Assessing Phenotypes, Genetic Diversity, and Population Structure of Shea Germplasm (Vitellaria paradoxa subsp. paradoxa C.F.Gaertn.) from Senegal and Burkina Faso

Vitellaria paradoxa subsp. paradoxa C.F.Gaertn., is one of the most important components of sub-Saharan agroforestry systems, providing to rural communities, especially women, with socio- economic, environmental, and nutritional benefits. Despite its importance, the species is threatened and remains semi-domesticated. To better preserve and improve this resource, the genetic diversity and structure of 88 mother trees originated from Senegal and Burkina Faso were studied by analysing 17 phenotypic traits and 3196 SNP markers. The results revealed similar level of observed heterozygosity (Ho) between the Senegalese and Burkinabe populations (Ho = 0.16), whereas the average number of alleles per population (Na) and the expected heterozygosity (He) ranged from 0.33 to 0.34 and 0.38 to 0.39, respectively, indicating moderate to low genetic diversity. Furthermore, the polymorphic information content ranged from 0.15 for Senegal to 0.25 for Burkina Faso. Both ADMIXTURE and cluster analysis delineated our collection into two groups depending on the origin. The AMOVA showed that the highest fraction of variation was within individual, indicating a very low genetic differentiation (Fst = 0.0006) between population. At the phenotypic level, the G2 cluster representing the Senegalese genepool recorded the highest performance in terms of nut and kernel attributes, cariten and unsaponifiable matters contents, while higher crude fat, Diglyceride, Triglyceride, and Triacylglycerol Mono Stearoyl Olein Stearin contents were observed in the Burkina Faso collection (G1). The present findings on the species’ genetic diversity and genetic structure constitute a good start to strengthen the species tree improvement and conservation programs.