Unveiling the Genomic Architecture of Phenotypic Plasticity Using Multiple GWAS Approaches Under Contrasting Conditions of Water Availability: A Model for Barley

Phenotypic plasticity is a key mechanism by which crops adjust to fluctuating environmental conditions, yet its genetic basis under drought remains poorly characterized in barley (<i>Hordeum vulgare</i>). We hypothesized that phenotypic plasticity under drought is controlled by a distinct, trait-specific genetic architecture that can be detected using complementary plasticity metrics and genome-wide association studies (GWAS). Here, we examined data from 1277 spring barley genotypes grown under well-watered and water-limited conditions to quantify plastic responses across two developmental traits (i.e., heading time, and maturity) and seven productivity-related traits (i.e., total dry matter, plant grain yield, grain number, grain weight, harvest index, vegetative dry weight, and grain-filling period). The experimental design, based on contrasting water regimes across a large diversity panel, allowed robust assessment of genotype-by-environment interactions. We combined five complementary plasticity estimators with four independent GWAS approaches to resolve the genomic architecture underlying trait-specific plasticity. Environmental effects dominated variation in yield-related traits, whereas developmental traits remained more genetically determined. The different plasticity metrics captured distinct but partially overlapping response dimensions, and their integration greatly increased the robustness of association signals. A total of 239 high-confidence SNPs obtained for top traits, those associated across metrics and methods, were enriched in coding regions and mapped to genes involved in osmoregulation, carbohydrate metabolism, hormonal pathways, and ion transport. A total of 27 high-confidence SNPs were located in coding regions, showing genotype-specific differences in the magnitude and even direction of phenotypic plasticity. These loci exhibited opposite allelic effects across water regimes, consistent with context-dependent antagonistic pleiotropy. The fact that candidate alleles for the plastic response modulate environmental sensitivity differently highlights that drought resilience arises from environment-contingent genetic architectures. Overall, these results provide a comprehensive framework for dissecting plasticity and identify concrete genomic targets for indirect selection targeting crop resilience with improved performance under increasingly variable water availability.