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

<p>Included in this dataset are SNP and fasta data for the Pea Single Plant Plus Collection (PSPPC) and the PSPPC augmented with 25 <em>P. fulvum</em> accessions. </p>
<p>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 + <em>P. fulvum</em> which refer to SNP data pertaining to the USDA PSPPC with 25 accessions of <em>Pisum fulvum</em> added. SNPs for each of these groups were called independently; therefore SNP names that are shared between the PSPPC and PSPPC + <em>P. fulvum</em> groups should NOT be assumed to refer to the same locus.</p>
<p>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 (<a href="http://www.maizegenetics.net/tassel">http://www.maizegenetics.net/tassel</a>). Explanations of fields (columns) in the VCF files are contained within commented (##) rows at the top of the file. </p>
<p>Descriptions of the first 11 columns in the hapmap file are as follows:</p>
<ul>
<li>rs#- Name of locus (i.e. SNP name)</li>
<li>alleles- Indicates the SNPs for each allele at the locus</li>
<li>chrom- Irrelevant for these datasets, since markers are unordered.</li>
<li>pos- Irrelevant for these datasets, since markers are unordered.</li>
<li>strand- Irrelevant for these datasets, since markers are unordered</li>
<li>assembly#- required field for hapmap format. NA for these datasets</li>
<li>center- required field for hapmap format. NA for these datasets</li>
<li>protLSID- required field for hapmap format. NA for these datasets</li>
<li>assayLSID- required field for hapmap format. NA for these datasets</li>
<li>panel- required field for hapmap format. NA for these datasets</li>
<li>QCcode- required field for hapmap format. NA for these datasets</li>
</ul>
<p>The fasta sequences containing the SNPs are also available for such downstream applications as development of primers for platform-specific markers.</p>
<p>For more information about this dataset, contact Clarice Coyne at Clarice.Coyne@usda.gov or coynec@wsu.edu. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: PSPPC SNPs in hapmap format.</p> <p>File Name: PSPPC.hmp<em>.txt</em></p><p><em>Resource Description: 66591 unanchored SNPs for the PSPPC collection in hapmap format</em></p><p><em>Resource Software Recommended: TASSEL,url: <a href="http://www.maizegenetics.net/tassel">http://www.maizegenetics.net/tassel</a> </em></p></li><em><br></em><li><em><p>Resource Title: PSPPC SNP FASTA Sequences.</p> </em><p><em>File Name: PSPPC.fa</em>.txt</p><p>Resource Description: FASTA sequences for each allele of the PSPPC SNP dataset</p></li><br><li><p>Resource Title: PPSPPC + P. fulvum SNPs in hapmap format.</p> <p>File Name: PSPPC+fulvums.hmp<em>.txt</em></p><p><em>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.</em></p><p><em>Resource Software Recommended: TASSEL,url: <a href="http://www.maizegenetics.net/tassel">http://www.maizegenetics.net/tassel</a> </em></p></li><em><br></em><li><em><p>Resource Title: PSPPC + P. fulvum SNP FASTA Sequences.</p> </em><p><em>File Name: PSPPC+fulvums.fa</em>.txt</p><p>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.</p></li><br><li><p>Resource Title: PSPPC + P. fulvum SNPs in vcf format.</p> <p>File Name: PSPPC+fulvums.vcf<em>.txt</em></p><p><em>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.</em></p><p><em>Resource Software Recommended: TASSEL,url: <a href="http://www.maizegenetics.net/tassel">http://www.maizegenetics.net/tassel</a> </em></p></li><em><br></em><li><em><p>Resource Title: PSPPC SNPs in vcf format.</p> </em><p><em>File Name: PSPPC.vcf</em>.txt</p><p>Resource Description: 66591 SNPs from the PSPPC in vcf format</p><p>Resource Software Recommended: TASSEL,url: <a href="http://www.maizegenetics.net/tassel">http://www.maizegenetics.net/tassel</a> </p></li><br><li><p>Resource Title: README.</p> <p>File Name: Data Dictionary.docx</p><p>Resource Description: These data are for the Pea Single Plant Plus Collection (PSPPC) and the PSPPC augmented with 25 <em>P. fulvum </em>accessions.</p>
<p>The 6 datasets can be divided into two groups. Group 1 consists of 3 datasets labeled “PSPPC” which refer to SNP data pertaining to the USDA Pea Single Plant Plus Collection. Group 2 consists of 3 datasets labeled “PSPPC + <em>P. fulvum</em>” which refer to SNP data pertaining to the PSPPC with 25 accessions of <em>Pisum fulvum </em>added. SNPs for each of these groups were called independently; therefore any SNP name that is shared between the PSPPC and PSPPC + <em>P. fulvum </em>groups should NOT be assumed to refer to the same locus.</p>
<p>For 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 (<a href="http://www.maizegenetics.net/tassel">http://www.maizegenetics.net/tassel</a>). </p>
<p>Explanations of fields (columns) in the VCF files are contained within commented (##) rows at the top of the file. </p>
<p>The first 11 columns required for the hapmap format are as follows:
rs#- Name of locus (i.e. SNP name)
alleles- Indicates the SNPs for each allele at the locus
chrom- N/A, since markers are unordered.
pos- N/A, since markers are unordered.
strand- N/A, since markers are unordered
assembly#- N/A
center- N/A
protLSID- N/A
assayLSID- N/A
panel- N/A
QCcode- N/A</p>
<p>The fasta sequences containing the SNPs are also available here for such downstream applications as development of primers for platform-specific markers.
</p></li></ul><p></p>

Tags: ars, data-gov, np301
Organization: Department of Agriculture