Phenotypic and genetic characterization of an unexplored yam (Dioscorea spp.) collection from Togo and development of a core collection

Abstract

Declining yam productivity and the erosion of traditional landraces threaten food security and genetic-resource conservation in Togo. We characterized 321 yam accessions representing six edible Dioscorea species ( D. rotundata , D. cayenensis , D. alata , D. dumetorum , D. esculenta and D. bulbifera ), dominated by D. rotundata , using 121 agro-morphological descriptors and disease/pest observations, and resequenced 294 accessions yielding 230,053 high-confidence SNPs for population-genomic analyses after filtering. Phenotypic analyses revealed extensive quantitative and qualitative variation, with strong interspecific differences yet substantial within-species diversity in D. rotundata . Genome-wide structure was driven primarily by species identity: the first two principal components explained 88.6% of the genetic variance, clearly separating D. alata and D. dumetorum , whereas D. rotundata and D. cayenensis clustered closely, consistent with their species complex. Under the common diploid-calling framework, comparative nucleotide-diversity estimates were highest in D. alata (π = 0.00282) and lowest in D. dumetorum (π = 0.00053). Hierarchical clustering of the 224 D. rotundata accessions resolved additional substructure, with ADMIXTURE cross-validation decreasing up to K = 10, and cluster-trait tests identified significant associations with emergence, stem, leaf and tuber traits. F st scans among D. rotundata genetic clusters highlighted 71 top 0.1% differentiated regions and 478 nearby genes enriched for dioscorin/storage proteins, cytochrome P450/redox and sugar-transport/carbon-allocation functions. A Partitioning Around Medoids-derived core collection of 118 accessions (40.1%) captured a large proportion of the diversity panel. Together, these analyses provide the first whole-genome diversity resource for the Togolese yam collection, resolve fine-scale diversity within D. rotundata , and deliver a quantitatively validated core set for conservation and breeding.