Genome-wide association study uncovers the genetic loci for yield-related traits in waxy rice

Improving yield potential is a critical goal for breeders; however, yield-related loci are still less understood in waxy rice, which seriously limited the precise development of high-yield cultivars. Here, we investigated six yield-related traits in a collection of 109 cultivated waxy rice accessions over two seasons and perform genome-wide association study using 1.81 million single nucleotide polymorphisms (SNPs) to elucidate the genetic basis underlying grain yield. Our analysis identified a total of 28 significant quantitative trait loci (QTLs), explaining 0.71-38.46% of phenotype variance. Of these, 17 was previously reported or contained genes known to govern the associated traits, while the remaining 11 appear to be novel alleles. Within the 28 QTLs, 379 residing genes were identified, and candidate yield-related genes in close proximity to the significant SNPs were extracted for haplotype analysis. The results showed that the genetic variations in Os09g0375700, Os09g0396300, and Os03g0609500 were highly associated with variations in thousand grain weight or panicle number. Our results dissected the possible genetic determinants of waxy rice yield and will be conducive to breed new cultivars with high yield in the future.