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Identifying and exploring significant genomic regions associated with soybean yield, seed fatty acids, protein and oil

Christopher J. Smallwood, Jason D. Gillman, Arnold M. Saxton, Hem S. Bhandari, Phillip A. Wadl, Benjamin D. Fallen, David L. Hyten, Qijian Song, Vincent R. Pantalone
Journal of crop science and biotechnology 2017 v.20 no.4 pp. 243-253
Glycine max, chromosomes, crop yield, field experimentation, genes, genomics, genotyping, inbred lines, linolenic acid, lipid content, pleiotropy, quantitative trait loci, single nucleotide polymorphism, soybean oil, soybeans, stearic acid, Tennessee
Soybean [Glycine max (L.) Merrill] yield and seed fatty acids, protein, and oil content are important traits for which an improved understanding of significant genomic regions would be useful. To accomplish this, a soybean population consisting of 203 F5 derived recombinant inbred lines (RILs) was developed and genotyped with 11,633 polymorphic single nucleotide polymorphisms (SNPs). Each RIL was grown in a single plot at Knoxville, TN in 2010; followed by replicated, multi-location field trials in 2013 and 2014. The data from 2010, 2013, and 2014 were analyzed together in order to detect quantitative trait loci (QTL) for these traits, and 30 total QTLs were detected. Five QTLs are candidates for confirmed status and one QTL is a candidate for positional confirmation. Many of the genes with mutations in close proximity to the fatty acid QTLs are involved in biological processes for fatty acids and/or lipids and could be considered possible candidate genes. Similarly, genes with mutations in genomic regions near yield, protein, and oil QTLs were plentiful and may contribute to the variation observed in these traits. Except for yield and stearic acid, each trait displayed pleiotropic effects with other traits in this study. Notable are the pleiotropic effects for oleic and linolenic acid on chromosomes 9, 13, and 19. Overall, the findings from this research contribute new information to the genetic understanding of soybean yield and seed fatty acids, protein and oil content. This understanding will be useful in making trait improvements.