Population genomic diversity and regional structure of lima bean ( Phaseolus lunatus L.) germplasm in Brazil
Josieli Lima da Silva, Ana Flávia Francisconi, João Victor da Silva Rabelo‐Araujo, Caroline Bertocco Garcia, Gabriela Corrêa Morais, Gérson do Nascimento Costa Ferreira, Vanessa Gomes de Moura, José Baldin Pinheiro, Maria Imaculada Zucchi, Marilia Lobo Burle, Verônica Brito da Silva, Gabriel Viana Ferraz, María Isabel Chacón Sánchez, Regina Lucia Ferreira Gomes, Marcones Ferreira Costa, Ângela Celis de Almeida LopesAbstract
Lima bean ( Phaseolus lunatus L.) is a crop of substantial social and economic importance, particularly in Brazilian smallholder agriculture. However, key knowledge gaps remain regarding the genomic diversity and population structure of the germplasm cultivated in Brazil. Here, we characterised 46 representative Brazilian accessions using single nucleotide polymorphism markers generated by genotyping‐by‐sequencing. The results revealed moderate genomic diversity, relatively high inbreeding and a clear pattern of regional population structure. The Southeast and Northeast populations exhibited the greatest allelic richness, while the South region contained the highest number of private alleles, highlighting distinct genetic resources. Population structure and clustering analyses identified well‐defined regional subgroups, consistent with historical dispersal routes. Regional differentiation shows that the genomic diversity of lima bean in Brazil is both heterogeneous and moderately structured. From an applied perspective, these findings support breeding strategies that combine Northeastern accessions with the unique alleles identified in the South. More broadly, this study highlights the value of expanded genomic analyses to clarify the species' evolutionary history and to guide the sustainable use of Brazilian germplasm.