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SNP data for 295 snap bean genotypes utilized in a study of snap bean genetic diversity published in Genes

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  • The accessions used in this study were comprised of 246 snap bean and 49 dry bean genotypes. Of these, 150 snap bean accessions came from the Common Bean Coordinated Agriculture Project Snap Bean Diversity panel, an assemblage of 59 Chinese snap bean genotypes obtained from a trip to China in 1991 by Michael Dickson (Cornell University), placed in the United States Dept. of Agriculture National Plant Germplasm System (USDA-NPGS) Plant Introduction collection at Pullman, WA, USA, but left uncatalogued and provided to the Oregon State University (OSU) Vegetable Breeding Program for evaluation, 19 genotypes obtained from the Misión Biológica de Galicia—Consejo Superior de Investigaciones Científicas (CSIC) (Pontevedra, Spain) collection, and 24 heirloom snap beans obtained from specialized seed catalogs and the family of Harvey Bruxvoort. For the dry beans, the 49 accessions chosen were selected based on having been previously reported to belong to one of six bean races. DNA of accessions was isolated, quantified and analyzed using Illumina Infinium Genechip BARCBEAN6K_3 platform. This SNP array consists of 5,398 allele-specific probes. The raw data was processed using GenomeStudio (v2.0.4) software (Illumina, San Diego, CA USA). Two marker positions contained greater than 20% missing data and were removed from the study resulting in 5,396 SNPs. Heterozygous positions were treated as missing data and four Chinese genotypes with greater than 20% missing data were removed from the study. No imputation of the data was conducted.
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  • Wallace, L., Arkwazee, H., Vining, K., & Myers, J. (2018). SNP data for 295 snap bean genotypes utilized in a study of snap bean genetic diversity published in Genes (Version 1) [Data set]. Oregon State University. https://doi.org/10.7267/3T945X17V
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  • Data used in the article Wallace, L., Arkwazee, H., Vining, K., & Myers, J. (2018). Genetic Diversity within Snap Beans and Their Relation to Dry Beans. Genes, 9(12), 587. https://doi.org/10.3390/genes9120587
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  • The following sources supported this research: USDA-NIFA-Bean CAP (2009-85606-05964), Del Monte Corp., and the Baggett-Frazier Vegetable Breeding and Genetics Endowment.
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Thumbnail Title Date Uploaded Visibility Actions
file details SNP_Data.csv 2018-11-28 Public Download
file details Table_S1_Passport_data_snap_bean_lines_final.csv 2018-11-28 Public Download
file details SNP_Data_Documentation.txt 2018-12-19 Public Download