Authors: Kaycie A Melville, Ashley N Egan, Yu Ya Liang
Mentors: Ashley N. Egan
Insitution: Utah Valley University
Phaseolus vulgaris (common bean) and P. lunatus (lima bean) provide protein and nutrition for millions of people across the globe. Native to the New World, these cultivated species present unique histories of multiple and independent domestications in Mesoamerica and the Andes. Brazil is the leading producer globally of these beans. With both wild and cultivated landraces present, Brazil may act as a secondary center of domestication for these two economically significant leguminous crops. Brazil's indigenous populations’ cultivation efforts may include both wild and cultivated germplasm, potentially contributing to the continued domestication of these crops to create novel shapes, sizes, and colors that are grown and hand-selected by the natives in these regions. To investigate Brazil as a secondary domestication center of beans, this research addresses several key questions: Are signals of past and current domestication processes discernible in current Brazilian cultivars of these species? Can we unravel the relationships between these Brazilian crops and their primary centers of domestication? What genetic differences are underpinning domestication? How diverse are Brazilian cultivars? How do they relate to wild and related material and species? This work focuses on 48 accessions of P. lunatus and P. vulgaris from Brazil, including wild material and two accessions from two related species, P. polystachios and P. filiformis from North America. Whole genomes were resequenced using Illumina sequencing and compared against the published genome of Phaseolus vulgaris to identify SNPs in each accession. Whole chloroplast genomes were also assembled and compared. Phylogenetic analyses, network analyses, population structure, and tests for neutral and positively selected mutations were conducted, revealing distinct clades for both P. vulgaris and P. lunatus with clear links to their Andean and Mesoamerican origins. Genetic diversity was assessed both within (cultivated vs wild) and between P. vulgaris and P. lunatus, demonstrating significant variations, not only between species but also within each species, suggesting the influence of diverse selection pressures and local adaptation during the domestication process. McDonald-Kreitman tests analyze and locate possible domestication genes from the library of SNP’s between outgroups (Phaseolus filiformis and Phaseolus polystachios) and between species. Overall, this research advances our understanding of the intricate process of domestication in P. vulgaris and P. lunatus, highlighting potential ongoing domestication in Brazilian cultivars, unraveling their genetic relationships, and shedding light on the complex interplay of genes that underpin domestication and diversity. These findings contribute to the broader understanding of crop evolution and have practical implications for crop improvement and conservation.