Population structure and diversity of common bean ( Phaseolus vulgaris L.) landraces in the Peruvian Amazon

Common bean ( Phaseolus vulgaris L.) is a globally important legume with significant nutritional and agronomic value. Genetic diversity in Amazonian landraces remains undercharacterized, limiting their utilization in breeding programs. Here we analyzed 647 accessions from the Peruvian Amazon using 18 morphological traits and 23,050 high-quality DArTseq single nucleotide polymorphisms (SNPs). Our results revealed two major genetic groups corresponding to Andean and Mesoamerican gene pools, each subdivided into distinct subgroups, exhibiting high allelic richness and structured diversity. Despite abundant polymorphic loci, observed heterozygosity was low, consistent with the species’ self-pollinating nature. These findings highlight the Peruvian Amazon as a reservoir of unique genetic variation, underscoring the need for integrated in situ and ex situ conservation strategies. This germplasm offers valuable resources for breeding programs targeting tropical adaptation and resilience, contributing to sustainable agriculture and food security.