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Background  Yams ( Dioscorea  spp.) are economically important food for millions of people in the humid and sub-humid tropics.  Dioscorea dumetorum  (Kunth) is the most nutritious among the eight-yam species, commonly grown and consumed in West and Central Africa. Despite these qualities, the storage ability of  D. dumetorum  is restricted by severe postharvest hardening of the tubers that can be addressed through concerted breeding efforts. The first step of any breeding program is bound to the study of genetic diversity. In this study, we used the Genotyping-By-Sequencing of Single Nucleotide Polymorphism (GBS-SNP) to investigate the genetic diversity and population structure of 44 accessions of  D. dumetorum  in Cameroon. Ploidy was inferred using flow cytometry and gbs2ploidy.    Results  We obtained on average 6371 loci having at least information for 75% accessions. Based on 6457 unlinked SNPs, our results demonstrate that  D. dumetorum  is structured into four populations. We clearly identified, a western/north-western, a western, and south-western populations, suggesting that altitude and farmers-consumers preference are the decisive factors for differential adaptation and separation of these populations. Bayesian and neighbor-joining clustering detected the highest genetic variability in  D. dumetorum  accessions from the south-western region. This variation is likely due to larger breeding efforts in the region as shown by gene flow between  D. dumetorum  accessions from the south-western region inferred by maximum likelihood. Ploidy analysis revealed diploid and triploid levels in  D. dumetorum  accessions with mostly diploid accessions (77%). Male and female accessions were mostly triploid (75%) and diploid (69%), respectively. The 1C genome size values of  D. dumetorum  accessions were on average 0.333 ± 0.009 pg and 0.519 ± 0.004 pg for diploids and triploids, respectively.    Conclusions  Germplasm characterization, population structure and ploidy are an essential basic information in a breeding program as well as for conservation of intraspecific diversity. Thus, results obtained in this study provide valuable information for the improvement and conservation of  D. dumetorum . Moreover, GBS appears as an efficient powerful tool to detect intraspecific variation.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1593-x) contains supplementary material, which is available to authorized users.

Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS)