Markers associated with soybean rust resistance and methods of use therefor

Abstract

Methods for conveying soybean rust (SBR) resistance into non-resistant soybean germplasm are provided. In some embodiments, the methods include introgressing SBR 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 SBR resistance. Also provided are single nucleotide polymorphisms (SNPs) associated with resistance to SBR; 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.

1 . A method for conveying resistance to soybean rust (SBR) into non-resistant soybean germplasm comprising introgressing SBR 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 an SBR resistance locus selected from the group consisting of Rpp1, Rpp2, Rpp3, Rpp4, and Rpp5. 
     
     
         2 . The method of  claim 1 , wherein the one or more nucleic acid markers are selected from the group consisting of SEQ ID NOs: 1-13, and informative fragments thereof. 
     
     
         3 . The method of  claim 1 , wherein the marker-assisted breeding comprises single nucleotide polymorphism (SNP) analysis. 
     
     
         4 . The method of  claim 1 , further comprising screening an introgressed soybean plant, or a cell or tissue thereof, for SBR resistance. 
     
     
         5 . A method for reliably and predictably introgressing soybean rust (SBR) resistance into non-resistant soybean germplasm comprising using one or more nucleic acid markers for marker-assisted breeding among soybean lines to be used in a soybean breeding program, wherein the nucleic acid markers are selected from the group consisting of SEQ ID NOs: 1-13, and informative fragments thereof, and introgressing the resistance into the non-resistant soybean germplasm. 
     
     
         6 . The method of  claim 5 , wherein the marker-assisted breeding comprises single nucleotide polymorphism (SNP) analysis. 
     
     
         7 . The method of  claim 5 , further comprising screening an introgressed soybean for SBR resistance. 
     
     
         8 . A method for producing an inbred soybean plant adapted for conferring, in hybrid combination with a suitable second inbred, resistance to soybean rust (SBR), the method comprising:
 (a) selecting a first donor parental line possessing a desired SBR resistance and having at least one of the resistant loci selected from a locus mapping to Rpp1 and mapped by one or more of the markers SEQ ID NOs: 1-3; a locus mapping to Rpp2 and mapped by one or more of the markers SEQ ID NOs: 4-6; a locus mapping to Rpp3 and mapped by one or more of the markers SEQ ID NOs: 7 and 8; a locus mapping to Rpp4 and mapped by one or more of the markers SEQ ID NOs: 9 and 10; and a locus mapping to Rpp5 and mapped by one or more of the markers SEQ ID NOs: 11-13;   (b) crossing the first donor parent line with a second parental line in hybrid combination to produce a segregating plant population;   (c) screening the segregating plant population for identified chromosoma loci of one or more genes associated with the resistance to SBR; and   (d) selecting plants from the population having the identified chromosomal loci for further screening until a line is obtained which is homozygous for resistance to SBR at sufficient loci to give resistance to SBR in hybrid combination.   
     
     
         9 . A method for selecting an soybean rust (SBR) resistant soybean plant, the method comprising:
 (a) genotyping one or more soybean plants with respect to one or more single nucleotide polymorphisms (SNPs), wherein the one or more SNPs correspond to one or more molecular markers selected from the group consisting of SEQ ID NOs: 1-13, and informative fragments thereof; and   (b) selecting a soybean plant that includes at least one resistance allele associated with the SNPs, thereby selecting an SBR resistant soybean plant.   
     
     
         10 . The method of  claim 9 , wherein the at least one resistance allele is associated with an allele having an A at nucleotide 428 of SEQ ID NO: 1; a T at position 895 of SEQ ID NO: 2; a G at position 932 of SEQ ID NO: 2; a T at position 57 of SEQ ID NO: 3; a G at position 213 of SEQ ID NO: 4; a G at position 441 of SEQ ID NO: 4; an A at position 70 of SEQ ID NO: 5; a T at position 348 of SEQ ID NO: 5; an A at position 715 of SEQ ID NO: 6; a C at position 377 of SEQ ID NO: 7; a T at position 100 of SEQ ID NO: 8; a G at position 113 of SEQ ID NO: 8; a T at position 147 of SEQ ID NO: 9; a C at position 205 of SEQ ID NO: 10; an A at position 102 at SEQ ID NO: 11; A T at position 159 of SEQ ID NO: 12; and/or a G at position 357 of SEQ ID NO: 13. 
     
     
         11 . A soybean rust (SBR) resistant soybean plant selected using the method of  claim 9 , or a cell, tissue culture, seed thereof. 
     
     
         12 . A method for selecting an soybean rust (SBR) resistant soybean plant, the method comprising:
 (a) isolating one or more nucleic acids from a plurality of soybean plants;   (b) detecting in said isolated nucleic acids the presence of one or more marker molecules associated with SBR resistance, wherein said marker molecule is selected from the group consisting of SEQ ID NOs: 1-13, informative fragments thereof, and any marker molecule mapped within 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 centiMorgans or less from said marker molecules; and   (c) selecting a soybean plant comprising said one or more marker molecules, thereby selecting an SBR resistant soybean plant.   
     
     
         13 . The method of  claim 12 , wherein said one or more marker molecules comprises an A at nucleotide 428 of SEQ ID NO: 1; a T at position 895 of SEQ ID NO: 2; a G at position 932 of SEQ ID NO: 2; a T at position 57 of SEQ ID NO: 3; a G at position 213 of SEQ ID NO: 4; a G at position 441 of SEQ ID NO: 4; an A at position 70 of SEQ ID NO: 5; a T at position 348 of SEQ ID NO: 5; an A at position 715 of SEQ ID NO: 6; a C at position 377 of SEQ ID NO: 7; a T at position 100 of SEQ ID NO: 8; a G at position 113 of SEQ ID NO: 8; a T at position 147 of SEQ ID NO: 9; a C at position 205 of SEQ ID NO: 10; an A at position 102 at SEQ ID NO: 11; A T at position 159 of SEQ ID NO: 12; and/or a G at position 357 of SEQ ID NO: 13. 
     
     
         14 . A method for producing seeds that result in soybean plants resistant to soybean rust (SBR), the method comprising:
 (a) providing a Glycine max plant which contains one or more alleles that confer resistance to SBR, which alleles are characterized one or more of five loci Rpp1-Rpp5, wherein:
 (i) Rpp1 is defined by the following markers: (1) a marker of about 459 by as set forth in SEQ ID NO: 1; (2) a marker of about 1101 by as set forth in SEQ ID NO: 2; and (3) a marker of about 443 by as set forth in SEQ ID NO: 3; or any part of a DNA sequence as in SEQ ID NOs: 82-84 linked within 1, 2, 5, or 10 cM to at least one of the markers of (1)-(3) conferring resistance to SBR; 
 (ii) Rpp2 is defined by the following markers: (4) a marker of about 471 by as set forth in SEQ ID NO: 4; (5) a marker of about 489 by as set forth in SEQ ID NO: 5; and (6) a marker of about 794 by as set forth in SEQ ID NO: 6; or any part of a DNA sequence as in SEQ ID NOs: 85-87 linked within 1, 2, 5, or 10 cM to at least one of the markers of (4)-(6) conferring resistance to SBR; 
 (iii) Rpp3 is defined by the following markers: (7) a marker of about 568 by as set forth in SEQ ID NO: 7; and (8) a marker of about 503 by as set forth in SEQ ID NO: 8; or any part of a DNA sequence as in SEQ ID NOs: 88 and 89 linked within 1, 2, 5, or cM to at least one of the markers of (7) and (8) conferring resistance to SBR; 
 (iv) Rpp4 is defined by the following markers: (9) a marker of about 769 by as set forth in SEQ ID NO: 9; and (10) a marker of about 513 by as set forth in SEQ ID NO: 10; or any part of a DNA sequence as in SEQ ID NOs: 90 and 91 linked within 1, 2, 5, or 10 cM to at least one of the markers of (9) and (10) conferring resistance to SBR; and 
 (v) Rpp5 is defined by the following markers: (11) a marker of about 281 by as set forth in SEQ ID NO: 11; (12) a marker of about 948 by as set forth in SEQ ID NO: 12; and (13) a marker of about 485 by as set forth in SEQ ID NO: 13; or any part of a DNA sequence as in SEQ ID NOs: 92-94 linked within 1, 2, 5, or 10 cM to at least one of the markers of (11)-(13) conferring resistance to SBR; 
   (b) crossing the Glycine max plant provided in step (a) with Glycine max culture breeding material; and   (c) collecting seeds resulting from the cross in step (b) that result in soybean plants which are resistant to SBR.   
     
     
         15 . The method of  claim 14 , further comprising detecting at least one allelic form of a polymorphic simple sequence repeat (SSR) or a single nucleotide polymorphism (SNP) associated with at least one of the one or more alleles that confer resistance to SBR. 
     
     
         16 . The method of  claim 15 , wherein the detecting comprises amplifying the marker locus or a portion of the marker locus and detecting the resulting amplified marker amplicon. 
     
     
         17 . The method of  claim 16 , wherein the amplifying comprises: (a) admixing an amplification primer or amplification primer pair with a nucleic acid isolated from the first Glycine max 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. 
     
     
         18 . The method of  claim 17 , wherein the nucleic acid is selected from DNA and RNA. 
     
     
         19 . The method of  claim 16 , wherein the amplifying comprises employing a polymerase chain reaction (PCR) or ligase chain reaction (LCR) using a nucleic acid isolated from the first soybean plant or germplasm as a template in the PCR or LCR. 
     
     
         20 . An improved soybean plant, seed, or tissue culture produced by the method of  claim 1 . 
     
     
         21 . An introgressed Glycine max plant or germplasm produced by the method of  claim 8 . 
     
     
         22 . 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 Glycine max marker comprising a nucleotide sequence of any of SEQ ID NOs: 1-13. 
     
     
         23 . The composition of  claim 22 , wherein said amplification primer pair comprises the nucleotide sequences of SEQ ID NOs: 14 and 15; SEQ ID NOs: 18 and 19; SEQ ID NOs: 22 and 23; SEQ ID NOs: 26 and 27; SEQ ID NOs: 30 and 31; SEQ ID NOs: 34 and 35; SEQ ID NOs: 38 and 39; SEQ ID NOs: 42 and 43; SEQ ID NOs: 46 and 47; SEQ ID NOs: 50 and 51; SEQ ID NOs: 54 and 55; SEQ ID NOs: 58 and 59; SEQ ID NOs: 62 and 63; SEQ ID NOs: 66 and 67; SEQ ID Nos: 70 and 71; SEQ ID Nos: 74 and 75; and SEQ ID Nos: 78 and 79.