Data from: A Community Resource for Exploring and Utilizing Genetic Diversity in the USDA Pea Single Plant Plus Collection

Metadata Updated: November 10, 2020

Included in this dataset are SNP and fasta data for the Pea Single Plant Plus Collection (PSPPC) and the PSPPC augmented with 25 P. fulvum accessions. These 6 datasets can be roughly divided into two groups. Group 1 consists of three datasets labeled PSPPC which refer to SNP data pertaining to the USDA Pea Single Plant Plus Collection. Group 2 consists of three datasets labeled PSPPC + P. fulvum which refer to SNP data pertaining to the USDA PSPPC with 25 accessions of Pisum fulvum added. SNPs for each of these groups were called independently; therefore SNP names that are shared between the PSPPC and PSPPC + P. fulvum groups should NOT be assumed to refer to the same locus. For analysis, SNP data is available in two widely used formats: hapmap and vcf. These formats can be successfully loaded into TASSEL v. 5.2.25 (http://www.maizegenetics.net/tassel). Explanations of fields (columns) in the VCF files are contained within commented (##) rows at the top of the file. Descriptions of the first 11 columns in the hapmap file are as follows:

rs#- Name of locus (i.e. SNP name) alleles- Indicates the SNPs for each allele at the locus chrom- Irrelevant for these datasets, since markers are unordered. pos- Irrelevant for these datasets, since markers are unordered. strand- Irrelevant for these datasets, since markers are unordered assembly#- required field for hapmap format. NA for these datasets center- required field for hapmap format. NA for these datasets protLSID- required field for hapmap format. NA for these datasets assayLSID- required field for hapmap format. NA for these datasets panel- required field for hapmap format. NA for these datasets QCcode- required field for hapmap format. NA for these datasets

The fasta sequences containing the SNPs are also available for such downstream applications as development of primers for platform-specific markers.

Access & Use Information

Public: This dataset is intended for public access and use. License: Creative Commons CCZero

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Dates

Metadata Created Date November 10, 2020
Metadata Updated Date November 10, 2020

Metadata Source

Harvested from USDA JSON

Additional Metadata

Resource Type Dataset
Metadata Created Date November 10, 2020
Metadata Updated Date November 10, 2020
Publisher Agricultural Research Service
Unique Identifier Unknown
Maintainer
Identifier b99c7cf3-a7c2-46c1-b02f-4f0d4ea60ffd
Data Last Modified 2019-08-23
Public Access Level public
Bureau Code 005:18
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Data Dictionary https://data.nal.usda.gov/dataset/data-community-resource-exploring-and-utilizing-genetic-diversity-usda-pea-single-plant-6
License https://creativecommons.org/publicdomain/zero/1.0/
Program Code 005:040
Source Datajson Identifier True
Source Hash ca86b0e67f2dacdae9d8e99af3dfa46f976f500f
Source Schema Version 1.1

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