Exploring the genetic diversity of common bean germplasm: insights into Andean gene pool variability

Abstract

Common bean (Phaseolus vulgaris) is among the most widely consumed legumes globally, with Brazil playing a crucial role in preserving and expanding its existing genetic diversity. This study aimed to characterize a subset of 863 common bean accessions from Brazil's Gene Banks, mainly of Andean origin. A germplasm collection was genotyped with 4275 SNPs using the EMBRAPA Multispecies 65KChip. Population structure analysis revealed two main groups: Andean (n = 558) and Middle American (n = 267), along with 38 admixed accessions. Andean group exhibited lower gene diversity (GD = 0.086), and allelic richness (A_R = 1.83) compared to the Middle American group (GD = 0.270, A_R = 1.98). Brazilian landraces in the Andean and Middle American groups showed potentially lower overall diversity, emphasizing the need for conservation efforts to preserve these genetic resources. The Andean Brazilian core collection (n = 221; GD = 0.095) encompasses the active collection diversity evaluated (n = 337; GD = 0.093). A total of 26 SNPs potentially under selection, mainly associated with plant development and defense, were identified. Georeferencing landraces using climate maps identified potentially valuable varieties adapted to drought (e.g., BGF0011779, BGF0012528, BGF0013826) and high temperatures and low-fertility soils (e.g., BGF0016128, BGF0013871), highlighting their relevance for conservation and sustainable use in breeding programs. Accessions' photographs showcased a wide range of morphological diversity, colors, types, shapes, and sizes of beans. Our findings reveal a significant genetic diversity among common bean germplasm, offering practical breeding opportunities and enhancing the value of gene bank collections. Certain landraces show potential for adapting to challenging climatic conditions, making them promising subjects for further adaptation studies.