Genome-Wide SNP Profiling Reveals Fine-scale Population Structure in Vitellaria paradoxa spp. paradoxa across the Guineo-Sahelian Eco-gradient

Abstract

Evaluating genetic diversity and population structure is important for understanding adaptation, evolution, and species conservation, especially under changing environments and disease conditions. Unfortunately, shea tree (Vitellaria paradoxa spp paradoxa) conservation strategies in Central Africa are rarely supported by molecular genetic studies. This study applies genotyping-by-sequencing (GBS) to evaluate genetic diversity and population structure in Shea trees across three West and Central African countries, focusing on conservation implications. We generated 12,771 high-quality filtered single nucleotide polymorphism (SNP) markers in the studied population. Within-population, expected heterozygosity (He) was low in all sampled populations, ranging from 0.05 to 0.08, indicating poor genetic diversity. Moreover, He of farmland trees was closer to savannah ones. Population structure analysis revealed three main clusters aligning with geographic regions, suggesting limited gene flow and distinct adaptive responses within each of the studied populations. Additionally, the molecular variance analysis indicated that most genetic variation in these samples was distributed within the populations (74.9%). In contrast to earlier studies conducted in Cameroon using microsatellite markers, which detected no population structure, this GBS study is the first to clearly distinguish admixed groups in western and northern Cameroon. Our findings offer a concrete framework for prioritizing conservation units in domestication programs.