Linking population structure, environment, and functional traits – towards an ecological genomics approach in common vetch (Vicia sativa)

How does intraspecific genetic diversity shape adaptive traits and ecological resilience across contrasting environments? Vicia sativa, a widespread nitrogen-fixing legume harboring untapped genetic variation relevant to adaptation across contrasting climates, provides a valuable model to address this question.

We analyzed 289 accessions from diverse Mediterranean regions via genotyping-by-sequencing and evaluated 17 ecologically relevant traits, including phenology, biomass allocation, and stress tolerance. Six traits were assessed in multi-site common garden experiments, revealing strong environmental effects and plastic responses under contrasting conditions.

Population structure inferred from 18K linkage-disequilibrium–pruned SNPs identified ten genetic clusters, partly inconsistent with traditional botanical classifications, highlighting complex patterns of admixture and suggesting historical gene flow and intricate population differentiation. Associations between admixture components and key environmental variables further indicated climate- and edaphic-driven differentiation across the species’ range.

Genome-wide association analyses using 320K SNPs detected 654 variants linked to adaptive traits, including 106 stable across environments. Notable candidates included variants in genes affecting flowering time and pleiotropic loci influencing multiple traits within a genomic region enriched for stress-response genes on chromosome 2.

Together, these results clarify the genetic architecture of adaptive traits in Vicia sativa, reveal soil- and climate-related population differentiation, and provide a framework for studying functional biodiversity and ecological resilience under environmental change.