Mining QTLs for elevated protein and other major seed composition traits from diverse soybean germplasm

Soybean is the world’s largest source of protein for animal feed and the second largest source of vegetable oil. Improving the seed protein of soybean without negatively affecting yield and oil content is an important goal for soybean breeders. A population consisting of 132 recombinant inbred lines (RILs) was developed by crossing an elite breeding line, G00-3213 with a plant introduction, PI 594458A, with elevated protein content. In 2016 and 2017, each of the RILs was grown as a single row in Watkinsville, GA, while in 2018, the population was grown at two locations. The seed composition of RILs was analyzed with near-infrared (NIR) spectroscopy. The RIL population was genotyped using the SoySNP6k BeadChip for quantitative trait locus (QTL) mapping. Significant genotype × environment interaction was observed. QTL analyses in and across four environments identified 16, 10, 10, 16, and 5 QTLs for protein, oil, sucrose, and normalized cysteine and methionine contents, respectively. QTLs for protein content identified on chromosomes (Chrs) 3, 6, 13, and 20 were detected in multiple environments. Eight genomic regions on Chrs 3, 6, 8, 10, 13, 17, and 20 were detected that influenced two to four traits, indicating that pleiotropic or linkage effects of these loci may influence multiple seed composition traits. The results of this research provide additional genomic resources for genetic improvement of seed composition and help breeders to better understand the environmental impacts on these QTLs.