[en] Shea tree (Vitellaria paradoxa) is a well-known carbon sink in Africa that requires a sustainable conservation of its gene pool and breeding. Shea has a substantial economic profits for sub-Saharan Africa countries and plays a crucial role in women autonomy. However, shea resources are under threat from human activities and climate change. This study investigates the genetic diversity, population structure, and fatty acid (FA) composition of superior shea trees in Côte d’Ivoire to support sustainable conservation and breeding programs. DArTseq technology identified 7,559 high-quality single nucleotide polymorphisms (SNPs) in 333 shea tree genotypes. Genetic diversity values (HE = 0.26; PIC = 0.24) suggest moderate diversity, and population structure analysis clustered these genotypes into three genetic groups. Analysis of molecular variance (AMOVA) revealed a low genetic differentiation (FST = 0.004), with significant gene flow (Nm = 59.02) among groups. A core set of 100 shea trees was proposed. In addition, a genome-wide association study (GWAS) on 122 trees identified 47 significant quantitative trait nucleotides (QTNs) associated with fat content (FC) and FA composition. Shea butter content ranged from 36% to 58%, with a notable correlation between oleic and stearic acids (-0.98). Pathway analysis highlighted 24 candidate genes involved in FA biosynthesis, with superior alleles for high FC more prevalent in high-fat trees (47.1%) compared to low-fat trees (14.3%). This research offers critical insights into the genetic factors influencing fat composition in shea trees, enhancing potential for molecular breeding programs aimed at improving high-fat cultivars and supporting sustainable conservation efforts.
