Molecular markers associated with chloride tolerant soybeans

Abstract

The present invention provides methods and compositions for the identification and selection of loci modulating phenotypic expression of a chloride tolerant trait in plant breeding. In addition, methods are provided for screening germplasm entries for the performance and expression of this trait.

We claim: 
     
         1 . A method of selecting a soybean plant that comprises a genotype associated with chloride tolerance, comprising:
 detecting in a soybean plant an allele in at least one genetic locus associated with chloride tolerance, wherein the genetic locus is on chromosome 3 and is flanked by loci FE704412 (SEQ ID NO: 1) and AW760852 (SEQ ID NO: 36).   
     
     
         2 . The method of  claim 1 , wherein said soybean plant or progeny thereof is exposed to a dosage of chloride sufficient to cause a detrimental effect in a soybean variety that is moderately sensitive or sensitive to chloride. 
     
     
         3 . The method of  claim 1 , wherein said genotype associated with a chloride tolerance comprises at least one polymorphic allele of at least one marker in a sub-region of said genetic locus that is flanked by loci BI972982 (SEQ ID NO: 2) and BI699634 (SEQ ID NO: 17). 
     
     
         4 . The method of  claim 3 , wherein said genotype associated with chloride tolerance comprises at least one polymorphic allele of at least one marker in said chromosome 3 region or sub-region comprises a TT allele of NS0205902 (SEQ ID NO: 13). 
     
     
         5 . The method of  claim 1 , wherein said genotype associated with a chloride tolerance comprises at least one polymorphic allele of at least one marker in a sub-region of said genetic locus that is flanked by loci BI699634 (SEQ ID NO: 17) and AW719859 (SEQ ID NO: 35). 
     
     
         6 . The method of  claim 5 , wherein said genotype associated with chloride tolerance comprises at least one polymorphic allele of at least one marker in said chromosome 3 region or sub-region comprises a GG allele of NS0203171 (SEQ ID NO: 31). 
     
     
         7 . A method for obtaining a soybean plant comprising in its genome at least one chloride tolerance locus, compromising the steps of:
 a. genotyping a plurality of soybean plants with respect to at least one genetic locus on chromosome 3 flanked by loci NGMAX006180041 (SEQ ID NO: 4) and NGMAX006184463 (SEQ ID NO:34); and   b. selecting a soybean plant comprising in its genome at least one genetic locus comprising a genotype associated with chloride tolerance.   
     
     
         8 . The method of  claim 7 , wherein said genotype associated with chloride tolerance comprises at least one polymorphic allele of at least one marker selected from the group consisting of NS0096117 (SEQ ID NO:8), NS0205902 (SEQ ID NO: 13), and NS0203171 (SEQ ID NO: 31). 
     
     
         9 . The method of  claim 8 , wherein said marker comprises a GG allele of NS0203171 (SEQ ID NO: 31). 
     
     
         10 . The method of  claim 8 , wherein said marker comprises a TT allele of NS0205902 (SEQ ID NO: 13) 
     
     
         11 . The method of  claim 7 , wherein said plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one chloride tolerance locus with a parent plant comprising at least one chloride sensitivity locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one chloride tolerance locus. 
     
     
         12 . The method of  claim 7 , wherein said population contains plants that contain a transgene that confers resistance to dicamba and/or a transgene that confers resistance to glyphosate. 
     
     
         13 . The method of  claim 7 , further comprising the step of assaying for the presence of at least one additional marker, wherein said additional marker is either linked or unlinked to said chromosome 3 genomic region. 
     
     
         14 . A method for producing a soybean plant comprising in its genome at least one introgressed chloride tolerance locus comprising the steps of:
 a. crossing a first soybean plant with a chloride tolerance locus with a second soybean plant comprising: a chloride sensitivity locus in a first chromosome genomic region flanked by loci NGMAX006180041 (SEQ ID NO: 4) and NGMAX006184463 (SEQ ID NO: 34) and at least one linked polymorphic locus not present in said first soybean plant to obtain a population segregating for the chloride tolerance loci and said linked polymorphic locus;   b. detecting at least two polymorphic nucleic acids in at least one soybean plant from said population, wherein at least one of said polymorphic nucleic acids is located in said first chromosome genomic region and wherein at least one of said polymorphic amino acids is a linked polymorphic locus not present in said first soybean plant; and   c. selecting a soybean plant comprising a genotype associated with chloride tolerance and at least one linked marker found in said second soybean plant comprising a chloride sensitivity locus but not found in said first soybean plant, thereby obtaining a soybean plant comprising in its genome an introgressed chloride tolerance locus.   
     
     
         15 . The method of  claim 14 , wherein at least one of said first or said second soybean plants comprises a transgene that confers resistance to dicamba and/or a transgene that confers resistance to glyphosate. 
     
     
         16 . The method of  claim 14 , wherein said population, said selected soybean plant, and/or progeny of said selected soybean plant is exposed to a dosage of chloride sufficient to cause a deleterious effect in a chloride sensitive variety. 
     
     
         17 . The method of  claim 14 , wherein said polymorphic nucleic acid detected in step (b) is detected with marker NS0203171 (SEQ ID NO: 31). 
     
     
         18 . The method of  claim 15 , wherein said polymorphic nucleic acid detected in step (b) comprises a GG allele of NS0203171 (SEQ ID NO: 31). 
     
     
         19 . The method of  claim 14 , wherein said polymorphic nucleic acid detected in step (b) is detected with marker NS0205902 (SEQ ID NO: 13). 
     
     
         20 . The method of  claim 15 , wherein said polymorphic nucleic acid detected in step (b) comprises a TT allele of NS0205902 (SEQ ID NO: 13). 
     
     
         21 . The method of  claim 14 , wherein said linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both. 
     
     
         22 . The method of  claim 14 , wherein said linked polymorphic locus is detected with a marker that is located within about 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of said chloride tolerance locus. 
     
     
         23 . The method of  claim 14 , wherein said linked polymorphic locus is detected with at least one marker selected from the group consisting of NS0096117 (SEQ ID NO:8), NS0205902 (SEQ ID NO: 13), and NS0203171 (SEQ ID NO: 31). 
     
     
         24 . A soybean plant made by the method of  claim 14 , wherein said soybean plant comprises an introgressed chloride tolerance locus. 
     
     
         25 . A soybean plant comprising an introgressed chloride tolerance locus, wherein at least one linked marker found in said soybean plant is characteristic of germplasm comprising a chloride sensitivity locus and is not associated with germplasm comprising the chloride tolerance locus. 
     
     
         26 . The soybean plant of  claim 25 , wherein said introgressed chloride tolerance locus comprises a GG allele of NS0203171 (SEQ ID NO: 31). 
     
     
         27 . The soybean plant of  claim 25 , wherein said introgressed chloride tolerance locus comprises a TT allele of NS0205902 (SEQ ID NO: 13).