Genetic Diversity Analysis of African Yam Bean (Sphenostylis stenocarpa Hochst. ex A. Rich) Accessions Using matK Gene Markers

The African yam bean (Sphenostylis stenocarpa (L.)) is an underutilized crop with significant agricultural and nutritional potential. However, limited genetic improvement efforts pose a risk of extinction, underscoring the urgent need for breeding programs. This study investigated the genetic variation of 18 S. stenocarpa accessions from the Genetic Resources Centre at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria, using the matK gene marker. Genomic DNA was extracted and amplified through polymerase chain reaction (PCR), with subsequent sequencing and analysis conducted using ChromasPro, MEGA 6.0.6, DnaSP version 5.1, and CodonCode Aligner. Phylogenetic analysis grouped the accessions into two major clusters, with sub-clusterings reflecting genetic variation. Linear genetic distances ranged from 0.08 to 2.13, with the shortest distance observed between TSs-119 (CAL-12) and TSs-38 (CAL-13), and the largest distance was between TSs-69 (CAL-2) and TSs-439 (CAL-17). DNA polymorphism analysis revealed two polymorphic sites among 54 nucleotide sites, resulting in high haplotype diversity (1.000) and moderate nucleotide diversity (0.396). SNP analysis identified 107 single nucleotide polymorphisms (SNPs), of which 81.31% were nonsynonymous mutations and 18.69% were synonymous. Transversion mutations (74.77%) were more prevalent than transitions (31.82%), indicating significant sequence variability among the accessions. These findings demonstrate substantial genetic differentiation within S. stenocarpa accessions and highlight the potential of the matK gene as a robust marker for genetic diversity studies. The results provide essential insights for future breeding efforts, genetic improvement, and conservation of this underutilized crop.