QTL mapping of starch, protein, and fatty acid traits reveals pleiotropic loci governing rice eating quality in a recombinant inbred lines population

UNLABELLED: Rice grain quality is a complex trait governed by multiple genetic factors. In this study, a high-density genetic map was constructed using a recombinant inbred line (RIL) population derived from a cross between two indica rice varieties, DL208 and ZS97, based on genotyping-by-sequencing. Three categories of grain quality traits, starch composition, storage protein content, and fatty acid composition, were systematically evaluated across two environments (Wuhan and Hainan). A total of 168 QTLs were identified, of which 30 were stably detected across both environments with concordant effect directions. These stable QTLs were further integrated with 6 ECQ-specific QTLs to yield 36 high-confidence QTLs for downstream analysis. Eleven QTL clusters with overlapping genomic regions were identified, suggesting pleiotropic regulation of multiple quality traits. The most prominent cluster on chromosome 6 (0-2.17 Mb) co-localized with the Wx gene and coordinately regulated amylose content, amylopectin content, and eating quality. Backcross introgression line (BIL) validation confirmed the genetic effects of six pleiotropic QTL clusters through pairwise phenotypic comparison. These findings provide a genetic framework for marker-assisted selection and quality improvement in indica rice breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01726-w.