Climate adaptation in Populus trichocarpa: key adaptive loci identified for stomata and leaf traits

Summary We investigated adaptive genetic variation in Populus trichocarpa , a potential biofuel feedstock crop, to better understand how physiological traits may influence tolerance to water limitation. Our study focused on leaf and stomatal traits, given their roles in plant–water relations and adaptation. Using a diversity panel of over 1300 genotypes, we measured 14 leaf and stomatal traits under control (well‐watered) and drought (water‐limited) conditions. We conducted genome‐wide association studies (GWAS), climate association analyses, and transcriptome (RNA‐seq) profiling to identify genetic loci associated with phenotypic variation and adaptation. Stomatal traits, including size and density, were correlated with the climate of origin, with genotypes from more arid regions tending to have smaller but denser stomata. GWAS identified multiple loci associated with trait variation, including a major‐effect region on chromosome 10 linked to stomatal size and abaxial contact angle. This locus overlapped with a tandem array of 3‐ketoacyl‐CoA synthase (KCS) genes and showed strong allele–climate and gene expression associations. Our findings reveal genetic and phenotypic variation consistent with local adaptation and suggest that future climates may favor alleles associated with smaller stomata, particularly under increasing aridity. This work provides insights into climate adaptation and breeding strategies for resilience in perennial crops.