Assessment of genetic diversity of six Nigerian states’ African yam bean ( Sphenostylis stenocarpa (Hochst ex. A. Rich) Harms) landraces using agronomic traits and DArTseq‐SNP markers

Abstract African yam bean (AYB), or sphenostylis stenocarpa (Hochst. Ex. A. Rich) Harms, is a leguminous crop with potential to enhance food security and agricultural sustainability. A total of one hundred Africa yam bean accessions from six Nigeria states were planted for agronomic evaluation. Out of 100 samples, ninety‐four accessions were genotyped using DArTseq approach and generated 2527 high‐quality single‐nucleotide polymorphism (SNP) polymorphic markers. The QC‐filtered markers had a call rate ≥0.80, marker reproducibility ≥0.95, minor allele frequency ≤0.01, and missing data ≤20%. The expected heterozygosity varied from 0.007 to 0.201 while the observed heterozygosity varied from 0.015 to 0.121. The overall inbreeding coefficient (FIS) was 0.623. The results revealed diversity within the AYB accessions for both the agronomic trait and SNP markers. Analysis of variance revealed significant variations ( p ≤ 0.05) in traits such as total seed weight, days to first flower, and pod length (PODL), suggesting genetic diversity within the population. Tropical Sphenostylis stenocarpa (TSs) accessions TSs‐513, TSs‐560, TSs‐526, TSs‐571, TSs‐581, TSs‐601, TSs‐602, and TSs‐582 exhibited excellent performance for some traits such as number of seeds per pod, PODL, and days to first flowering. Neighbor‐joining cluster analysis grouped the AYB population into four main clusters, where majority of Abia, Enugu, and Cross River states AYB accessions were grouped together with their origin. Population structure analysis results were consistent with the cluster analysis. The comprehensive view of genetic diversity and population structure analysis, highlights both genetic distinctness between geographical origin and relationship among accessions. The results of genetic diversity and population structure analysis confirmed that there is substantial genetic variation among the AYB accessions. These results provide valuable insights for AYB breeding in sub‐Saharan Africa, enabling the selection of diverse parental lines, maintaining genetic variability, and enhancing adaptability. Understanding genetic structure enables efficient germplasm conservation and the development of improved, resilient breeding populations.