Yam genetic diversity in Sub-Saharan Africa: implications for conservation and breeding

Yam (Dioscorea spp.) encompasses diverse species, including several staple food crops, of which a few were domesticated on the African continent. This study assessed yam genetic diversity in Sub-Saharan Africa (SSA) to inform breeding and conservation initiatives. A diverse collection of 1,247 yam accessions representing six species (D. rotundata, D. alata, D. praehensilis, D. bulbifera, D. cayenensis, and D. dumetorum) sourced from six African countries (Benin, Côte d'Ivoire, Democratic Republic of Congo, Ghana, Nigeria, and Uganda) was used in this study. Genetic diversity was assessed using 7,648 single-nucleotide polymorphism (SNP) markers, selected from previously sequenced datasets between the Consultative Group on International Agricultural Research (CGIAR) and National Agricultural Research and Extension Systems (NARES) collaboration. Findings showed a substantial inter- and intra-specific variation in African yam germplasm, with observed heterozygosity ranging from 0.165 to 0.464 and an average polymorphic information content (PIC) of 0.324 across populations. Population structure was assessed using ADMIXTURE (with cross-validation error for optimal K), DAPC (with BIC for K), and an IBS-based Neighbor-Joining (NJ) tree. Analysis of molecular variance (AMOVA) indicated moderate differentiation among countries (FST = 0.07), and higher differentiation among species (average FST = 0.14). Clustering patterns and phylogenetic analysis revealed the presence of evolutionary relationships among D. cayenensis, D. praehensilis, and D. rotundata, providing insights into D. rotundata domestication history in West Africa. These findings enhance our understanding of genetic relationships within the Dioscorea genus.