Submitted to: Journal of Plant Genome Sciences
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/14/2013
Publication Date: 12/1/2013
Citation: Fallen, B.D., Nyinyi, C.N., Allen, F.L., Kopsell, D.A., Saxton, A.M., Chen, P., Kantsartzi, S.K., Cregan, P.B., Hyten, D.L., Pantalone, V.R. 2013. Soybean amino acid QTL detected using the Universal Soy Linkage Panel 1.0 with 1536 SNPs. Journal of Plant Genome Sciences. 1(3):68-79. Interpretive Summary: Soybean meal is an important component of animal feed and the quantity of protein and the quality of the protein in the meal is important to animal nutrition. The objective of this research was to determine the positions of genes, also referred to as quantitative trait loci (QTL), that control the quantity of the various amino acids that make-up the soybean seed protein. A total of 282 progeny from a cross of the soybean cultivars Essex and Williams 82 were planted at three field locations along with the parents and check cultivars. The seed harvested from these field experiments was analyzed for each of 18 amino acids and significant differences among the progeny were found for the level of each amino acid. A total of 1536 single nucleotide polymorphism (SNP) DNA markers was used to analyze each of the progeny and the parents. The combined analysis of the DNA marker data and the amino acid data detected a total of 10 genes/QTL on six different chromosomes that were associated with variation in seed amino acid content. The SNP DNA markers in close proximity to the QTL/genes in the 10 regions can be used by plant breeders and geneticists in marker assisted selection to identify soybean progeny with increased levels of specific amino acids.
Technical Abstract: Soybean [Glycine max (L.) Merr.] is an integral component of U.S. agriculture and the use of soybean in animal feed is important to the viability of the global agricultural industry. However, few studies have been conducted to evaluate genomic regions controlling amino acid composition is soybean. Designing soybean seed composition that will benefit animal production is essential. The objective of this study was to identify genomic regions controlling essential and non-essential amino acid composition in soybean seed. To achieve this objective, 282 F5:9 recombinant inbred lines (RIL) developed from a cross of Essex × Williams 82 were used. Ground soybean seed samples were analyzed for amino acids and significant differences (p < 0.05) were found among genotypes in the population for all amino acid concentrations. The Universal Soy Linkage Panel (USLP) 1.0 with 1536 single nucleotide polymorphism (SNP) DNA markers was used to genotype the 282 RILs and identify 480 polymorphic genetic markers. The software R/qtl was used to identify candidate quantitative trait loci (QTL), which were validated using R/MQM. A total of ten QTL were detected on chromosomes 5, 7, 9, 10, 13 and 20 that explained 5 to 14 % of the total phenotypic variation for a particular amino acid. Using SNPs from the USLP 1.0 to detect QTL for amino acids in soybean provides additional information to select genotypes with enhanced amino acid profiles that will benefit animal production.