Novel genetic loci associated with disease resistance in soybeans

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.

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; and   f. 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); and   d) 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; 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.   
     
     
         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)