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Seed coat cracking (SCC), particularly the Type-I irregular cracking, is critical in determining the quality of appearance and commercial value of soybean seeds. The objective of this study was to identify the quantitative trait loci (QTLs) for SCC with high-density genetic map. One hundred sixty-seven recombinant inbred lines (RILs) developed from a cross between Uram (SCC-resistant) and Chamol (SCC-susceptible) were evaluated for SCC over 2 years (2016–2017). The QTL analysis identified 12 QTLs located on chromosomes 2 (D1b), 6 (C2), 8 (A2), 9 (K), 10 (O), 12 (H), 19 (L), and 20 (I). Out of the 12 QTLs,  qSC2-1 ,  qSC9, SC10-1 ,  qSC10-2 , and  qSC12  were novel QTLs and the other seven QTLs ( qSC2-2 ,  qSC2-3 ,  qSC6 ,  qSC8 ,  qSC19-1 ,  qSC19-2 , and  qSC20 ) were found to co-localize with the previously identified QTLs. The mean SCC of the RILs of early maturity group was significantly higher than that of the late maturity group, suggesting an association between SCC and maturity loci. In addition, although 10 QTLs were distantly located from the maturity loci ( E1 ,  E3 ,  E4 ,  E7 , and  E10 ),  qSC10-1  and  qSC10-2  co-localized with the maturity loci  E2 . The results obtained in this study provide useful genetic information on SCC which could be used in the SCC breeding programs.

High-density linkage map reveals QTL for Type-I seed coat cracking in RIL population of soybean [Glycine max (L.) Merr.]