Genome-wide SNP association analysis reveals the genomic signature of local adaptation in natural populations of European beech (Fagus sylvatica L.)

• Site-specific SNP variants reveal distinct patterns of local adaptation in European beech populations across climatic gradients. • Climatic fluctuations and human activities shape the local adaptation signals observed in beech populations. • Results inform adaptive forest management and support targeted conservation and assisted migration strategies. • Broad-scale genomic signatures indicate selection driven by complex climatic variables, with adaptive SNPs involved in both temperature and precipitation responses. • Unmanaged and less-intensively managed forests maintain higher private SNP diversity, emphasizing the role of forest structure and low-impact practices in supporting local adaptation. • Reduced-impact silvicultural approaches may promote the persistence of adaptive alleles, enhancing long-term resilience to climate change. Understanding the dynamics and mechanisms of local adaptation in natural populations provides the basis for predicting responses to environmental changes, including those associated to global climate change. European beech (Fagus sylvatica L.) is one of the most economically and ecologically important deciduous trees in Europe. Nevertheless, little is known about its genomic adaptive diversity and adaptive potential. Genetic differentiation in beech sites associated with environmental adaptation was assessed by genotyping 1384 single nucleotide polymorphisms (SNPs) in candidate genes. The study included 153 beech individuals from 12 populations located in Italy, Slovenia, and Croatia, with diverse bio-geoclimatic conditions. PCA-based and the Fst -based method of differentiation (PCAdapt and LEA) and two different Environmental Association Analysis approaches (Latent Factor Mixed Model and Samβada) were used to identify loci with significant correlations with bioclimatic indicators. The results obtained in this study allowed us to identify signature of regional and local environment adaptation. Specific patterns of local adaptation were observed for each studied population. We identified allelic variants associated with the response to precipitation fluctuations and drought periods during the growing season. Particularly interesting is the observation of differences in the presence and effect of allelic variants among different sites, likely due to adaptation to the local environment and the different silvicultural history of each observed population.