Mapping QTLs For 1000-grain Weight In Hybrid Rice And Outcrossing-related Traits In Male Sterile Lines

Grain weight is a key determinant of grain yield in rice, while outcrossing, stigma exertion and panicle enclosure are critical factors determining hybrid rice seed production. This study consists of two parts. One was using populations in isogenic backgrounds, derived from maintainer line Zhenshan 97 and restorer line Milyang 46 of Shanyou 10, a popular three-line rice hybrid, for dissection of quantitative trait loci(QTL) for grain weight. The other was using 217 rice cytoplasmic male sterile(CMS) lines for genome-wide association study(GWAS) for outcrossing and its related traits. The results can be summarized as follows.In linkage mapping study, three sets of populations with overlapping segregating regions in isogenic backgrounds of Zhenshan 97 B were established in the generations of BC2F5, BC2F6 and BC2F7, derived from Zhenshan 97 B and Milyang 46, and used for dissection of QTL for 1000-grain weight. The results showed that two QTLs linked in repulsion phase on the long arm of chromosome 1 were separated. One was located between simple sequence repeat(SSR) markers RM11437 and RM11615, having a smaller additive effect with the enhancing allele from the maintainer line Zhenshan 97 and a partially dominant effect for increasing grain weight. The other was located between SSR markers RM11615 and RM11800, having a larger additive effect with the enhancing allele from the restorer line Milyang 46 and a partially dominant effect for increasing grain weight. When the two QTLs segregated simultaneously, a residual additive effect with the enhancing allele from Milyang 46 and an over-dominance effect for increasing grain weight were detected. This suggests that dominant QTL linked in repulsion phase might play an important role in heterosis in rice.In genome-wide association study, 217 rice CMS lines and their corresponding maintainer lines were used. The maintainer lines were used for genotyping and as the pollinator in evaluating the seed-setting rate of the CMS plants, and the CMS lines were used for trait measurement. Based on 43,394 single nucleotide polymorphism(SNP) markers, 59 and 57 lines were assigned into Groups 1 and 2, respectively, while the remaining 101 entries went into the mixed group. Such large number of mixed group showed a broad gene exchange between the two subgroups. The results also showed that the linkage disequilibrium(LD) decay varied greatly among different chromosomes with a range from 975 to 2,690 kb. For seed-setting rate(SS), panicle enclosure rate(PE), total stigma exertion rate(TSE), single stigma exertion rate(SSE), and double stigma exertion rate(DSE), GWAS with correction for population structure and kinship were used. A total of 154 significant associations(P < 0.001) for these five traits were identified, located in 27 QTLs including 10 for SS, 11 for stigma exertion, and 6 for PE. Six of the QTLs detected for SS on chromosomes 4, 8, and 10 were tightly linked to QTL for sigma exertion or/and panicle enclosure with the same allelic direction for SS and sigma exertion but opposite direction for SS and PE. QTL clusters of this kind could be targeted to improve the efficiency in the outcrossing of female parents in hybrid rice breeding. Our study also indicates that GWAS-based QTL mapping can complement and enhance previous QTL information for understanding the genetic relationship between outcrossing and its related traits.