Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

BACKGROUND: African Yam Bean (AYB) is an understudied and underutilized tuberous legume of tropical West and Central African origin. In these geographical regions, both seeds and tubers of AYB are important components of people’s diets and a potential target as a nutritional security crop. The understanding of the genetic diversity among AYB accessions is thus an important component for both conservation and potential breeding programs. RESULTS: In this study, 93 AYB accessions were obtained from the International Institute of Tropical Agriculture (IITA) genebank and genotyped using 3722 SNP markers based on Restriction site-Associated DNA sequencing (RAD-Seq). Genetic data was analysed using multiple clustering methods for better understanding the distribution of genetic diversity across the population. Substantial genetic variability was observed in the present set of AYB accessions and different methodologies demonstrated that these accessions are divided into three to four main groups. The accessions were also analysed for important agronomic traits and successfully associated with their genetic clusters where great majority of accessions shared a similar phenotype. CONCLUSIONS: To our knowledge, this is the first study on predicting genotypic-phenotypic diversity relationship analysis in AYB. From a breeding perspective, we were able to identify specific diverse groups with precise phenotype such as seed or both seed and tuber yield purpose accessions. These results provide novel and important insights to support the utilization of this germplasm in AYB breeding programs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-03302-0.