Phenotypic and genetic bases of variable drought stress response in a widely adapted allotetraploid species

Abstract Premise Understanding how plants adapt to spatial and temporal variation in water availability is central to predicting their responses to climate change. However, the genetic and physiological mechanisms underlying local adaptation to drought remain poorly understood, particularly in polyploid species. We investigated these mechanisms in Trifolium repens (white clover), a recently evolved allotetraploid characterized by broad ecological tolerance, global distribution, and extensive variation in life‐history traits. Methods We evaluated drought response in genotypes from three climatically distinct North American locations (Minnesota, Missouri, and Florida), focusing on fitness‐related traits and subgenomic gene expression. We used a quantitative trait locus (QTL) mapping population derived from Minnesota and Florida genotypes to characterize the genetic architecture of drought‐divergent traits. Results Genotypes showed divergent drought responses in biomass allocation, flowering time, and photosynthesis. Transcriptomic data revealed genotype‐specific expression responses, with parallel regulation across homeologous gene pairs and equal subgenomic contributions. Variability in cyanogenesis, a chemical defense, had no detectable effect on fitness‐related traits. QTL analysis identified a major locus on Chromosome 4 with antagonistic pleiotropy across environments, consistent with local adaptation; this QTL partially overlaps genomic regions previously associated with aridity gradients in a landscape genomics analysis. Conclusions Adaptive divergence in white clover under drought reflects differences in life history, energy allocation, and physiology. Parallel homeolog regulation underscores balanced subgenomic expression in this young polyploid. A key QTL with environment‐dependent effects provides evidence for the genetic basis of local adaptation. These findings highlight how polyploid species can evolve context‐dependent strategies to cope with climate‐induced stresses.