Verification and fine-mapping of QTLs conferring days to flowering in soybean using residual heterozygous lines

The results of QTL mapping based on a primary mapping population should be further verified and refined for its real utilization in marker-assisted selection or map-based cloning. The primary mapping population contains 114 BC1F1 plants of the backcross between Essex (maturity group V, MG V) as the donor parent and ZDD2315 (MG II) as the recurrent parent. In this study, a genetic linkage map with 250 SSR markers spanning a total length of 2963.5 cM on 25 linkage groups (LG) was constructed using software MAPMAKER3.0. Six kinds of genetic statistical models of 4 softwares, i.e. WinQTL Cartographer Version 2.5, IciMapping Version 2.0, MapQTL Version 5.0 and QTLnetwork Version 2.0, were used to map QTLs conferring days to flowering of the BC1F3 lines. Nine QTLs were mapped on 6 different linkage groups (LG). Of those, 6 QTLs were detected by at least two different genetic statistical models, while the other three were detected by only one procedure. Among the three QTLs, Flwdt7 was mapped between Sat_213 and Satt643 on LG C2 with only 11.0% contribution rate. For confirmation of Flwdt7, 5 RHL populations were developed through selfing eight BC1F5 plants heterozygous at seven markers around the locus. The RHL populations with the same segregating loci were bulked and used to construct a secondary linkage map of the specific segment using software JoinMap® 3.0. The genetic distances among the markers on the specific segment became shorter than those of the whole genome map. On the secondary map, Flwdt7 was mapped between Satt277 and Satt489, next to its primary interval Sat_213-Satt643, with distance 1.40 cM to Satt277 and 0.45 cM to Satt489, confidence interval narrowed to 2.7 cM, and contribution rate increased to 36.8%. The results were confirmed with significance analysis among marker genotypes on individual loci and comparison analysis of target marker intervals among near isogenic lines (plants). Thus the strategy by using residual heterozygous lines for QTL fine-mapping on target segments based on primary whole genome scanning with multiple mapping models was demonstrated to be effective.