Quantitative trait locus mapping for water-soluble protein content in soybean across six environments

Water-soluble protein is an important component of soybean seeds and is usually used as an indicator of soybean quality, especially in soybean food processing. Compared with studies on seed protein or oil content, genetic studies on water-soluble protein content (WSPC) in soybean have lagged. Therefore, to identify genes associated with WSPC in soybean seeds, we systematically performed a quantitative trait locus (QTL) mapping study based on a recombinant inbred line population consisting of 237 lines derived from Zheng 92116 and Williams 82 and SNP or InDel markers from a genotyping-by-sequencing protocol. As a result, the WSPC at 3 locations from 2016 to 2017 ranged from 26.69 to 40.35% and was normally distributed in each environment. A genetic map consisting of 6,597 markers distributed in 20 linkage groups was constructed. By using the iciMapping and QTL.gCIMapping programs, a total of 20 QTLs with a PVE (proportion of phenotypic variance explained) ranging from 1.86 to 30.03%, distributed throughout 9 chromosomes, were detected, including 2 major QTLs. Among the 20 QTLs, 9 were stable; these QTLs were detected by both programs and/or in two or more datasets and usually presented relatively high LOD and PVE values. Compared with previous studies, 8 of the 20 QTLs above were newly identified, and the other 12 QTLs were the same or identical to the WSPC QTLs reported previously. To identify potential genes underlying WSPC, the QTL with the largest effect, i.e., qWSPC5-3, was selected for further analysis on the basis of the RNA-seq datasets, and the expression profiles of the 27 genes within this interval were analyzed. These results shed new light on the genetics of WSPC in soybean and may also provide important information for improving the functional quality of soybean varieties for breeders.