Decoding rice starch viscosity via GWAS reveals novel loci for eating and cooking quality

The Rapid Viscosity Analyzer (RVA) has emerged as a useful tool for comprehensive and objective evaluation of rice eating and cooking quality (ECQ), offering precise quantification of starch viscosity properties during simulated cooking processes. To dissect the genetic basis of ECQ, we performed genome-wide association studies (GWAS) on 439 genetically diverse rice accessions across two environments and identified 10 robust quantitative trait loci (QTLs) associated with RVA profile parameters. Six loci (qRVA-1.1, qRVA-1.2, qRVA-3, qRVA-5, qRVA-8 and qRVA-11) were linked to six RVA profile properties, displaying their importances in the regulation of RVA parameters. Notably, qRVA-6.1 co-localizes with Wx locus, a canonical regulator of amylose content (AC) and gel consistency (GC), and influenced breakdown value (BDV), cold paste viscosity (CPV), consistence value (CSV), hot paste viscosity (HPV) and setback value (SBV). Two novel loci, qRVA-2 and qRVA-10 were associated with retrogradation dynamics (SBV/CSV) and starch stability (BDV/CPV), respectively. Through haplotype-based analysis, we prioritized six candidate genes (LOC_Os01g65780, LOC_Os01g65880, LOC_Os02g53620, LOC_Os03g40440, LOC_Os10g34520 and LOC_Os11g01580) harboring nonsynonymous mutations or structural variations significantly altered RVA profiles, highlighting their potential as key regulators of starch viscosity properties. By integrating RVA phenotyping with genetic mapping, this study provides novel insights into the molecular mechanisms underlying ECQ and delivers valuable QTLs and candidate genes for breeding rice varieties with superior culinary characteristics.