, genetic editing (e.g. CRISPR or TALEN or MegaNucleases) and/or by any other nucleic acid transfer system.


In some embodiments, the disease resistant soybean seed comprises a non-naturally occurring variety of soybean. In some embodiments, the soybean seed is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.


The disease resistant soybean seed may be produced by a disease resistant soybean plant identified, produced or selected by the methods of the present invention. In some embodiments, the disease resistant soybean seed is produced by a disease resistant soybean or wild glycine plant (e.g. Glycine tomentella) plant comprising any one of chromosomal intervals corresponding to SEQ ID NOs: 1-5.


A disease resistant soybean seed of the present invention may comprise, be selected by or produced by use of one or more markers from Tables 1-5 of the present invention.


In some embodiments, the disease resistant soybean seed may comprise within its genome, a marker associated with enhanced ASR tolerance, wherein said marker is located within a chromosomal interval selected from the group consisting of:


1) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or


2) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.;


3) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or


4) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;


5) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5.;


6) a chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM or in close proximity from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5.


EXAMPLES

The following examples are not intended to be a detailed catalog of all the different ways in which the present invention may be implemented or of all the features that may be added to the present invention. Persons skilled in the art will appreciate that numerous variations and additions to the various embodiments may be made without departing from the present invention. Hence, the following descriptions are intended to illustrate some particular embodiments of the invention, and not to exhaustively specify all permutations, combinations and variations thereof.


Example 1 Identification of ASR Resistant Wild Glycine Lines

Multiple wild glycine (Glycine tomentella) lines were evaluated for ASR resistance against sixteen rust strains collected across a diverse range of environments. The rust data were generated using single pustule derived isolates from USDA-ARS (FL Q09, FL Q12, LABR13, FLQ11) and field populations (FL Q15, FLQ16, RTP1, RTP2, Vero, GA15, UBL, BR south and BR central), the screening was carried out in contained facilities. Of the Glycine tomentella lines screened for ASR resistance, the following Glycine tomentella lines showed broad resistance against all ASR strains tested: PI441001, PI441008, PI446958, PI509501, PI583970, and PI483224.


Each Glycine tomentella line was evaluated over a multiple day course of infection and rated at various time points using a rust rating scale based on groupings modified from Burdon and Speer, TAG, 1984 (see FIG. 6). Each Glycine tomentella accession was screened >2 times with ˜4 plants each time in North & South America using a large diverse panel of rust isolates.


Example 2 Allele Mining & Associations to PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 ASR Loci

Resistant parent lines (i.e. PI441001, PI441008, PI446958, PI509501, PI583970, and PI483224) were crossed with a susceptible Glycine tomentella line and F1 plants were generated (See Table 5). F1 plants were self-fertilized to generate F2 seed. F2 seed was harvested from the selfed F1 plant. Around 200 F2 seed were sown and leaf tissue from each plant was collected for genotyping studies. Each line was inoculated with Phakopsora pachyrhizi to determine the resistance/susceptible phenotype of each F2 individual. Tissue from 50 resistant F2s and 50 susceptible F2s were combined in separate pools and genomic DNA was prepared from each pool. Illumina sequencing libraries were prepared from DNA for each of the pools and each library was sequenced in two Illumina HiSeq2000 2×100 bp Paired-End (PE) lanes. The average yield per sample was 383 million read pairs, which equals 77 gigabases of sequence per library. The sequencing reads were trimmed to remove bases with PHRED quality scores of <15.


Quality trimmed reads were aligned to the PI441001, PI441008, PI583970, and PI483224 reference genome sequence using GSNAP (WU and NACU 2010) as paired-end fragments. If a pair of reads could not be aligned together, they were treated as singletons for alignment. Reads were used in subsequent analyses if they mapped uniquely to the reference (<2 mismatches every 36 bp and less than 5 bases for every 75 bp as tails).


SNPs were filtered prior to BSA analysis based on read depth, with SNPs having between 40 and 200× read depth being retained. A Chi-square test was used to select SNPs with significantly different read counts between the two alleles in the two pools. An empirical Bayesian approach (LIU et al. 2012) was used to estimate the conditional probability that there is no recombination between each SNP marker and the causal locus in both the resistant pool and in the susceptible pool. The probability of the linkage between the SNP and the causal gene is the geometric mean of these two conditional probabilities. Around 1000 SNPs were found to have possible linkage to the target locus. A subset of these putatively linked SNPs were used to fine map the locus using phenotyped F2 individuals. See references: LIU, S., C.-T. YEH, H. M. TANG, D. NETTLETON AND P. S. SCHNABLE, 2012 Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq). PLoS ONE 7: e36406 & Wu, T. D., and S. Nacu, 2010 Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.









TABLE 5







Plant Crossings and Study Type














Genome
F2: Resistant to



PI#
PI #
Size
Susceptible


Species
(male)
(female)
(Gb)
Ratio






G. tomentella

PI441001
PI441010
2
3:1



G. tomentella

PI441001
PI441011
2
3:1



G. tomentella

PI441001
PI441010
2
3:1



G. tomentella

PI583970
PI441007
2
3:1



G. tomentella

PI583970
PI441010
2
3:1



G. tomentella

PI583970
PI441011
2
3:1



G. tomentella

PI448224
PI441010
2
3:1



G. tomentella

PI441008
PI441010
2
7:9









1. PI441001 Data2Bio LLC (Ames, Iowa) Lab Methodology for gBSA-Seq Analysis for Tetraploid Soybean.

    • Chromosome discovery for causal loci in the tetraploid soybean population, PI441001 was carried out using Data2Bio′s Genomic Bulked Segregant Analysis (gBSA) technology. It was theorized that ASR resistance is controlled by a single dominant allele. Four libraries were generated from DNA samples extracted from two susceptible tissue pools and two resistant tissue pools. These pools were then sequenced in eight (8) Illumina HiSeq2000 2×100bp Paired-End (PE) lanes. A summary of the reference genomes used for subsequent analyses, read processing from raw data to quality trimming, alignment, SNP discovery and SNP impact are demonstrated in FIGS. 1-5 for population 441001. After various filtering steps 110,503 informative SNPs were identified in the PI441001 genome as being significantly associated with ASR resistance. A Bayesian approach was then used to calculate trait-associated probabilities. Next, physical maps of trait-associated SNPs (probability cutoff at 0.01) for the top contigs were created (FIG. 1). Two scaffolds, 46840 and 49652, were identified in PI441001 (SEQ ID NOs: 1 and 2 respectively). SNPs from these enriched scaffolds were mapped to the public Glycine max genome. In both populations, most of the SNPs from the top scaffolds clustered on small portions of Chr05 and Chr08 (see FIG. 4).



2. PI583970 Data2Bio LLC (Ames, Iowa) Lab Methodology for gBSA-Seq Analysis for Tetraploid Soybean

    • Chromosome discovery for loci in the tetraploid soybean population, PI583970 was carried out using Data2Bio′s Genomic Bulked Segregant Analysis (gBSA) technology. Two libraries were created from RNA samples extracted from one susceptible tissue pool and one resistant tissue RNA pool. After various filtering steps 59,014 informative SNPs were identified in the PI583970 genome that were significantly associated with ASR resistance. A Bayesian approach was then used to calculate trait-associated probabilities. Next, a physical map of trait-associated SNPs on contigs was created. The clustering of these SNPs suggests that the resistance loci is located in or near scaffold 000819F (see FIG. 7; Scaffold 001084F is SEQ ID NO: 4). The context sequences associated with these SNPs were also aligned to the public Glycine max genome to create a chromosome-level understanding of the mapping interval. The chromosomal positions of the trait-associated (ASR resistance) SNPs were then displayed graphically. Most of the SNPs from scaffold 001084F mapped and clustered on a small region of Chr05 (see FIG. 8). The data suggest that the loci responsible for ASR resistance maps within or near the interval 0.11 to 0.30 Mbp on scaffold 001084F (FIG. 9).



3. PI483224 Data2Bio LLC (Ames, Iowa) Lab Methodology for gBSA-Seq Analysis for Tetraploid Soybean

    • Chromosome discovery for causal loci in the tetraploid soybean population, PI483224 was carried out using Data2Bio′s Genomic Bulked Segregant Analysis (gBSA) technology. Two libraries were created from DNA samples extracted from one susceptible tissue pool and one resistant tissue pool (PI483224). After various filtering steps 428,263 informative SNPs were identified in the PI483224 genome to be significantly associated with ASR resistance. A Bayesian approach was then used to calculate trait-associated probabilities. Next, a physical map of trait-associated SNPs on contigs was created. The clustering of these SNPs indicates that the ASR resistance loci is located on or near scaffold 002687F (see FIG. 10). The context sequences associated with these SNPs were also aligned to the public Glycine max genome to create a chromosome-level understanding of the mapping interval. The chromosomal positions of the trait-associated (ASR resistant) SNPs were displayed graphically. Most of the SNPs from scaffold 002687F mapped to a small region of Chr05 (See FIG. 11). Data indicates that the ASR loci may map within or near the interval 0.17 to 0.36 MB on scaffold 002687F (see FIG. 12 and SEQ ID NO: 3).


Example 3 Embryo Rescue & Introgression of R Gene Intervals into Glycine max Lines

Embryo rescue is performed (as described below) and chemical treatment to induce chromosome doubling is applied in order to generate amphidiploid shoots. If the amphidiploid plants are fertile they will be used to backcross with Glycine max. Backcrossing with Glycine max and subsequent embryo rescue will need to be performed for several generations in order to gradually eliminate the perennial Glycine tomentella chromosomes eventually resulting in ASR resistant Glycine max plant


Wide crosses were carried out using Elite Syngenta soybean (Glycine max) lines (RM 3.7 to 4.8). The elite soybean lines are used as the females (pollen recipients) and multiple accessions of Glycine tomentella are used as the males or pollen donors. Selecting flowers from the Glycine tomentella plant containing anthers at the proper developmental stage is important. New, fully-opened, brightly colored flowers hold anthers with mature pollen. The pollen should appear as loose, yellow dust. These flowers are removed from the Glycine tomentella plant and crossed with the elite Glycine max plant for pollination. Pollen from the Glycine tomentella plants should be used within 30 minutes of flower removal. It is also important to identify and select elite soybean flower buds that are ready for pollination. A soybean flower bud is generally ready when it is larger in size when compared to an immature bud. The sepals of the soybean blossoms are lighter in color and the petals are just beginning to appear. First, use a pair of fine-tipped tweezers to carefully detach the sepals from the flower bud to expose the outer set of petals. Then, gently grasp and remove the petals (5 in total) from the flower exposing the ring of stamens surrounding the pistil. Since the stigma is receptive to pollen 1 day before the anthers begin shedding pollen it is important to recognize the stage development of “female ready, male not ready”. When pollinating soybean flowers at this developmental stage it is not necessary to emasculate the female flower. Locate the stigma on the elite soybean flower. Then using 1 male flower, carefully peel off the petals to expose the anthers and gently dust the pollen grains onto the stigma of the soybean flower. Care should be taken not to damage the stigma at any time during this process. Starting the day after pollination a hormone mixture is sprayed onto the pollinated flower and eventual developing F1 pod 1X every day until harvest. The pollinated flower or pod is saturated with a light mist of the hormone mixture, taking care not to cause the flower/pod to prematurely detach from the plant. The mixture contains 100 mg GA3, 25 mg 1-Naphthaleneacetic acid (NAA) and 5 mg kinetin/L distilled water. Application of these hormones aid in the retention of the developing pod and in increased pod growth. The above described wide cross methodology results in success rates significantly higher than that reported in the literature. Further, no emasculation of female flowers is necessary, which saves time and reduces risk of damage to the stigma.


Harvest: Pods from wide crosses are harvested at approximately 14 to 16 days post pollination. (Harvest dates in the literature suggest 19 to 21 days, however the above method allows for faster harvest time and more robust pods.). Pods are collected and counted according to wide cross combination to determine crossing success. The average crossing success across multiple soybean females and 5 different accessions of Glycine tomentella is approximately 40%. The wide cross pods can contain 1 to 3 seeds but generally 2 seeds are found in each F1 pod. The above described methodology allows for pod harvest at 14 to 16 days after pollination, ˜5 days earlier than described in literature.


Embryo rescue: Harvested pods are collected and brought back to the lab to be sterilized. The pods are first rinsed with 70% EtOH for 2 to 3 minutes and then placed in 10% Clorox bleach for an additional 30 minutes on a platform shaker at approximately 130 RPM. Finally, the pods are rinsed multiple times with sterile water to remove any residual bleach. Embryo isolation can begin immediately following pod sterilization or pods can be stored at 4° C. for up to 24 hours prior to embryo isolation. The sterilized pods are next taken to a laminar flow hood where the embryos can be rescued. Individual pods are placed in a sterile petri dish and opened using a scalpel and forceps. An incision is made along the length of the wide cross pod away from the seed. The pod can then be easily opened to expose the seed. Alternatively, two pair of forceps can be used to separate the pod shell. Carefully remove the seed from the pod and place in a sterile petri dish under a dissection microscope. Very fine forceps are needed to isolate the embryo from the seed. With forceps in one hand, gently hold the side of the seed away from the embryo, with the hilum facing up. Use another pair of forceps in the other hand to remove the seed coat from the side of the seed containing the embryo. Peel off the membrane surrounding the embryo and push the embryo up from its bottom side. Embryos should be past the globular developmental stage and preferably past the early heart developmental stage (middle to late heart stage, cotyledon stage and early maturation stage embryos are desired). Isolated embryos are transferred to embryo rescue medium such as Soy ER1-1 (i.e. 3.1g B5 basal salt, Gamborg's, lml B5 vitamins 1000×, 40 g sucrose [C12H22O11], 0.25g casein hydrolysate, 0.25ml BAP, 0.75g MgCl2*6H20, 20ml glutamine 25mg/ml, 0.1g serine [C3H7NO3], 4 ml Asparagine 25mg/ml and 0.05ml of IBA 1 mg/ml) Murashige and Skoog Medium (MS) and Gamborg's B-5 media (Bridgen, 1994) may also be used as embryo rescue medium. Embryos can be treated to induce chromosome doubling at this time. (See below for chromosome doubling details.) Isolated embryos remain on embryo rescue medium for 21 to 30 days at 24° C. Embryos may remain in the dark for the entire incubation on ER1-1, they also can be incubated in the dark and later completed in the light, or may spend the entire incubation in the light. There is not a callus induction stage in this protocol, shoots are developed directly from the embryos which allows for faster turnaround time, plantlet survival and better quality results. The above described embryo rescue method involves direct shoot regeneration from embryos, rather than regeneration through embryogenesis, thus making plant recovery quicker (shoot recovery in approximately 2-3 months, compared to reported up to 1 year timeline in the literature). Further, the following protocol does not require culture in the dark following transfer to germination medium nor does the above protocol require a transfer to rooting medium.


Chromosome doubling treatments: Either colchicine of trifluralin can be used to induce chromosome doubling. Ideally, late heart stage wide cross embryos (or larger) are chemically treated to induce chromosome doubling at any time from immediately following isolation up to 1 week post isolation. The doubling agent can be mixed in either solid or liquid medium and applied for several hours or up to a few days. Trifluralin is used at a concentration of 10-40uM in either solid or liquid media. Alternatively, colchicine is used at a concentration of 0.4-1 mg/ml in either solid or liquid media. Following chemical treatment, embryos are transferred to fresh embryo rescue medium.


Shoot regeneration: Developing embryos are transferred from rescue medium to germination medium such as Soy ER GSMv2 (i.e. 3.2g Schenk and Hilderbrandt Basal salt mixture, lg Myo-inositol [C6H12O6], 5ml Thiamine 1 mg/ml, 0.5 ml pyridoxine 1 mg/ml, 10 g sucrose [C12H22O11], and 7.5g purified agar) for approximately 3 to 5 weeks in the light at 24° C. Alternatively, developing embryos may be transferred from rescue medium to elongation medium such as Soy E1 0 No TCV (i.e. 4.3g MS Basal salt Mixture [MSP01], 5 ml MS iron 200×, 30g Sucrose [C12H22O11], lg MES [C6H13NO4S], 8g purified agar, lml B5 vitamins 100×, 2ml glutamine 25mg/ml, 0.50 ml zeatin riboside, trans isomers 1 mg/ml, 0.1ml IAA 1 mg/ml, 0.2 ml GA3 5mg/ml, 1.5 ml timentin 100 mg/ml, 0.3ml cefotaxime 250mg/ml, 0.5ml vancomycin 100 mg/ml) Shoots can be kept on medium for approximately 3 to 5 weeks in the light at 24° C. Developing shoots may be transferred from media plates to Phytocons containing either germination or elongation medium for further shoot development. Established shoots having suitable roots are moved to soil.


Ploidy Analysis: Ploidy analysis is conducted using a flow cytometer. Leaf tissue for ploidy analysis is collected from small shoots either in culture or after establishment in soil. Tissue is collected on dry ice and stored at −80° C. until analysis, or collected on wet ice and analyzed the same day. A sample size of 0.5cm2 is sufficient. Samples are prepared according to the instructions in the Sysmex kit (Sysmex Inc., Kobe Japan). Each sample set contains an untreated F1 plant (not treated to induce chromosome doubling) as a control.


Example 4 ASR Resistance Trait Introgression

Amphidiploid lines generated from the wide cross (i.e. Glycine tomentella crossed with Glycine max) followed by embryo rescue as described in Example 3 were backcrossed multiple times with a recurrent elite Glycine max lines. It is known in the art that multiple backcrosses are needed to generate fertile hybrid lines, in particular the literature suggests that a BC3 generation is necessary. In this case it was determined that an additional backcrosses are necessary, BC4 in the case of G. tomentella×G. max to generate fertile hybrid plants. Fl hybrid plants produced by the methods as described above were created from wide crosses comprising PI441001, PI441008, PI446958, PI509501, PI583970, and PI483224. F1 plants were next crossed as a female with a male recurrent G. max plant to perform a first backcross (BC1 progeny). BC1 Progeny were further backcrossed for multiple generations (e.g. BC2). BC plants are evaluated for ASR resistance, chromosome numbers and in some cases lines are genotyped through use of molecular markers as described herein to detect the presence of chromosome intervals corresponding to SEQ ID NOs 1-5 or any marker identified in Tables 1-5.


The above examples clearly illustrate the advantages of the invention. Although the present invention has been described with reference to specific details of certain embodiments thereof, it is not intended that such details should be regarded as limitations upon the scope of the invention except as and to the extent that they are included in the accompanying claims.


Throughout this application, various patents, patent publications and non-patent publications are referenced. The disclosures of these patents, patent publications and non-patent publications in their entireties are incorporated by reference herein into this application in order to more fully describe the state of the art to which this invention pertains.

Claims
  • 1. An elite Glycine max plant having in its genome a chromosomal interval from a wild glycine plant, wherein said chromosomal interval confers increased Asian soy rust (ASR) resistance as compared to a control plant not comprising said chromosomal interval.
  • 2. The plant of claim 1, wherein the chromosomal interval comprises SEQ ID NOs: 1, 2, 3, 4, 5, or a portion of any thereof wherein said portion confers in said plant increased ASR resistance.
  • 3. The plant of claim 1, wherein the chromosomal interval comprises a SNP marker associated with increased ASR resistance wherein said SNP marker corresponds with any one of the favorable SNP markers as listed in Tables 1-5.
  • 4. The plant of claim 3, wherein the chromosomal interval is derived from Glycine tomentella chromosome 5 at an approximate mapping interval of 0.02-1.19 Mb.
  • 5. The plant of claim 5, wherein the chromosomal interval corresponds to a position within the Glycine tomentella genome that comprises any one of SEQ ID NOs: 1-5.
  • 6-9. (canceled)
  • 10. The plant of claim 1, wherein the plant is a agronomically elite Glycine max plant having a commercially significant yield and/or commercially susceptible vigor, seed set, standability or threshability.
  • 11. The plant of claim 1, wherein said interval is introduced into said plant genome by a wide cross between a Glycine max and Glycine tomentella line followed by embryo rescue to create amphidiploid hybrid lines capable of being backcrossed with a Glycine max line to create an elite Glycine max plant.
  • 12-15. (canceled)
  • 16. A ASR resistant agronomically elite Glycine max plant having commercially significant yield, wherein said plant comprises an introgression from a Glycine tomentella accession P1441001, P1441008, P1446958, P1509501, P1583970, P1483224, or progeny thereof, wherein the introgression comprises a ASR resistance conferring QTL linked to at least one marker located on the chromosome equivalent to Glycine max chromosome 5 and wherein said marker is closely linked with or located within a chromosome interval corresponding to and defined by any one of SEQ ID NOS: 1-5.
  • 17. (canceled)
  • 18. (canceled)
  • 19. An agronomically elite Glycine max plant comprising an ASR resistance allele which confers increased resistance to ASR, and wherein the ASR resistance allele comprises at least one single nucleotide polymorphism (SNP) selected from the group of favorable SNPs described in any one of Tables 1-5.
  • 20-22. (canceled)
  • 23. A plant cell, seed or plant part derived from the plant of claim 1 .
  • 24. A progeny plant from the plant of claim 1.
  • 25. (canceled)
  • 26. (canceled)
  • 27. A method of producing a Glycine plant having increased resistance to Asian soybean rust (ASR), the method comprising the steps of: a. crossing a Glycine max plant with a ASR resistant Glycine tomentella plant;b. generating soybean pods from the cross of a);c. isolating embryos from the pods of b) and placing said embryos onto embryo rescue medium, wherein there is no callus induction;d. transferring the embryos of c) onto germination medium or elongation medium and collecting shoots from said embryos;e. growing the collected shoots of d) on germination or elongation medium; andf. transferring established shoots of e) to soil, thereby producing a Glycine plant having increased resistance to ASR.
  • 28. The method of claim 27, wherein the Glycine tomentella plant of step a) comprises in its genome a chromosomal interval corresponding to any one of SEQ ID NOs: 1-5 or a portion thereof.
  • 29. (canceled)
  • 30. The method of claim 27, wherein the Glycine tomentella line is any one of P1441001, P1441008, P1446958, P1509501, P1583970, P1483224, or a progeny thereof or a amphidiploid hybrid.
  • 31. (canceled)
  • 32. The method of claim 27, further comprising the step of molecular marker selection, wherein an isolated genomic nucleic acid from either the parent plants of a), the embryo of c) or the shoot or resultant plant of f) are analyzed for the presence of a allele that associates with increased ASR resistance and further wherein said allele is closely linked with or located within the chromosome intervals corresponding to SEQ ID NOs: 1-5.
  • 33-35. (canceled)
  • 36. The method of claim 27, wherein the pods of b ) are treated with a hormone mixture comprising GA3, NAA and Kinetin.
  • 37. The method of claim 27, wherein the pods are collected prior to 19 days after pollination.
  • 38. The method of claim 27, wherein the embryos and/or shoots are treated with a chromosome doubling agent in any one of steps e)-h) to create amphidiploid plants capable of being backcrossed with a domestic annual Glycine cultivar to produce at least one backcross generation (BC1).
  • 39. The method of claim 38, wherein the chromosome doubling agent is either colchicine or trifluralin.
  • 40-42. (canceled)
  • 43. A method of producing a Glycine max plant having increased resistance to Asian soybean rust (ASR), the method comprising the steps of: a. providing a first Glycine max plant comprising in its genome a chromosomal interval corresponding to any one of SEQ ID NOs: 1-5, wherein said first Glycine max plant has increased resistance to ASR;b. crossing the Glycine max plant of a) with a second Glycine max plant not comprising said chromosomal interval;c. selecting a progeny plant from the cross of b) by isolating a nucleic acid from said progeny plant and detecting within said nucleic acid an allele that associates with increased ASR resistance and further wherein said allele is closely linked with or located within the chromosome intervals corresponding to any one of SEQ ID NOs: 1-5, thereby producing a Glycine max plant having increased resistance to ASR.
  • 44-47. (canceled)
  • 48. The method of claim 43, wherein the Glycine tomentella chromosome interval is derived from any one of plant accessions: P1441001, P1441008, P1446958, P1509501, P1583970, P1483224, or a progeny thereof.
  • 49. (canceled)
  • 50. A method of producing a Glycine max plant with increased ASR resistance, the method comprising the steps of: a) isolating a nucleic acid from a Glycine max plant;b) detecting in the nucleic acid of a) at least one molecular marker associated with increased ASR wherein said molecular marker is located within 20 cM, 10 cM, ScM, 1 cM 0.5 cM, or closely linked with a chromosomal interval corresponding to a genomic region from Glycine tomentella chromosome 5 comprising any one of SEQ ID NOs: 1-5, or a portion thereof, wherein said portion confers to a plant increased ASR resistance;c) selecting a plant based on the presence of the molecular marker detected in b); andd) producing a Glycine max progeny plant from the plant of c) identified as having said allele associated with increased ASR resistance.
  • 51-58. (canceled)
  • 59. A primer diagnostic for ASR resistance, wherein said primer can be used in a PCR reaction to indicate the presence of an allele associated with ASR resistance, wherein said allele is any favorable allele as described in Tables 1-5.
  • 60-64. (canceled)
  • 65. A method for producing a hybrid between a first parent plant of a wild perennial Glycine species and a second parent plant that is a domestic annual Glycine cultivar, wherein said hybrid is capable of being backcrossed with a domestic annual Glycine cultivar to produce at least on plant of a first backcross generation, or progeny thereof, said method comprising: a. providing at least one wild perennial Glycine parental plant (wg) and at least one domestic annual Glycine parental plant (dg);b. allowing parent plants to flower;c. crossing said wg plant with dg plant;d. generating pods from the cross of c);e. isolating embryos from the pods of d) and placing said embryos onto embryo rescue medium, wherein there is no callus induction;f. transferring the embryos of e) onto germination medium or elongation medium and collecting shoots from said embryos;g. growing the collected shoots of f) on germination or elongation medium; andh. transferring established shoots of e) to soil, thereby producing a hybrid between a first parent plant of a wild perennial Glycine species and a second parent plant that is a domestic annual Glycine.
  • 66. The method of claim 65, wherein said wg is selected from the group consisting of G. canescens, G. argyrea, G. clandestine, G. latrobeana, G. albicans, G. aphyonota, G. arenaria, G. curvata, G. cyrtoloba, G. dolichocarpa, G. falcate, G. gracei, G. hirticaulis, G. lactovirens, G. latifolia, G. microphylla, G. montis-douglas, G. peratosa, G. pescadrensis, G. pindanica, G. pullenii, G. rubiginosa, G. stenophita, G. syndetika, and G. tomentella.
  • 67. The method of claim 66, wherein the wild perennial Glycine parental plant is Glycine tomentella.
  • 68. The method of claim 67, wherein the wild perennial Glycine carries a desirable agronomic trait.
  • 69. (canceled)
  • 70. The method of claim 65, wherein the domestic annual Glycine is Glycine max.
  • 71-84. (canceled)
  • 85. A amphidiploid plant produced by the method of claim 65-84.
  • 86. A domestic annual Glycine plant derived from the plant of claim 85.
  • 87-92. (canceled)
RELATED APPLICATIONS

This Application claims the benefit of U.S. Provisional Application No. 62/347,945, filed 9 Jun. 2016, the contents of which are incorporated herein by reference.

PCT Information
Filing Document Filing Date Country Kind
PCT/US2017/036712 6/9/2017 WO 00
Provisional Applications (1)
Number Date Country
62347945 Jun 2016 US