Genome-Wide Association Study for Yield and Yield related traits reveals Marker–Trait Associations in Germplasm lines of Rice

Rice germplasm has abundant genetic diversity, which provides a feasible solution for mapping loci of multiple traits simultaneously. In this study, a set of 72 rice germplasm lines were evaluated for yield and yield-related traits, and significant phenotypic variation was observed among the lines. Three accessions with high yield performance were identified. The germplasm set comprised five sub-populations and genome-wide association study (GWAS) identified a total of 6 marker-trait associations (MTAs) for the studied traits. These MTAs were located on rice chromosomes 1, 3, 7, 9, and 12 and explained the trait phenotypic variances ranging from 17.8 to 26.3%. Six novel MTAs were identified for yield and yield-related traits. A total of 28 putative annotated candidate genes were identified in a genomic region spanning ∼200 kb around the MTAs respectively. Among the important genes underlying the novel MTAs were OsFBK12, bHLH, WRKY, HVA22, and ZmEBE-1 , which are known to be associated with the identified novel QTLs. These MTAs provide a pathway for improving high yield in rice genotypes through molecular breeding.