Soy gene cluster regions and methods of use

Abstract

Methods for conveying pathogen resistance into non-resistant soybean germplasm are provided. In some embodiments, the methods include introgressing pathogen resistance into a non-resistant soybean using one or more nucleic acid markers for marker-assisted breeding among soybean lines to be used in a soybean breeding program, wherein the markers are linked to and/or associated with pathogen resistance. Also provided are single nucleotide polymorphisms (SNPs) associated with resistance to pathogens; soybean plants, seeds, and tissue cultures produced by any of the disclosed methods; seed produced by the disclosed soybean plants; and compositions including amplification primer pairs capable of initiating DNA polymerization by a DNA polymerase on soybean nucleic acid templates to generate soybean marker amplicons.

What is claimed is: 
     
         1 . A method for producing a soybean plant having improved resistance to  Phytophthora , the method comprising the steps of:
 (a) isolating at least one nucleic acid from a soybean plant selected from a population of soybean plants;   (b) detecting in the nucleic acid of (a) at least one allele of a marker locus associated with improved resistance to  Phytophthora , wherein the marker locus localizes within a chromosomal interval on soy chromosome 13 and comprises a T at nucleotide 251 of SEQ ID NO: 20, a T at nucleotide 251 of SEQ ID NO: 21, an A at nucleotide 251 of SEQ ID NO: 22, and a C at nucleotide of 101 SEQ ID NO: 27;   (c) selecting a first soybean plant from the population of (a) based on the presence of the allele detected in (b);   (d) crossing the first soybean plant of (c) with a second soybean plant wherein said second soybean plant does not comprise the allele or marker locus of (b) associated with improved  Phytophthora  resistance;   (e) collecting seed from the cross of (d); and   (f) growing a soybean progeny plant from the seed of (e), wherein said soybean progeny plant comprises in its genome said allele or marker locus associated with improved resistance to  Phytophthora , thereby producing a soybean progeny plant with improved resistance to  Phytophthora.      
     
     
         2 . The method of  claim 1 , wherein the chromosomal interval comprises at least two alleles associated with improved resistance to  Phytophthora , the at least two alleles selected from the group consisting of a T at nucleotide 251 of any of SEQ ID NO: 6, 7, 9, 10, 11, 13, 15, 16, 17, 18, 19, 20, 21, or 22, and a C at nucleotide 101 of SEQ ID NO: 27. 
     
     
         3 . The method of  claim 1 , wherein the detecting comprises detecting at least one allelic form of a polymorphic simple sequence repeat (SSR) or a single nucleotide polymorphism (SNP). 
     
     
         4 . The method of  claim 1 , wherein the detecting comprises amplifying the marker locus or a portion of the marker locus and detecting the resulting amplified marker amplicon. 
     
     
         5 . The method of  claim 4 , wherein the amplifying comprises: (a) admixing an amplification primer or amplification primer pair with a nucleic acid isolated from the first plant, 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. 
     
     
         6 . A method of identifying a soybean plant having improved resistance to  Phytophthora , the method comprising:
 (a) isolating at least one nucleic acid from a soybean plant selected from a population of soybean plants; and   (b) detecting in the nucleic acid of (a) at least one allele of a marker locus associated with improved resistance to  Phytophthora , wherein the marker locus comprises one of a T at nucleotide 251 of SEQ ID NO: 20, a T at nucleotide 251 of SEQ ID NO: 21, an A at nucleotide 251 of SEQ ID NO: 22, and a C at nucleotide of 101 SEQ ID NO: 27.   
     
     
         7 . The method of  claim 6 , wherein the marker locus localizes within a chromosomal interval on soy chromosome 13 and 
     
     
         8 . A composition comprising an amplification primer pair capable of initiating DNA polymerization by a DNA polymerase on a  Glycine max  nucleic acid template to generate a  Glycine max  marker amplicon, wherein the  Glycine max  marker amplicon corresponds to a  Glycine max  marker comprising a nucleotide sequence of any of SEQ ID NOs: 6, 7, 9, 10, 11, 13, 15, 16, 17, 18, 19, 20, 21, or 22, or 27, and wherein the  Glycine max  marker is associated with improved resistance to  Phytophthora.    
     
     
         9 . The composition of  claim 8 , wherein the amplification primer pair comprises:
 (i) SEQ ID NO: 53 and one of SEQ ID NO: 51 or SEQ ID NO: 52, when the amplicon comprises SEQ ID NO: 6;   (ii) SEQ ID NO: 56 and one of SEQ ID NO: 54 or SEQ ID NO: 55, when the amplicon comprises SEQ ID NO: 7;   (iii) SEQ ID NO: 62 and one of SEQ ID NO: 60 or SEQ ID NO: 61, when the amplicon comprises SEQ ID NO: 9;   (iv) SEQ ID NO: 65 and one of SEQ ID NO: 63 or SEQ ID NO: 64, when the amplicon comprises SEQ ID NO: 10;   (v) SEQ ID NO: 68 and one of SEQ ID NO: 66 or SEQ ID NO: 67, when the amplicon comprises SEQ ID NO: 11;   (vi) SEQ ID NO: 74 and one of SEQ ID NO: 72 or SEQ ID NO: 73, when the amplicon comprises SEQ ID NO: 13;   (vii) SEQ ID NO: 80 and one of SEQ ID NO: 78 or SEQ ID NO: 79, when the amplicon comprises SEQ ID NO: 15;   (viii) SEQ ID NO: 83 and one of SEQ ID NO: 81 or SEQ ID NO: 82, when the amplicon comprises SEQ ID NO: 16;   (ix) SEQ ID NO: 86 and one of SEQ ID NO: 84 or SEQ ID NO: 85, when the amplicon comprises SEQ ID NO: 17;   (x) SEQ ID NO: 89 and one of SEQ ID NO: 87 or SEQ ID NO: 88, when the amplicon comprises SEQ ID NO: 18;   (xi) SEQ ID NO: 92 and one of SEQ ID NO: 90 or SEQ ID NO: 91, when the amplicon comprises SEQ ID NO: 19;   (xii) SEQ ID NO: 95 and one of SEQ ID NO: 93 or SEQ ID NO: 94, when the amplicon comprises SEQ ID NO: 20;   (xiii) SEQ ID NO: 98 and one of SEQ ID NO: 96 or SEQ ID NO: 97, when the amplicon comprises SEQ ID NO: 21;   (xiv) SEQ ID NO: 101 and one of SEQ ID NO: 99 or SEQ ID NO: 100, when the amplicon comprises SEQ ID NO: 22; or   (xv) SEQ ID NO: 116 and one of SEQ ID NO: 114 or SEQ ID NO: 115, when the amplicon comprises SEQ ID NO: 27.   
     
     
         10 . A composition comprising an amplification primer pair capable of initiating DNA polymerization by a DNA polymerase on a  Glycine max  nucleic acid template to generate a  Glycine max  marker amplicon, wherein the  Glycine max  marker amplicon corresponds to a  Glycine max  marker comprising a nucleotide sequence of any of SEQ ID NOs: 7, 34, or 35.