This documentation file was generated on 2018-11-28 by James R. Myers ------------------- # GENERAL INFORMATION ------------------- 1. Title of Dataset: 295 snap bean diversity panel SNP data 2. Creator Information 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; Conceptualization, Methodology, Validation, Formal analysis, Investigation, Writing: original draft, review and editing, Visualization. Name: Haidar Arkwazee Institution: University of Sulaimani College, School or Department: Department of Horticulture Address: P.O. Box 334 Sulaimani 334, Kurdistan, IRAQ Email: arkwazee1983@gmail.com ORCID: Role: Former Ph.D. graduate research assistant; Investigation, Writing: review and editing Name: Kelly Vining Institution: Oregon State University College, School or Department: Department of Horticulture Address: 4017 Ag. & Life Sci. Bldg., Corvallis, OR 97331 USA Email: kelly.vining@oregonstate.edu ORCID: Role: co-Principal Investigator; Methodology, Formal analysis, Writing: review and editing. 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 Role: Principle Investigator; Conceptualization, Methodology, Formal Analysis, Resources, Data curation, Writing: original draft, review and editing, Visualization, Supervision, Project administration, Funding acquisition. 3. Collaborator information 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: 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 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 Abstract: 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. 3. Date of data collection: The Bean CAP Snap Bean Diversity Panel DNA isolated in 2009. Chinese and Spanish accessions, and some snap bean accession DNA was collected in 2013, and the dry bean race accessions, heirloom materials and eight Spanish line DNA was collected in 2018. Beadchip analysis was conducted in 2018. 4. Source of accessions: All accessions are detailed in the file Table_S1_Passport_data_snap_bean_lines_final.csv. Bean CAP Snap Bean Diversity Panel: Documentation for this panel is also found in Kleintop, A. E., Myers, J. R., Echeverria, D., Thompson, H. J., & Brick, M. A. (2016). Total Phenolic Content and Associated Phenotypic Traits in a Diverse Collection of Snap Bean Cultivars. Journal of the American Society for Horticultural Science, 141(1), 3-11. Chinese accessions: 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. Accessions available from JRM. Spanish accessions: Provided by Antonio de Ron from the Misión Biológica de Galicia Consejo Superior de Investigaciones Científicas (CSIC) (Pontevedra, Spain) collection. Heirloom snap beans: Obtained from various commercial sources or maintained within the OSU Vegetable Breeding Program. Source by variety information can be found in accompanying Table_S1_Passport_data_snap_bean_lines_final.csv file, which can also be found as a supplemental file to the derivative manuscript (Wallace, L.; Arkwazee, H.; Vining, K.; Myers, J.R. Genetic Diversity within Snap Beans and Their Relation to Dry Beans. Genes 2018, 9, 587.). Dry bean races: Obtained from the USDA-NPGS Western Region 6 Plant Introduction (PI) collection. These are accessible through the Germplasm Resources Information Network (GRIN) database (https://npgsweb.ars-grin.gov/gringlobal/search.aspx). 5. Funding sources that supported the collection of the data: USDA-NIFA-Bean CAP (2009-85606-05964), Del Monte Corp., and the 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: Wallace, L.; Arkwazee, H.; Vining, K.; Myers, J.R. Genetic Diversity within Snap Beans and Their Relation to Dry Beans. Genes 2018, 9, 587. http://dx.doi.org/10.3390/genes9120587 3. Recommended citation for the data: 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 4. Dataset Digital Object Identifier (DOI) 10.7267/3t945x17v -------------------------- VERSIONING AND PROVENANCE -------------------------- 1. Last modification date 2018-11-25 -------------------------- METHODS -------------------------- Methods for data collection and analysis are described in Wallace, L.; Arkwazee, H.; Vining, K.; Myers, J.R. Genetic Diversity within Snap Beans and Their Relation to Dry Beans. Genes 2018, 9, 587. http://dx.doi.org/10.3390/genes9120587 --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: SNP_Data.csv Short description: Data set containing 295 common bean accessions and their genotype for 5,396 SNPs B. Filename: Table_S1_Passport_data_snap_bean_lines_final.csv Short description: Data file containing full accession names, source, phenotypic descriptions and historical information (where known) for 295 common bean accessions."Label" column in this file corresponds to "Accession" column in SNP_Data.csv. 2. Formats Datasets are in comma separated variable (csv) format. ----------------------------------------- TABULAR DATA-SPECIFIC INFORMATION FOR: SNP_Data.csv ----------------------------------------- 1. Number of variables: 5,397 columns (one column for accession names and 5,396 columns for SNPs ordered by SS ID number). 2. Number of cases/rows: 295 data rows ordered by accession name. 3. Data codes: Code/symbol: SS[#########] Definition: NCBI SNP ID. Code/symbol: A or T Definition: Adenine or Thymine DNA base at SNP site in Phaseolus vulgaris genome. Code/symbol: N Definition: missing data (accessions heterozygous for a SNP were coded as missing data). ----------------------------------------- TABULAR DATA-SPECIFIC INFORMATION FOR: Table_S1_Passport_data_snap_bean_lines_final.csv file ----------------------------------------- 1. Long description Passport information on 295 genotypes utilized in this study of snap bean genetic diversity. Data are a combination of field notes, Plant Variety Protection applications, and ASHS Cultivar Descriptions for North America (http://cucurbitbreeding.com/todd-wehner/publications/vegetable-cultivar-descriptions-for-north-america/; verified 10/08/18). Accessions are listed in the order in which they were analyzed in Structure and fastStructure. Bean race identifiers are appended to the names of the landrace dry beans. The appended identifiers are J (Jalisco), D (Durango), M (Mesoamerica), G (Guatemala), P (Peru), C (Chile), and NG (Nueva Granada). 2. Variable List Accession #: Number assigned to diversity panel accessions. Label: Abbreviated name Complete correct name: full accession name Pod traits: Class of bean (dry, snap, Romano, wax, semi-snap, purple podded snap) Plant habit: pole (indeteriminate climber) half runner (indeterminate non-climber), bush determinate. Source: Source of accession PI #: Plant introduction number assigned by USDA-NPGS and searchable in GRIN (https://npgsweb.ars- grin.gov/gringlobal/search.aspx). Origin: Original breeder or seed company originally offering the cultivar. Type: processing, fresh market or dual purpose Sieve Class: Pod sieve size classification ? generally the median sieve size class. For more information on grading processing beans for sieve size, see Myers, James R., and James R. Baggett. "Improvement of snap bean." In Common bean improvement in the twenty-first century, pp. 289-329. Springer, Dordrecht, 1999. Similar: Cultivar most similar to accession, either by ancestry or by resemblance. PVP#: Plant Variety Protection certificate number. A searchable database of PVP certificates is available at https://www.ams.usda.gov/datasets/plant-variety. Release date: Date cultivar was introduced commercially. Notes: Any additional information on origins and history.