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Soybean is valued in foods, animal feed and some industrial applications, and agronomic traits are important targets for soybean breeding. In this study, two sets of recombinant inbred line (RIL) populations were used to map yield and quality trait quantitative trait loci (QTLs) across three environments. In total, we detected 37 QTLs in two RIL populations grown in three locations. In the 3613 RIL population, three QTLs related to quality traits and 13 related to yield traits were identified among the 16 QTLs. In the 6013 population, we identified six QTLs related to quality traits and 15 related to yield traits. Among these QTLs, some genomic regions showed pleiotropic effects on yield and quality traits. We further identified candidate genes from these regions. Our results lay the foundation for producing high-yielding soybean with excellent quality traits via molecular breeding.

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