Genome‐Wide Association Study Identifies Key QTL and Genes for Rice Processing Traits

Abstract

ABSTRACT Rice processing quality, a key driver of consumer acceptance and global market competitiveness, is primarily determined by two critical parameters: brown rice rate (BRR) and milled rice rate (MRR). Despite their significant agricultural importance, the genetic mechanisms underpinning these traits remain poorly understood. This study analysed 447 genetically diverse rice accessions from the 3K Rice Genomes Project across multiple environments. Significant variation in processing traits was observed, with BRR from 73.1% to 79.3% and MRR from 58.3% to 74.3%. Seven quantitative trait loci (QTL) were identified via genome‐wide association studies (GWAS), including four novel loci ( qBRR10 , qBRR10‐1 , qMRR5 and qMRR11‐1 ) and three loci co‐localized with functionally validated genes ( OsGME2 , du3 and OsPK5 ). These results confirm the reliability of the analytical framework. Haplotype‐based stratification revealed statistically significant variations in traits ( p < 0.05) across subpopulations, with distinct geographic clustering patterns identified through cluster analysis. This study enhances the molecular understanding of mechanisms regulating processing quality and delivers specific genetic targets for marker‐assisted breeding, establishing a foundation for developing superior rice cultivars with enhanced processing traits.