• african crops
• climate change adaptation
• genome-environment association
• genomic diversity

The climate crisis presents major challenges for agricultural systems of sub-Saharan Africa. The continent’s rich diversity of crop varieties holds significant potential for enhancing climate resilience of farming and ensuring food security. In this study, we explored genomic diversity of five African crop species—Eragrostis tef (teff), Vigna unguiculata (cowpea), Hordeum vulgare (barley), Oryza sativa (rice), and Sorghum bicolor (sorghum) — across eight African countries. We used population-scale passport information, analyzing the climatic diversity at sampling sites of 2,470 georeferenced samples.
Although the structure of our dataset indicates a significant risk of sampling bias, principal component analysis (PCA) and clustering analyses still revealed intraspecific crop diversity within the same sampling area. Genome–environment association (GEA) analyses were performed on five species with high-quality genotyping data, identifying candidate loci linked to major abiotic stressors such as prolonged drought, temperature extremes, and soil nutrient limitations. Notable adaptation signals included nocturnal heat stress response in E. tef and H. vulgare, alleles associated with drought and soil nitrogen content in V. unguiculata, and evidence of edaphic adaptation in S. bicolor and O. sativa.