10.25338/B8KP45
Gepts, Paul
0000-0002-1056-4665
University of California, Davis
Kuzay, Saarah
University of California, Davis
Hamilton, Paige
0000-0001-6828-1708
University of California, Davis
Is the USDA core collection of common bean representative of genetic
diversity of the species, as assessed by SNP diversity?
Dryad
dataset
2019
Amplified Fragment Length Polymorphism
Neighbor-Joining Analysis
Principal Coordinate Analysis
Randomly Amplified Polymorphic
Restriction Fragment Length Polymorphism
Single Nucleotide Polymorphism
Simple Sequence Repeat
plant species
USDA
USDA NIFA AFRI BeanCAP
#2009-01929
2019-01-17T18:59:30Z
2019-01-17T18:59:30Z
en
45231250 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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).