S02 - Session O6 - Uncovering the genetic diversity and population structure of yam (Dioscorea spp.) core collection using DArTseq SNP in IITA genebank

Authors: Rajneesh Paliwal *, Michael Abberton, Badara Gueye, Benjamin Faloye

Yam ( Dioscorea spp.) is a widely cultivated edible starchy tuber food crop for millions of people in sub-Saharan Africa (SSA) by small-scale farmers. West Africa produces over 90% of yam world production. Plant genetic resources, especially landraces and wild relatives, are crucial resources to conserve natural genetic diversity and provide a source of novel climate-adaptive traits essential for sustainable crop improvement and future food security. Knowledge of detailed genetic diversity is a key pillar for crop improvement programs. The Genetic Resources Center (GRC) of the International Institute of Tropical Agriculture (IITA), based in Ibadan, Nigeria, conserves an international collection of 5839 germplasm of nine different yam species, mainly landraces of D. rotundata and D. alata . A set of 947 accessions of nine different yam species, including yam core collection (812 accessions) and wild relatives originating from 12 African countries, were used to genotype using DArTseq genotype-by-sequencing (GBS), a cost-effective next-generation sequencing method. The DArTseq-GBS data, derived from 947 yam accessions of IITA genebank, generated 80K SNPs across the genome. In the present study, the genetic diversity and population structure of the IITA yam core collection was analyzed with high-quality 48K SNPs. The results of genetic diversity showed a wide variation both within and between the species. Results from neighbour-joining cluster analysis and principal component analysis were consistent in diverse yam core collection. The phylogenetic relationship shows the correspondence of accessions with their different species information, and all the wild-relative species were clustered separately from D. alata and D. rotundata . The structure analysis showed six subpopulations (K=6) among the yam accessions. These results will be beneficial for selecting appropriate landrace/wild-relative to develop climate-resilient yam varieties and improve germplasm conservation methods.