Method to identify disease resistant quantitative trait loci in soybean and compositions thereof

1. A method of producing a population of soybean plants or seeds comprising ASR (Asian Soybean Rust) resistance locus 1, wherein said ASR resistance locus 1 is also present in soybean accession PI 200492, said method comprising:

genotyping a first population of soybean plants or seeds, said first population of soybean plants or seeds comprising ASR resistance locus 1;

selecting from said first population one or more soybean plants or seeds comprising said ASR resistance locus 1 based upon said genotyping; and

producing from said selected one or more soybean plants or seeds a second population of soybean plants or seeds comprising said ASR resistance locus 1.

2. The method of claim 1 , wherein said ASR resistance locus 1 is localized to linkage group G.

3. The method of claim 2 , wherein said ASR resistance locus 1 is mapped within 10 centimorgans or less from a SNP marker selected from the group consisting of

NS0093250 capable of being identified with probes with SEQ ID NOs: 100 and 101,

NS0119710 capable of being identified with probes with SEQ ID NOs: 102 and 103,

NS0103004 capable of being identified with probes with SEQ ID NOs: 104 and 105,

NS0099454 capable of being identified with probes with SEQ ID NOs: 106 and 107,

NS0102630 capable of being identified with probes with SEQ ID NOs: 108 and 109,

NS0102915 capable of being identified with probes with SEQ ID NOs: 110 and 111,

NS0102913 capable of being identified with probes with SEQ ID NOs: 112 and 113,

NS0123728 capable of being identified with probes with SEQ ID NOs: 114 and 115,

NS0129943 capable of being identified with probes with SEQ ID NOs: 116 and 117,

NS0102168 capable of being identified with probes with SEQ ID NOs: 118 and 119,

NS0092723 capable of being identified with probes with SEQ ID NOs: 120 and 121,

NS0098177 capable of being identified with probes with SEQ ID NOs: 122 and 123,

NS0127343 capable of being identified with probes with SEQ ID NOs: 124 and 125, and

NS0101121 capable of being identified with probes with SEQ ID NOs: 126 and 127.

4. The method of claim 1 , wherein said ASR resistance locus 1 confers a slow rust phenotype.

5. The method of claim 1 , wherein said ASR resistance is resistance to Phakopsora pachyrhizi or Phakopsora meibomiae.

6. The method of claim 1 , wherein said second population of soybean plants or seeds comprise one or more agronomic traits selected from the group consisting of herbicide tolerance, increased yield, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, mycoplasma disease resistance, modified oils production, high oil production, high protein production, germination and seedling growth control, enhanced animal and human nutrition, lower raffinose, environmental stress resistance, increased digestibility, production of industrial enzymes, production of pharmaceutical proteins, production of pharmaceutical peptides, production of pharmaceutical small molecules, improved processing traits, improved flavor, improved nitrogen fixation, improved hybrid seed production, reduced allergenicity, and improved production of biopolymers and biofuels.

7. The method of claim 1 , wherein said second population of soybean plants or seeds comprise one or more traits selected from the group consisting of insect resistance, glyphosate resistance, resistance to Soybean Cyst Nematode, resistance to Meloidogyne javanica , resistance to Meloidogyne arenaria , resistance to Meloidogyne hapla , resistance to Meloidogyne incognita , resistance to Diaporthe phaseolorum var. caulivora , and resistance to Corynespora cassiicola.

8. The method of claim 1 , wherein said second population of soybean plants or seeds are transgenic.

9. The method of claim 1 , wherein said genotyping uses one or more markers selected from the group consisting of a simple sequence repeat (SSR) marker, an AFLP marker, an RFLP marker, an RAPD marker, a phenotypic marker, a SNP, an isozyme marker, and microarray transcription profile.

10. The method of claim 1 , wherein said genotyping involves a molecular marker located within 10 centimorgan from said ASR resistance locus 1.

11. The method of claim 1 , wherein said genotyping involves a molecular marker located within 5 centimorgan from said ASR resistance locus 1.

12. The method of claim 1 , wherein said genotyping uses one or more methods selected from the group consisting of polymerase chain reaction (PCR), Ligase Chain Reaction (LCR), Oligonucleotide Ligation Assay (OLA), allele-specific oligomers, branched DNA technology, transcription-based amplification systems, isothermal amplification methods, and Single Strand Conformation Polymorphism (SSCP) analysis.

13. The method of claim 1 , wherein said genotyping comprises detecting one or more SNP polymorphisms.

14. The method of claim 13 , wherein said genotyping comprises a primer-extension assay.

15. The method of claim 13 , wherein said genotyping comprises a GOOD assay.

16. The method of claim 13 , wherein said genotyping uses one or more methods selected from the group consisting of oligonucleotide hybridization, Taq-Man assay, molecular beacon, electronic dot blot assay, and denaturing high-performance liquid chromatography.

17. The method of claim 1 , wherein said genotyping involves a SNP marker selected from the group consisting of

NS0093250 capable of being identified with probes with SEQ ID NOs: 100 and 101,

NS0119710 capable of being identified with probes with SEQ ID NOs: 102 and 103,

NS0103004 capable of being identified with probes with SEQ ID NOs: 104 and 105,

NS0099454 capable of being identified with probes with SEQ ID NOs: 106 and 107,

NS0102630 capable of being identified with probes with SEQ ID NOs: 108 and 109,

NS0102915 capable of being identified with probes with SEQ ID NOs: 110 and 111,

NS0102913 capable of being identified with probes with SEQ ID NOs: 112 and 113,

NS0123728 capable of being identified with probes with SEQ ID NOs: 114 and 115,

NS0129943 capable of being identified with probes with SEQ ID NOs: 116 and 117,

NS0102168 capable of being identified with probes with SEQ ID NOs: 118 and 119,

NS0092723 capable of being identified with probes with SEQ ID NOs: 120 and 121,

NS0098177 capable of being identified with probes with SEQ ID NOs: 122 and 123,

NS0127343 capable of being identified with probes with SEQ ID NOs: 124 and 125, and

NS0101121 capable of being identified with probes with SEQ ID NOs: 126 and 127.

18. The method of claim 1 , wherein said genotyping involves a marker within 10 centimorgans or less from a SNP marker selected from the group consisting of

NS0093250 capable of being identified with probes with SEQ ID NOs: 100 and 101,

NS0119710 capable of being identified with probes with SEQ ID NOs: 102 and 103,

NS0103004 capable of being identified with probes with SEQ ID NOs: 104 and 105,

NS0099454 capable of being identified with probes with SEQ ID NOs: 106 and 107,

NS0102630 capable of being identified with probes with SEQ ID NOs: 108 and 109,

NS0102915 capable of being identified with probes with SEQ ID NOs: 110 and 111,

NS0102913 capable of being identified with probes with SEQ ID NOs: 112 and 113,

NS0123728 capable of being identified with probes with SEQ ID NOs: 114 and 115,

NS0129943 capable of being identified with probes with SEQ ID NOs: 116 and 117,

NS0102168 capable of being identified with probes with SEQ ID NOs: 118 and 119,

NS0092723 capable of being identified with probes with SEQ ID NOs: 120 and 121,

NS0098177 capable of being identified with probes with SEQ ID NOs: 122 and 123,

NS0127343 capable of being identified with probes with SEQ ID NOs: 124 and 125, and

NS0101121 capable of being identified with probes with SEQ ID NOs: 126 and 127.