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An Evaluation of the Representativity of the USDA Core Collection of Common Bean as Assessed by SNP Diversity

Citation

Gepts, Paul; Kuzay, Saarah; Hamilton, Paige (2019), An Evaluation of the Representativity of the USDA Core Collection of Common Bean as Assessed by SNP Diversity, UC Davis Dash, Dataset, https://doi.org/10.25338/B8KP45

Abstract

In this article, we present the results of an analysis of the genetic diversity of a USDA core collection of common bean. This collection was analyzed with a SNP chip platform of some 5,400 markers distributed over the 11 chromosomes (Pv01 to Pv11) of the species (Song et al. 2015). Results were compated with those obtained using  SSR markers (McClean et al. 2012). We determine the representativity of this collection using a combination of prior results and suggest several targets to improve the diversity of the domesticated common bean gene pool in this core collection.

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