Flag leaf serves as an essential source of assimilates during grain filling, thereby contributing to grain yield up to 48%. Thus, high-throughput phenotyping of flag leaves is crucial to determine their physiological and genetic basis of yield formation and drought adaptation. Here, we utilized 200 wheat cultivars to identify droughtadaptive loci underlying candidate genes associated with flag leaf biomass and photosynthesis-related traits using a genome-wide association study (GWAS). GWAS revealed 21 significant marker-trait associations for key photosynthetic traits in response to drought stress. Analysis of linkage disequilibrium (LD) in these SNPs intervals discovered 103 significant SNPs that established distinct LD blocks containing a total of 382 candidate genes putatively involved in physiological processes, including photosynthesis and water responses. Further, in silico transcript analysis identified two candidate genes in locus AX-580365925 on chromosome 4B, those were found to be highly expressed under drought and associated with protontransporting ATP synthase activity and stress response pathways. Accordingly, we identified significant allelic haplotype differences on this same locus. The tolerant haplotype (higher chlorophyll content under drought) representing major allele was more abundant and stably increased photosynthetic efficiency and yield under drought scenarios. Collectively, this study offers new adaptive loci and beneficial alleles to reshape the flag leaf physiological and associated photosynthetic components for better yield and sustainability to water-deficit stress.

Background The frequency of droughts has dramatically increased over the last 50 years, causing yield declines in cereals, including wheat. Crop varieties with efficient root systems show great potential for plant adaptation to drought stress, however; genetic control of root systems in wheat under field conditions is not yet well understood. Results Natural variation in root architecture plasticity (phenotypic alteration due to changing environments) was dissected under field-based control (well-irrigated) and drought (rain-out shelter) conditions by a genome-wide association study using 200 diverse wheat cultivars. Our results revealed root architecture and plasticity traits were differentially responded to drought stress. A total of 25 marker-trait associations (MTAs) underlying natural variations in root architectural plasticity were identified in response to drought stress. They were abundantly distributed on chromosomes 1 A, 1B, 2 A, 2B, 3 A, 3B, 4B, 5 A, 5D, 7 A and 7B of the wheat genome. Gene ontology annotation showed that many candidate genes associated with plasticity were involved in water-transport and water channel activity, cellular response to water deprivation, scavenging reactive oxygen species, root growth and development and hormone-activated signaling pathway-transmembrane transport, indicating their response to drought stress. Further, in silico transcript abundance analysis demonstrated that root plasticity-associated candidate genes were highly expressed in roots across different root growth stages and under drought treatments. Conclusion Our results suggest that root phenotypic plasticity is highly quantitative, and the corresponding loci are associated with drought stress that may provide novel ways to enable root trait breeding.