Hidden Reservoirs of Genetic Diversity in Common Bean: Wild Populations and Local Landraces Reveal the Evolutionary Legacy of Domestication in Guerrero, Mexico

The common bean (Phaseolus vulgaris L.) is a key crop for food security in Mexico, yet its genetic resources remain poorly characterized in small farmers’ agricultural fields where landraces are actively conserved. Using genotyping-by-sequencing, we assessed genetic diversity, population structure, and gene flow among wild populations (W), traditional landraces (L), and commercial varieties exchanged through local markets (M). We analyzed 73 individuals and 11,701 SNPs. Population genetic analyses revealed moderate differentiation between wild populations and cultivated forms (landraces and markets) (FstL-W = 0.249 and FstM-W = 0.20), whereas landraces and market varieties were weakly differentiated (FstL-M = 0.024). Wild populations exhibited the highest genetic diversity, with the greatest expected heterozygosity (HeW = 0.25) but also the highest (FisW = 0.339). Cultivated forms showed similar expected heterozygosity between them (HeL = 0.228; HeM = 0.233), which was only slightly lower than that estimated in wild populations, although levels exceeded those previously reported for Guerrero and other Mexican regions. Gene flow was limited between wild and cultivated forms but high between landraces and market varieties (NmL-M = 10.15), highlighting the role of seed exchange networks in maintaining connectivity and diversity. These findings underscore the importance of conserving wild populations, landraces, and traditional seed systems to strengthen crop resilience and food security under climate change.