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Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity?

Gepts, Paul1; Kuzay, Saarah1; Hamilton, Paige1

Published Jan 17, 2019; Updated Jan 16, 2020 on Dryad. https://doi.org/10.25338/B8KP45

Data files

Jan 17, 2019 version files 7.49 MB
Jan 16, 2020 version files 45.23 MB

Abstract

Core collections are envisioned to be a representative subset of larger germplasm collections. They were introduced to facilitate the characterization and use of these germplasm collections. The common bean (Phaseolus vulgaris) core collection of the USDA Western Regional Plant Introduction Station was one of the first ones to be established in the early 1990s. Here, we evaluate the representativity of this common bean collection in light of the availability of a SNP platform and new information about genetic diversity of the species, including phaseolin and seed type data. SNP diversity was studied with a combination of STRUCTURE, Principal Coordinate Analysis (PCoA), and Neighbor-Joining Analysis (NJA). STRUCTURE analyses were conducted for K = 3 and K =7, based on the ad hoc statistic ΔK. The K = 3 analysis recognized the split between Andean and Mesoamerican domesticates and the subdivision of the Mesoamerican domesticates into high- (Durango/Jalisco) and low-altitude (Mesoamerica) ecogeographic races. The K = 7 analysis further subdivided the Andean group identified for K = 3, as well as the high-altitude group from the Mesoamerican gene pool. It also identified smaller groups consisting of Mesoamerican wild beans. PCoA and NJA confirmed the STRUCTURE results and highlighted the existence of presumed hybridization among groups. Our results suggest that this core collection should be updated by adding domesticated categories, developing a separate wild common bean core collection, and developing cores for specific purposes.Core collections are envisioned to be a representative subset of larger germplasm collections. They were introduced to facilitate the characterization and use of these germplasm collections. The common bean (Phaseolus vulgaris) core collection of the USDA Western Regional Plant Introduction Station was one of the first ones to be established in the early 1990s. Here, we evaluate the representativity of this common bean collection in light of the availability of a SNP platform and new information about genetic diversity of the species, including phaseolin and seed type data. SNP diversity was studied with a combination of STRUCTURE, Principal Coordinate Analysis (PCoA), and Neighbor-Joining Analysis (NJA). STRUCTURE analyses were conducted for K = 3 and K =7, based on the ad hoc statistic ΔK. The K = 3 analysis recognized the split between Andean and Mesoamerican domesticates and the subdivision of the Mesoamerican domesticates into high- (Durango/Jalisco) and low-altitude (Mesoamerica) ecogeographic races. The K = 7 analysis further subdivided the Andean group identified for K = 3, as well as the high-altitude group from the Mesoamerican gene pool. It also identified smaller groups consisting of Mesoamerican wild beans. PCoA and NJA confirmed the STRUCTURE results and highlighted the existence of presumed hybridization among groups. Our results suggest that this core collection should be updated by adding domesticated categories, developing a separate wild common bean core collection, and developing cores for specific purposes.