Fine mapping and candidate gene analysis of qGL10 affecting rice grain length

Abstract

Grain size influences the yield and quality of rice (Oryza sativa L.), and grain length is one of the component traits of grain size. In this study, a near-isogenic line LB3 with long grain size was constructed using japonica rice cultivar 02428, with short grain size, as the recipient parent and indica rice cultivar ZYX, with long grain size, as the donor parent, by multi-generation backcrossing and selfing. BSA-seq was used for preliminary QTL mapping and InDel markers were developed to fine map the locus. The major QTL, tentatively named qGL10, for grain length was located in a 128.45 kb region of chromosome 10. Combined with haplotype analysis of rice varieties, expression pattern analysis of candidate genes suggested LOC_Os10g39130 (OsMADS56) as a candidate gene. Sequence alignment of OsMADS56 in 02428 and LB3 revealed that there were 15 SNPs in the promoter region and four in the coding region. Further haplotype analysis suggested that SNP9 (G/A) located in the TGTCACA motif might account for the different expression levels of OsMADS56 in 02428 and LB3. These results lay a foundation for the application of qGL10 in molecular breeding of new rice varieties.

Keywords

• Rice
• Grain length
• QTL mapping
• Haplotype analysis