Genome‐wide association analysis to identify QTLs and candidate genes associated with grain yield and its related traits under low light conditions in rice ( Oryza sativa L.)

Low-light (LL) stress caused by persistent cloud cover during the Kharif season significantly reduces rice (Oryza sativa L.) grain yield (GY) by limiting photosynthesis, impairing assimilate production, and affecting reproductive development. To dissect the genetic basis of LL tolerance, 192 diverse rice genotypes were evaluated across contrasting light environments (LL and normal light under Rabi and Kharif seasons) and genotyped using a high-density 44K single nucleotide polymorphism array. Integrating phenotypic and genomic data enabled a multi-tiered analysis from quantitative trait locus (QTL) discovery to gene identification and haplotype dissection. Genome-wide association analysis identified 305 QTLs associated with GY and 11 related traits, including 148 LL-specific and 32 stable QTLs expressed across both seasons. Forty-two candidate genes were localized within major QTL intervals, and 12 were identified as hub genes based on their key roles in photosynthesis, light perception, hormone signaling, and starch biosynthesis. These included Gn1a, OsPsbS1, OsAGPL2, OsLhcb1, OsAUX1, OsSBDCP1, OsNPF5.16, OsPHYA, OsPHYB, OsGIF1, HY5, and OsYUC11. Expression profiling confirmed stronger induction of OsPHYA (∼2.5-fold) and OsPsbS1 (∼2.8-fold) in LL-tolerant genotypes like Purnendu and Swarnaprabha compared to susceptible lines. Haplotype analysis revealed several superior alleles, such as PHYA-Hap2 and OsPsbS1-Hap3, that were consistently associated with higher spikelet fertility, greater grain number, increased biomass, and improved GY under LL, with top-performing haplotypes enhancing yield by 12%-18%. Genotypes carrying these haplotypes (e.g., Purnendu, Swarnaprabha, and Chamarmani) represent valuable breeding donors. Overall, this study provides the first genome-wide identification of LL-specific haplotypes in rice, together with biologically validated hub genes. These findings offer actionable genomic targets and donor resources for developing LL-resilient, high-yielding cultivars suited to changing climate and light-limited environments.