Nested Association Mapping to Identify Seed Composition QTL in Diverse Soybean Lines
Abstract
Soybeans are economically the most important legume grown worldwide. It provides quality protein and oil to food and feed markets in addition to being used for industrial products. The value of soybean could be enhanced by increasing protein, oil, and sucrose contents, while lowering anti-nutritional compounds such as oligosaccharides. Understanding the genetic and environmental factors controlling soybean seed composition is an essential prerequisite for such an endeavor. Three separate studies were initiated to understand the underlying genetics governing soybean seed compositional traits. The first study was conducted to identify Quantitative Trait Loci (QTL) controlling seed protein and oil contents in the SoyNAM multi-parent population through a Genome-Wide Association Study (GWAS). The SoyNAM population was created by generating recombinant inbred lines from crossing the hub parent IA3023 to forty other parents representing elite public germplasm. Over 40,000 seed samples from 5486 recombinant inbred lines were evaluated in eight environments for seed protein and oil concentrations using NIR spectroscopy. Using GWAS, we identified thirteen QTL highly associated with seed protein content distributed over nine different chromosomes and marked by 49 SNPs. Twenty-two out of 49 SNPs were located within the 39.6–40.2 Mbp region of chromosome 9, a region previously reported to be associated with seed protein content. We refined the seed protein QTL region to 0.56 Mbp compared to a previously reported 5–8 Mbp. Of the thirteen seed protein QTL, six were novel and were located on chromosomes 11, 13, 14, 15, and 18. GWAS also identified twelve QTL significantly associated with seed oil content on eight different chromosomes tagged by 109 SNPs. Six of the twelve seed oil QTL were new and were situated on chromosomes 2, 11, 15, 18, and 20. The QTL detected for protein and oil explained 15% and 23% of the phenotypic variations, respectively. The second study was performed to identify quantitative trait loci (QTL) controlling seed sucrose, raffinose, and stachyose content in a set of 140 SoyNAM recombinant inbred lines (RILs), developed from the cross of two elite soybeans lines IA3023 and LD02-4485. Composite interval mapping (CIM) identified three QTL for sucrose content: one on chromosome 1 and two on chromosome 3. The QTL on chromosome 1 explained 10% of the phenotypic variation while the two QTL on chromosome 3 each explained 22% phenotypic variation in the sucrose content. The CIM also displayed a QTL for raffinose content on chromosome 6 and it explained 6% of phenotypic variation. This study identified novel QTL that can be validated for use in developing soybean lines with higher concentrations of sucrose and reduced levels of raffinose and stachyose. The last study focused on Multi-Environment Trial (MET) analyses for both seed protein and oil contents. The result from the GGE-biplot analyses revealed that selection based on mean and stability was appropriate for the SoyNAM parental genotypes. The most stable and desirable genotypes for seed protein content were LG92-1255, CL0J173-6-8, PI398881, PI561370, Prohio, PI427136, LG03-3191, PI507681B and genotypes LG03-2979, U03-100612, Prohio, LD02-4485, IA3023, LG04-4717, LG92-1255 were most desirable for seed oil content. LG94-1128 and 5M20-2-5-2 for seed protein content and NE3001 and LG05-4317 for seed oil content were unstable even though high yielding.
Degree
Ph.D.
Advisors
Rainey, Purdue University.
Subject Area
Agronomy
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