This documentation file was generated on 2019-10-08 by James R. Myers ------------------- # GENERAL INFORMATION ------------------- 1. Title of Dataset: Bean CAP Snap Bean Diversity Panel SNP Data 2. Creator Information Name: James R. Myers Institution: Oregon State University College, School or Department: Horticulture Address: 4017 Ag & Life Sciences Bldg. Email: james.myers@oregonstate.edu ORCID: 0000-0003-0976-144X Role: Principle Investigator; Conceptualization, Methodology, Resources – selected accession for diversity panel, Data curation – maintains seed & data for diversity panel. Name: Lyle Wallace Institution: University of Wisconsin-Madison College, School or Department: Horticulture (USDA-ARS) Address: 1575 Linden Dr., Madison, WI 53705 USA Email: lw2671@gmail.com ORCID: Role: Former Ph.D. graduate research assistant; Methodology Formal analysis. Name: Samira Mafi Moghaddam Institution: Plant Resilience Institute, Michigan State University, East Lansing, MI 48824; College, School or Department: Department of Plant Biology, Address: Plant Resilience Institute, Department of Plant Biology, Michigan State University, East Lansing, MI 48824 Email: smafi@msu.edu ORCID: Role: Methodology Formal analysis – performed imputation. 3. Collaborator information Name: Phil McClean Institution: North Dakota State University College, School or Department: Department of Plant Science Address: North Dakota State University Loftsgard Hall Plant Sciences Fargo, ND 58105. Email: phillip.mcclean@ndsu.edu ORCID: Role: Principle Investigator; Conceptualization, Methodology, Resources. Name: Qijan Song Institution:USDA-ARS College, School or Department: USDA-ARS - Soybean Genomics and Improvement Laboratory Address: Bldg. 006 Rm. 100, 10300 Baltimore Ave, Beltsville, MD 20705, USA Email: qijian.song@ars.usda.gov ORCID: Role: Investigation - Conducted Illumina Beadchip analysis to generate SNPs 3. Contact Information Name: James R. Myers Institution: Oregon State University College, School or Department: Department of Horticulture Address: 4017 Ag. & Life Sci. Bldg., Corvallis OR 97331 USA Email: james.myers@oregonstate.edu ORCID: https://orcid.org/0000-0003-0976-144X ------------------- CONTEXTUAL INFORMATION ------------------- 1. Abstract for the dataset The accessions used to create the Snap Bean Diversity Panel were 149 snap bean accessions selected from North American and European germplasm. This panel was developed with support from the Common Bean Coordinated Agriculture Project (USDA-NIFA grant no. 2009-85606-05964). A modified CTAB procedure was used to extract genomic DNA and the resulting DNA samples were analyzed on an Illumina Infinium Genechip BARCBEAN6K_3 platform. The single nucleotide polymorphism (SNP) array utilized was composed of 10,546 allele-specific probes. The raw data was initially processed on GenomeStudio (v2.0.4) software (Illumina, San Diego, CA, USA). Two marker SNP positions contained greater than 20% missing data and were removed from the study. All missing data for the remaining SNPs was imputed using fastPHASE software (v1.4), including heterozygous SNPs which were treated as missing data. SNPs not assigned to a genomic position in Phytozome12 (Phaseolus vulgaris, version 2.1) were removed from the study resulting in 10,073 remaining SNPs. 2. Context of the research project that this dataset was collected for. The Bean CAP was a project to genotype and phenotype common bean diversity panels consisting of both dry and snap beans. The main phenotypic focus was on nutritional traits. 3. Date of data collection: The Bean CAP Snap Bean Diversity Panel DNA isolated in 2009. 4. Geographic location of data collection: Snap bean accessions are maintained by the OSU Vegetable Breeding and Genetics Program, Oregon State University, Corvallis, OR 97331. 5. Funding sources that supported the collection of the data: USDA-NIFA-Bean CAP (2009-85606-05964), Baggett-Frazier Vegetable Breeding and Genetics Endowment -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: This work is licensed under a Creative Commons Attribution 4.0 International License. 2. Links to publications related to the dataset: Myers, J.R., L.T. Wallace, S.M. Moghaddam, A.E. Kleintop, D. Echeverria, H.J. Thompson, M.A. Brick, and P.E. McClean. 2019. Improving the health benefits of snap bean: Genome wide association studies of total phenolic content. Nutrients (in press). 3. Links to other publicly accessible locations of the data: 4. Recommended citation for the data: Myers, J., Wallace, L., & Moghaddam, S. M. (2019). BeanCAP snap bean diversity panel SNP data (Version 1) [Data set]. Oregon State University. https://doi.org/10.7267/m900p1589 5. Dataset Digital Object Identifier (DOI) 10.7267/M900P1589 6. Limitations to reuse: none. -------------------------- VERSIONING AND PROVENANCE -------------------------- 1. Last modification date 2019-09-18 4. Additional related data collected that was not included in the current data package: Passport data for the Snap Bean Diversity Panel Accessions can be found in the ScholarsArchive file Table_S1_Passport_data_snap_bean_lines_final.csv. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Methods for collection, generation and processing of data are found in Myers, J.R., L.T. Wallace, S.M. Moghaddam, A.E. Kleintop, D. Echeverria, H.J. Thompson, M.A. Brick, and P.E. McClean. 2019. Improving the health benefits of snap bean: Genome wide association studies of total phenolic content. Nutrients (in press). --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: BeanCAP_Snap_Bean_Diversity_Panel_SNP_data.csv Short description: Data set containing 149 common bean accessions and their genotypes for 10,073 SNPs. 3. Formats Comma separated variable (csv) format. ----------------------------------------- TABULAR DATA-SPECIFIC INFORMATION FOR: BeanCAP_Snap_Bean_Diversity_Panel_SNP_data.csv ----------------------------------------- 1. Number of variables: 153 columns consisting of SS ID no., Sequence ID no., Chromosome, Physical location on chromosome, followed by 149 columns of snap bean accessions arrange alphabetically. 2. Number of cases/rows: 10,074 rows (one row for column names and 10,073 row for SNPs ordered by chromosome and physical location on the chromosome.) 3. Missing data codes: (no missing data) 4. Variable List A. Name: SS ID no. Description: NCBI SNP ID B. Name: SC ID no. Description: Alternate SNP ID no. C. Name: Chromosome Description: chromosome number (1-11 for Phaseolus vulgaris genome). D. Name: Physical position on chrom. Description: Location in base pair (bp) on chromosome. E. Name: Accession name Description: Accession names for 149 snap bean accessions arranged alphabetically. Data consists of A (Adenine) or T (Thymine) DNA base at SNP site in Phaseolus vulgaris genome.