Unveiling hidden genetic resources: genomic insights for crop improvement in underutilized and cultivated African crops

Abstract Bambara groundnut (Vigna subterranea) and snake tomato (Trichosanthes cucumerina) are underutilized African crops valued for their nutritional quality and resilience to harsh environments. Despite their agronomic importance, molecular data on key stress-related genes remain limited, constraining their integration into modern breeding programs. Previously validated primers targeting genes associated with drought tolerance (NAC), disease resistance (Ph-3, Ty-3), starch biosynthesis (CYP79D1), and phytic acid metabolism (MIPS) were evaluated through PCR and Sanger sequencing. Tomato and cassava served as positive controls and phylogenetic anchors. Amplicons were analyzed using standard sequence-quality workflows, multiple sequence alignment, and phylogenetic reconstruction. Most primer pairs produced clear, single amplicons in both crops, with snake tomato exhibiting particularly strong cross-species amplification. Sequencing confirmed locus specificity and revealed conserved regions enabling primer transferability. Phylogenetic analyses grouped Bambara groundnut and snake tomato sequences with their expected legume and cucurbit clades, validating the evolutionary placement of the amplified loci. These outcomes demonstrate that the targeted genes are conserved across species and suitable for molecular characterization. The successful amplification and sequencing of key stress-related genes provide foundational genomic information for Bambara groundnut and snake tomato. These results confirm that conserved gene regions can be exploited for molecular marker development, comparative genomics, and future breeding programs aimed at enhancing stress resilience in underutilized crops.