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.

For more information about this dataset, contact Clarice Coyne at Clarice.Coyne@usda.gov or coynec@wsu.edu.