Integrating natural variation through GWAS – genetics of drought and flood tolerance in grass pea reveal independent yet interconnected mechanisms

Grass pea (Lathyrus sativus L.) is a grain legume of increasing importance in the Mediterranean region due to its outstanding tolerance to abiotic stresses such as salinity, heat, drought, and flooding, outperforming many other legume species. Despite established natural phenotypic variation in response to water-related stresses, the genetic basis of this resilience remains poorly understood, hindering precision breeding for single and combined stress tolerance. A genome-wide association study was conducted here to investigate the genetic architecture of water stress responses in grass pea. Previously, phenotypic data, including gas exchange, chlorophyll a fluorescence, photosynthetic pigments, leaf water status, and biomass partitioning traits, were assessed under well-watered, mild drought, and partial submergence conditions across 194 representative grass pea accessions worldwide. The data were associated with 5,651 single nucleotide polymorphisms (SNPs) using linear mixed models under a restricted maximum likelihood framework, incorporating population structure and the newly assembled L0007 genome. A total of 130 unique SNPs associated with at least one trait-treatment combination or with trait variation between stress and control conditions, providing a valuable resource for precision breeding of multi-stress tolerance in grass pea. The loci associated with drought and waterlogging were largely non-overlapping, suggesting distinct genetic bases for the two stress tolerances. However, some common mechanisms, such as redox regulation and carbohydrate metabolism, emerged among the identified candidate genes, highlighting some interconnectedness of biological pathways involved in grass pea responses to water stress. Genotypic-phenotypic data associations suggest that the documented tolerance to water deficit and to waterlogging in grass pea is achieved through independent molecular mechanisms that might nevertheless overlap.