Genome wide association mapping and haplotype analysis identify genetic loci and candidate genes associated with yield related traits in rice (Oryza sativa L.)

Rice ( Oryza sativa L.) is one of the most important staple crops worldwide, and improving grain yield remains a major objective of rice breeding programs. Yield is a complex quantitative trait influenced by multiple agronomic characteristics, including grain yield per plant (GY), seed setting rate (SSR), plant height (PH), and thousand grain weight (TGW). In this study, a natural population comprising 265 rice accessions was evaluated during two consecutive growing seasons (2022-2023) at one field location, and genome-wide association studies (GWAS) conducted using 4454137 high-quality single nucleotide polymorphisms (SNPs). Best linear unbiased prediction (BLUP) values estimated across the two year-environments were used for association analysis using a mixed linear model (MLM). A total of 102 significant SNPs were identified and consolidated into 20 quantitative trait loci (QTLs), including five associated with GY, four with SSR, ten with PH, and one with TGW. Among them, several loci were co-localized with previously reported genes associated with yield related traits, thereby supporting the reliability of the GWAS results. Candidate gene identification and haplotype analysis further revealed four prioritized genes: LOC_Os09g28230 (GID1L2) for GY, LOC_Os05g09500 for SSR, LOC_Os03g06930 for PH, and LOC_Os02g09170 for TGW. Significant phenotypic differences among haplotypes supported the potential involvement of these genes in regulating the natural trait variation. These findings provide insights into the genetic basis of rice yield related traits and offer genetic resources for future validation and breeding. However, because the present study included only two year-environments at one field location, additional multi-environment validation is required before the broader environmental reproducibility or breeding adaptation.