Fine Mapping and Candidate Gene Prediction of the Quantitative Trait Locus qPL8 for Panicle Length in Rice

Rice panicle is the sink organ where assimilation product accumulates, and its morphology determines the rice yield. Panicle length has been suggested as a yield-related trait, but the genetic factor for its control is still limited. In this study, we carried out fine-mapping of qPL8, a QTL identified for panicle length in our previous work. Near isogenic line (NIL) with qPL8 exhibited elongated panicle without obvious effect on other panicle elements. With five key recombinants from NIL population, the locus was finally narrowed down to a 278-kb region, where 44 genes are annotated. By comparing the genomic sequence of two parents, 17 genes were identified with SNPs or InDels variations in the coding region. Expression analysis showed that eight genes were up-regulated in the NIL with qPL8. Considering both the coding variation and expression status, several candidate genes for the locus were identified, and OsMADS37 was raised as the most possible candidate. Interestingly, an expression QTL (eQTL) also resides in the locus, leading to a cluster of gene expression variation in the region. This study will facilitate the application of qPL8 locus in rice breeding for yield potential.