Abstract
Rice chromosome segment substitution lines (CSSLs) are ideal for creating natural variation and dissecting complex quantitative traits. In addition, it builds a bridge for molecular breeding and accurate identification of quantitative trait loci (QTLs). In this study, to construct an indica rice library of single-segment substitution lines (SSSLs) spanning the whole genome, a rice CSSL-Z691 carrying four substitution segments (4.07 Mb of average length) was identified by marker-assisted selection (MAS) from indica restorer line "Jinhui35" in the "Xihui18" genetic background. Compared with large panicle type Xihui18, seed setting ratio, grain width, and 1000-grain weight increased in Z691. In contrast, the number of primary branches, spikelet number per panicle, grain number per panicle, grain length, rate of length to width, and yield per plant decreased in Z691. Then, 11 QTLs were identified in the secondary F(2) population from Xihui18/Z691. Again, four QTLs (qGW6, qGL4, qRLW4, and qGWT4) were validated by three SSSLs (S1-S3) developed in F(3). In addition, 11 new QTLs were detected by the three SSSLs that were not identified in the F(2) population. Moreover, the different QTLs in D1-D3 showed various genetic models. Some QTLs, e.g., qGWT6 (a = 0.96 g) and qGWT7 (a = -0.29 g), displayed independent inheritance, while others exhibited various epistatic interactions. Thus, it is vital to identify different QTLs and their genetic models. Resolving the epistasis effects among different QTLs is crucial for screening QTLs for breeding by design. Finally, qGL4 and qGW6 were fine-mapped to 160- and 240-kb intervals on chromosomes 4 and 6, and two candidate genes were determined by DNA sequencing. These results provide valuable genetic and breeding materials for cloning qGL4 and qGW6 and for future molecular breeding by design.