Togo’s Hidden Yam Diversity Revealed by Whole-Genome Sequencing of 321 Accessions

Yams are more than a staple crop in West Africa; they are woven into the cultural fabric of the region, featuring in festivals, marriage customs and ancestral rituals. Yet in Togo, the productivity of this ancient crop is slipping, and the traditional farmer-selected landraces that carry centuries of adaptation are quietly disappearing from fields and village stores. A new study published in BMC Plant Biology offers the most detailed portrait to date of what is at stake. A team led by Hona Sèwanou Elom Kinglo of the Institut Togolais de Recherche Agronomique, working with collaborators at the University of Lomé, Lushan Botanical Garden and CIRAD in France, has assembled, characterized and genetically decoded a national collection of 321 yam accessions spanning six edible species of the genus Dioscorea. The work, funded by CORAF, Togo’s Ministry of Agriculture through the Food Systems Resilience Program, and the French National Research Agency, delivers the first whole-genome diversity resource for the Togolese yam collection and a compact core set designed to safeguard that diversity for future breeding.

The scale of the phenotyping effort alone sets the study apart. The researchers scored their accessions using 121 agro-morphological descriptors, covering everything from emergence timing and stem architecture to leaf shape and tuber characteristics, alongside systematic observations of disease and pest symptoms. The collection was dominated by Dioscorea rotundata, the white Guinea yam that anchors West African yam culture, but it also embraced D. cayenensis, the yellow Guinea yam; D. alata, the water yam of Asian origin; D. dumetorum, the bitter yam; D. esculenta, the lesser yam; and D. bulbifera, the aerial yam whose tubers grow above ground. Across this panel, the phenotypic analyses revealed extensive variation in both quantitative traits, such as yield-related measurements, and qualitative descriptors such as tuber flesh color and shape. Strong differences separated the species from one another, but crucially, the team found substantial diversity hiding within D. rotundata itself, suggesting that Togolese farmers have maintained a remarkable reservoir of variation in their most prized crop.

To peer beneath the visible traits, the researchers resequenced the genomes of 294 accessions. After stringent filtering, they retained 230,053 high-confidence single nucleotide polymorphisms, or SNPs, which served as molecular landmarks scattered across the yam genome. This is the first time the Togolese collection has been examined at such resolution, and the results were striking. A principal component analysis showed that the first two components together explained 88.6 percent of the genetic variance, an unusually clean separation driven primarily by species identity. D. alata and D. dumetorum stood apart as clearly distinct genomic lineages, while D. rotundata and D. cayenensis clustered closely together, a pattern consistent with the long-recognized species complex that links these two Guinea yams and complicates efforts to classify them as fully independent species.

The genomic data also allowed the team to quantify how much genetic variation each species carries. Under a common diploid-calling framework, comparative nucleotide diversity, denoted by the statistic pi, was highest in D. alata at 0.00282 and lowest in D. dumetorum at 0.00053. In practical terms, this means the water yam accessions in the collection harbor roughly five times more sequence-level variation than the bitter yam accessions, a difference that may reflect the contrasting demographic histories of an introduced crop versus a more narrowly cultivated native one. For breeders, such estimates are more than academic bookkeeping; they indicate which parts of the collection are most likely to harbor rare alleles for disease resistance, tuber quality or climate resilience, and which species may require the most urgent conservation attention before their limited diversity slips away entirely.

Because D. rotundata dominates both the collection and Togolese agriculture, the researchers drilled deeper into its internal structure. Hierarchical clustering of the 224 D. rotundata accessions resolved additional substructure within the species, and an ADMIXTURE analysis, a standard tool for detecting ancestry components in genomic data, showed cross-validation error decreasing up to K equals 10, indicating that the white Guinea yam in Togo is not a single homogeneous population but a mosaic of up to ten genetic groups. When the team tested these genetic clusters against the morphological data, they identified significant associations with emergence, stem, leaf and tuber traits. In other words, the invisible genetic partitions carved out by the SNP data correspond to real, measurable differences in how the plants grow and what their tubers look like, evidence that farmer selection and local adaptation have left detectable signatures across the genome.

Perhaps the most intriguing part of the study is the search for the genomic basis of this differentiation. The researchers scanned for regions of the genome that were unusually divergent between the D. rotundata genetic clusters, using Fst, a measure of genetic differentiation between populations. Their scans highlighted 71 regions in the top 0.1 percent of differentiation, with 478 genes located nearby. Functional enrichment analysis of these genes pointed to three compelling categories: dioscorin and other storage proteins, which are the dominant proteins in yam tubers and directly shape nutritional and culinary quality; cytochrome P450 enzymes and associated redox functions, a large enzyme family involved in defense chemistry and stress responses; and sugar transporters governing carbon allocation, the plumbing that determines how photosynthate is partitioned into the harvested tuber. The convergence of these functional themes suggests that the differentiation among Togolese white yam clusters is not random drift but touches genes tied to the very traits farmers care about.

Characterizing diversity is only useful if that diversity can be conserved and exploited, and maintaining hundreds of accessions is expensive for a national program with limited resources. This is where the core collection concept comes in. A core collection is a carefully chosen subset that captures, as efficiently as possible, the genetic breadth of the full panel. Using the Partitioning Around Medoids algorithm, a clustering method that selects representative central individuals from each group, the team derived a core set of 118 accessions, about 40.1 percent of the diversity panel. Quantitative validation showed that this subset retained a large proportion of the variation present in the full collection, both at the molecular level and across the agro-morphological descriptors. For Togo’s genebank and breeding programs, this means that the most essential material can be prioritized for regeneration, distribution and genotyping without sacrificing the raw material needed for future crop improvement.

The implications extend well beyond Togo’s borders. Yam is a crop of enormous importance across West and Central Africa, yet it has historically been under-researched compared with cereals and legumes, partly because of its polyploid complexity, long breeding cycle and vegetative propagation. Datasets like this one, combining deep phenotyping with hundreds of thousands of genome-wide SNPs, provide the raw material for genome-wide association studies, genomic prediction and marker-assisted selection in a crop where such tools remain nascent. The fine-scale structure resolved within D. rotundata could help breeders choose genetically complementary parents for crossing, maximizing heterosis or combining desirable tuber traits, while the differentiated genomic regions flagged by Fst scans offer candidate loci for traits ranging from tuber protein content to stress adaptation.

There is also a conservation urgency underlying the science. Declining yam productivity and the erosion of traditional landraces threaten both food security and genetic-resource conservation in Togo, as the authors note. Every landrace lost represents an irreplaceable combination of alleles shaped by generations of farmer selection in specific microenvironments. By documenting and genotyping this collection now, the researchers have effectively frozen a snapshot of that diversity before it disappears, and the open-access publication of the data means that researchers worldwide can interrogate it. The study stands as a model for other countries in the yam belt, demonstrating that a national collection, even one from a small West African nation, can yield genome-scale insights when paired with modern sequencing and rigorous statistical analysis.

From a field in Togo to a validated core of 118 accessions, the journey described in this study illustrates how classical botany, farmer knowledge and genomics can converge on a single goal: keeping a vital crop’s genetic heritage alive and usable. As climate pressure intensifies and demand for resilient staples grows, the humble yam, long overshadowed in global research, is finally getting the molecular attention it deserves, and Togo’s farmers may be among the first to benefit from what its genome has to say.

Subject of Research: Phenotypic and whole-genome characterization of Togolese yam germplasm and development of a core collection

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

Article References: Kinglo, H. S. E., Ayisah, D. K., Bouka, E. O. C., Nazir, M. F., & Dossa, K. (2026). Phenotypic and genetic characterization of an unexplored yam (Dioscorea spp.) collection from Togo and development of a core collection. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10096-6

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10096-6

Keywords: yam, Dioscorea, genetic diversity, whole-genome resequencing, SNPs, core collection, agro-morphological traits, Togo, plant breeding, germplasm conservation, Dioscorea rotundata, nucleotide diversity