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Increasing the yield of soybean ( Glycine max  L. Merrill) is a main aim of soybean breeding. The 100-seed weight is a critical factor for soybean yield. To facilitate genetic analysis of quantitative traits and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population consisting of 194 chromosome segment substitution lines (CSSLs) was developed. In these lines, different chromosomal segments of the Chinese cultivar Suinong 14 were substituted into the genetic background of wild soybean ( Glycine soja  Sieb. & Zucc.) ZYD00006. Based on these CSSLs, a genetic map covering the full genome was generated using 121 simple sequence repeat (SSR) markers. In the quantitative trait loci (QTL) analysis, twelve main effect QTLs ( qSW-B1 -1/2/3,  qSW-D1b -1/2,  qSW-D2 -1/2,  qSW-G -1/2/3,  qSW-M -2 and  qSW-N -2) underlying 100-seed weight were identified in 2011 and 2012. The epistatic effects of pairwise interactions between markers were analyzed in 2011 and 2012. The results clearly demonstrated that these CSSLs could be used to identify QTLs, and that an epistatic analysis was able to detect several sites with important epistatic effects on 100-seed weight. Thus, we identified loci that will be valuable for improving soybean 100-seed weight. These results provide a valuable foundation for identifying the precise location of genes of interest, and for designing cloning and marker-assisted selection breeding strategies targeting the 100-seed weight of soybean.

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QTL Location and Epistatic Effect Analysis of 100-Seed Weight Using Wild Soybean (Glycine soja Sieb. &amp; Zucc.) Chromosome Segment Substitution Lines