Physiological signatures but no evidence for universal genomic predictors of extreme drought responses in European beech

Following a severe 2018 drought affecting much of Europe, European beech (Fagus sylvatica) exhibited patchy canopy dieback. To investigate the drivers of this mortality, we used a paired case-control design across Swiss forests, integrating phenotypic assessments and genomic analyses. Phenotypically, crown transparency and discoloration were used to classify tree damage state, while several other characteristics were measured to evaluate whether paired, neighboring damaged and undamaged trees were otherwise comparable, and to identify physiological stress signatures. Elevated leaf calcium content and red edge reflectance in dried leaves emerged as robust indicators of physiological stress. Genomic association models using reference-based SNP markers and reference-free k-mers were heavily confounded by micro-environmental variance and local population stratification even within our geographically limited study region. Our cross-validated genomic outliers showed no spatial overlap with predictive drought-associated loci previously identified in an independent German cohort. These findings indicate that drought survival in European beech is not governed by a universal set of major-effect alleles. Instead, tree performance appears highly context-dependent, likely shaped by micro-environmental heterogeneity and phenotypic condition. However, our results do not exclude polygenic drought responses involving multiple small-effect loci.