QTL analysis of net-like cracking in soybean seed coats

There are two types of seed coat cracking that are controlled genetically in soybean: Type I with irregular cracks and Type II with net-like cracks. This study was conducted to determine the genetic basis of Type II cracking using DNA markers. A F-2 population and F-3 lines derived from a cross between Uzuramame with black seed coats having net-like cracking, and a Clark mutant line with black seed coats were used in this study. Degree of cracking in each seed was scored by cracking index (no cracking, 0 to severe cracking, 4) and was averaged per plant (average cracking index, ACl). One morphological and 189 SSR markers were analyzed and assigned to 31 linkage groups spanning 2463 cM. Two QTLs for ACT (ncr1 and ncr2) were identified in molecular linkage group C 1 with a distance of about 62 cM. The ncr1 and ncr2 had LOD scores of 5.90 and 8.61, accounting for 16.0 and 32.4% of phenotypic variation, respectively. The alleles from Uzuramame at the QTLs conferred increased ACl. The effects of QTLs identified in the F-2 population were confirmed in the F-3 lines. No epistatic interaction was observed between the QTLs.