Unveiling the genetic loci for a panicle developmental trait using genome-wide association study in rice

Panicle size has a high correlation with grain yield in rice. There is a bottleneck to identify the additional quantitative trait loci (QTL) for panicle size due to the conventional traits used for QTL mapping. To identify more genetic loci for panicle size, a panicle developmental trait (LNTB, the length from panicle neck-knot to the first primary branch in the rachis) related to panicle size was identified and the genetic loci were investigated using genome-wide association study (GWAS). Three populations including two subspecies, Indica and Japonica and the whole population were used to perform GWAS by the linear mixed model. Nineteen significant associations were totally identified in the whole population. One locus was examined in both Indica and Japonica. Four associations identified in the present study were near the cloned panicle related genes. Hd16 (Heading date 16) and DST (Drought and salt tolerance) were examined for LNTB. These results indicate that LNTB was also an ideal trait for GWAS to identify the underlying QTLs for panicle size. The associations not related to the cloned genes need to be further validated by the bi-parental populations. Dissecting the favorable alleles of these associations could be helpful for breeding by marker assisted selection in rice.