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

Citation

Gepts, Paul; Kuzay, Saarah; Hamilton, Paige (2020), Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity?, Dryad, Dataset, https://doi.org/10.25338/B8KP45

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.

Methods

Plant material:

The current core collection for common bean held at the Western Regional Plant Introduction Station of the USDA in Pullman, WA, is an amalgamation of an original collection focused mainly on Mesoamerican gene pool accessions (n = 224) with a subsequent addition of Central (n = 101) and South American (n = 97) accessions for a total of n = 422 [USDA, ARS, National Genetic Resources Program. Germplasm Resources Information Network - (GRIN). [Online Database] National Germplasm Resources Laboratory, Beltsville, Maryland. Available: http://www.ars-grin.gov/cgi-bin/npgs/html/desc.pl?83085 (06 October 2014)]. Plants were grown in the greenhouse to produce leaf tissue for DNA extraction. One plant per accession was analyzed because the emphasis is on determining genetic diversity patterns across broad groups of accessions, rather than within accessions. For various reasons, including photoperiod sensitivity and other causes of lack of adaptation UC Davis greenhouse conditions, only 363 entries of the core collection could be studied. A subset of these 363 accessions is also maintained at the Genetic Resources Unit (GRU) at the Centro Internacional de Agricultura Tropical (Cali, Colombia). The database maintained by the GRU was used to retrieve, when available, seed photos and information on the type of phaseolin seed protein of share accessions.

SNP genotyping

Bean DNA samples were genotyped with the Illumina (Illumina Inc., San Diego, CA, USA) BARCBean6K_3 Infinium SNP array (Song et al. 2015) which permits the analysis of 5,398 SNP markers distributed across the 11 pairs of common bean chromosomes. The BACBean6K_3 BeadChips were scanned with the Illumina BeadStation 500G.  SNP calling was conducted with the genotyping module V2011.1 of the GenomeStudio software (Illumina Inc., San Diego, CA, USA).

Funding

USDA NIFA AFRI BeanCAP, Award: #2009-01929