QTL Analysis Of Rice Cooking Traits And Fine-mapping Of A Gel Consistency Gene QGC-10

China was the first country to take advantage of heterosis in hybrid rice production. The superhybrid rice cultivar ‘Liangyou Peijiu’(LYP9), a pioneer two-line hybrid rice, is an excellent parentalmaterial for genetic studies on both rice yield and grain quality. In this study, a RILs (RecombinantInbred Lines) population, derived from ‘LYP9’(PA64S×93-11), was used to detect quantitative trait loci(QTLs) relevant to rice cooking traits as well as rice grain gel consistency. The results are as follows:1. Based on2,622high-quality SNP markers via re-sequencing parental lines and the132LYP9RIL individuals, we successfully constructed one high-density SNP genetic map, covering1381.9cMon genetics with the average internal distance0.392cM.2. Using the QTL software of Mapping Version1.0, we identified totally23cooked-rice-relatedQTLs, including cooked rice size, cooked/soaked rice length expansion rate, width expansion, cookedrice elongation index and so on.3. These detected cooked–rice-related QTLs were distributed on rice chromosome1,2,4,5,6,7,8,9, and11. Among them, qGL7, locating on chromosome7between SNP7-177and SNP7-121, is amajor QTL controlling both rice grain and cooked-rice grain length. Additionally, we find a hot geneticspot on top of rice chromosome6involving in Wx functional region.4. RT-PCR indicated that, although obvious expression level variations could be detected in theendosperm of93-11and during different stages of grain filling, the gene expression patterns were thesame; i.e., the expression level of Wx increased substantially during the primary filling stage andreached a maximum at12d after flowering, then decreased gradually. Moreover, the expression levelof Wx was lower in93-11than that in PA64s, especially at12d and20d after flowering.5.3QTLs for rice grain gel consistency were identified on chromosome5,6,10. Among them,qGC-6and qGC-10were the two main QTLs controlling grain gel-consistency, and detected in bothHangzhou and Hainan while the phenotypic variation they contributed are both above10%.6. Combining the high-density genetic map and phenotypic analysis of F7lines, we selected threetarget RIL individuals (F7-5, F7-23, F7-28) with a homozygous genetic background of qGC-10. Thoseselected lines were backcrossed three times with PA64S, and we successfully constructed the BC3F2population.7. We screened F7population derived from ‘LYP9’ with molecular markers to further fine-mapqGC-10. Based on the re-sequencing information, we developed more Indel markers in qGC-10targetgenetic region and finally narrowed qGC-10to350kb between GC19and GC25.