DOI: 10.25338/b8kp45
title: Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity?

description: 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.
description: 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 <i>et al.</i>
 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).