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.
\nThese 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.
\nFor 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.
\nDescriptions of the first 11 columns in the hapmap file are as follows:
\nThe fasta sequences containing the SNPs are also available for such downstream applications as development of primers for platform-specific markers.
\nFor more information about this dataset, contact Clarice Coyne at Clarice.Coyne@usda.gov or coynec@wsu.edu.
Resource Title: PSPPC SNPs in hapmap format.
File Name: PSPPC.hmp.txt
Resource Description: 66591 unanchored SNPs for the PSPPC collection in hapmap format
Resource Software Recommended: TASSEL,url: http://www.maizegenetics.net/tassel
Resource Title: PSPPC SNP FASTA Sequences.
File Name: PSPPC.fa.txt
Resource Description: FASTA sequences for each allele of the PSPPC SNP dataset
Resource Title: PPSPPC + P. fulvum SNPs in hapmap format.
File Name: PSPPC+fulvums.hmp.txt
Resource Description: 67400 SNPs from the PSPPC augmented with 25 P. fulvum accessions in hapmap format. SNP names are independent and unrelated to plain PSPPC SNP files.
Resource Software Recommended: TASSEL,url: http://www.maizegenetics.net/tassel
Resource Title: PSPPC + P. fulvum SNP FASTA Sequences.
File Name: PSPPC+fulvums.fa.txt
Resource Description: FASTA sequences for each allele of the PSPPC + P. fulvum SNP dataset. SNP names are independent and unrelated to plain PSPPC SNP files.
Resource Title: PSPPC + P. fulvum SNPs in vcf format.
File Name: PSPPC+fulvums.vcf.txt
Resource Description: 67400 SNPs from the PSPPC augmented with 25 P. fulvum accessions in vcf format. SNP names are independent and unrelated to plain PSPPC SNP files.
Resource Software Recommended: TASSEL,url: http://www.maizegenetics.net/tassel
Resource Title: PSPPC SNPs in vcf format.
File Name: PSPPC.vcf.txt
Resource Description: 66591 SNPs from the PSPPC in vcf format
Resource Software Recommended: TASSEL,url: http://www.maizegenetics.net/tassel
Resource Title: README.
File Name: Data Dictionary.docx
Resource Description: These data are for the Pea Single Plant Plus Collection (PSPPC) and the PSPPC augmented with 25 P. fulvum accessions.
\nThe 6 datasets can be divided into two groups. Group 1 consists of 3 datasets labeled \u201cPSPPC\u201d which refer to SNP data pertaining to the USDA Pea Single Plant Plus Collection. Group 2 consists of 3 datasets labeled \u201cPSPPC + P. fulvum\u201d which refer to SNP data pertaining to the PSPPC with 25 accessions of Pisum fulvum added. SNPs for each of these groups were called independently; therefore any SNP name that is shared between the PSPPC and PSPPC + P. fulvum groups should NOT be assumed to refer to the same locus.
\nFor analysis, SNP data is available in two widely used formats: hapmap and vcf. These files were successfully loaded into the standalone version of TASSEL v. 5.2.25 (http://www.maizegenetics.net/tassel).
\nExplanations of fields (columns) in the VCF files are contained within commented (##) rows at the top of the file.
\nThe first 11 columns required for the hapmap format are as follows:\nrs#- Name of locus (i.e. SNP name)\nalleles- Indicates the SNPs for each allele at the locus\nchrom- N/A, since markers are unordered.\npos- N/A, since markers are unordered.\nstrand- N/A, since markers are unordered\nassembly#- N/A\ncenter- N/A\nprotLSID- N/A\nassayLSID- N/A\npanel- N/A\nQCcode- N/A
\nThe fasta sequences containing the SNPs are also available here for such downstream applications as development of primers for platform-specific markers.\n