Association Mapping of Rice Flag Leaf Primary Metabolism Uncovers Major Multitrait Qtls Related to Yield Performance Under Drought

Abstract

Rice (Oryza sativa) is the primary food for over one-third of the global population, yet its productivity is increasingly threatened by drought. To better understand the metabolic basis of drought tolerance and grain yield, we performed a metabolic profiling on a panel of 271 indica rice accessions grown under well-watered (WW) and water-deficit (WD) field conditions. The WW field remained flooded, while the WD field experienced 14 days without irrigation at 50% flowering, followed by re-watering until maturity. Flag leaf samples were analyzed using untargeted gas chromatography-mass spectrometry (GC-MS) metabolomics and a total of 89 primary metabolites were annotated and quantified. The rice accessions were genotyped via genotype-by-sequencing (GBS), generating a 47K SNP map available for genome-wide association studies (GWAS). We identified 184 QTLs associated with the variation in the metabolite values: 114 under WD, 70 under WW, and 19 shared across conditions. Four high-density regions (HDRs), each harboring ≥4 metabolite QTLs, were found on chromosomes 1, 4, and 11. Principal component 1 (PC1) of each HDR-associated metabolites correlated strongly with grain yield. Fine mapping using a 1.5 million SNP map revealed 35 candidate genes within HDRs, including promising targets such as IAAS (Os01t0785400), NSP1 (Os01t0784900), proteases (Os04t0477900, Os04t0479800), and CYPs (Os04t0480650, Os04t0480700). These genes and HDRs represent valuable candidates for breeding drought-resilient, high-yielding rice varieties.