GWAS of flag leaf primary metabolites uncovers metabolic QTL hubs linked to grain yield stability under drought in field-grown indica rice

A genome-wide association study of 271 indica rice accessions grown under either well-watered or drought-stressed conditions has uncovered metabolic quantitative trait loci (mQTLs) linked to grain yield stability during reproductive-stage drought. The study identified 180 metabolite mQTLs, with 93 unique to drought conditions, 68 to well-watered conditions, and 19 present in both scenarios, suggesting a primary role for genetics in stress response.

Genome-wide association studies of 89 annotated polar metabolites revealed only four marginal QTLs influencing grain yield, with no overlap between these and the mQTLs. Four high-density regions of mQTLs were pinpointed: HDR1-1, HDR1-2, HDR4, and HDR11. The HDR1-2 and HDR4 regions, both activated under drought, were found to be associated with tricarboxylic acid cycle intermediates, amino acids, and polyphenol oxidase, respectively.

Rice accessions possessing favorable haplotypes at both HDR1-2 and HDR4 yielded 21.5% more grains under drought stress compared to those with unfavorable haplotypes. Even accessions with favorable haplotype variants at only one locus demonstrated a significant reduction in yield loss under drought conditions. Haplotype-guided variant detection identified major-impact variants in candidate genes, paving the way for metabolically defined targets in breeding drought-resistant rice varieties.