Identification and mapping of stable QTL for protein content in soybean seeds

Protein and oil are two primary traits in soybean, which affect the quality of soyfood, feed, and oil products. The objectives of this research were to identify and validate quantitative trait loci (QTL) for seed protein. Crosses were made between two high-protein and two low-protein lines, R05-1415 × R05-638 designated as Population 1, and V97-1346 × R05-4256 as Population 2. A total of 242 and 214 recombinant inbred lines were developed for QTL mapping in populations 1 and 2, respectively. The F2 plants from the mapping populations were genotyped with simple sequence repeat (SSR) and/or single nucleotide polymorphism (SNP) markers. Seeds from F2:3, F2:4, and F2:5 lines were evaluated for seed protein content at three locations for 3 years accounting for five environments. A total of 120 polymorphic SSR markers and 526 polymorphic SNP markers were used to construct linkage maps. One major protein QTL on chromosome 20 was identified in both populations across all five environments and accounted for 20–42 % of protein content variation. Four protein QTL were identified on chromosome 1, 5, and 14, which accounted for 10–16 % of the total variation in protein content. These identified QTL along with linked SSR/SNP markers in this study would be of great value in facilitating marker-assisted selection for seed protein content in soybean breeding programs.