Population genomics of Acacia senegal (L.) Willd: adaptive variation in its natural range in Niger

Abstract Acacia senegal (L.) Willd. is a widespread dryland tree valued for its ecological roles and economic significance in gum Arabic production. In Niger, the species spans a sharp east–west environmental gradient across three major basins, varying in rainfall and temperature. To assess how environmental factors shape genetic structure and local adaptation, we applied a genotyping-by-sequencing (GBS) approach to 81 individuals sampled from natural populations across the western, central, and eastern regions. We found a low differentiation within basins but higher divergence between western and eastern populations. We identified 162 candidate SNPs showing signature of selection, of which two (SNP1282, SNP3577) were consistently detected across the three different methods used. These environmental association analyses revealed significant correlations between allele frequencies, annual precipitation and maximum temperature, suggesting divergent selection pressures across the gradient. The distinctiveness of eastern populations, combined with their exposure to arid conditions, highlights their importance for conservation. These findings provide information into climate-driven adaptation in A. senegal and support targeted management of its genetic resources under projected environmental change.