Data Sets for Download

Entire Panzea database as a mysqldump output: [download]. The database uses the GDPDM schema. For information on the GDPDM schema, please visit the GDPDM Home Page

All germplasm passport data as a tab-delimited text file: [download]

• All Phenotypic data as a tab-delimited text file: [download]


• Phenotypic trait genetic means and heritabilities for our maize Nested Association Mapping population (measured in Summer 2006):
  • Genetic means: [download]
  • Trait heritabilities: [download]
  
  
• NEW: Flowering times (mean, min, max) for NAM families summarized within and across 8 summer environments [download]

• All sequence data (formatted as alignments) as a tab-delimited text file: [download]


• Pointers to all alignments as a tab-delimited text file: [download]


• Sequence tracefiles generated by the project are available at: ftp://ftp.panzea.org/pub/panzea/tracefiles.

• All SNP data as a tab-delimited text file:
  • Sorted by marker name: [download]
  • Sorted by plant (accession & source): [download]
  
  
• All SSR data as a tab-delimited text file:
  • Sorted by marker name: [download]
  • Sorted by plant (accession & source): [download]
  
  
• Q martrix showing population structure data for the maize associaton mapping panel. Population structure was estimated using SSRs and the STRUCTURE algorithm. An Excel file with pedigree information is available [download], as is a text file readable by TASSEL software [download]. The following paper has more details about these estimates of population structure:

  Flint-Garcia, S.A., A.-C. Thuillet, S.M. Romero, J. Yu, G. Pressoir, S. Mitchell, J. Doebley, S. Kresovich, M.M. Goodman and E.S. Buckler. 2005. Maize association population: a high resolution platform for QTL dissection. Plant Journal, 44: 1054-1064.    [pdf]

• Data files (genotypes, phenotypes, plant information, kinship matrix and principle components describing population structure) from the study below:

  Weber, A.L., W.H. Briggs, J. Rucker, B.M. Baltazar, J. Sanchez-Gonzalez, P. Feng, E. Buckler and J. Doebley. 2008. The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): New evidence from association mapping. Genetics (in press). [download zip archive of data]   

In each context sequence, the target SNP is indicated in square brackets [ ], and other polymorphisms with curly brackets { } or with IUPAC ambiguity codes

• Context sequences for all of our functional SNPs to date with successful assays (3110 SNPs, including 98 redundant SNPs): [download]


• Context sequences for functional SNPs developed by Pioneer Hybrid International, Inc. (640 SNPs): [download]


• Context sequences for the SNPs successfully genotyped in our maize Nested Association Mapping population (1180 SNPs, including 26 redundant SNPs): [download]


• Context sequences for our "2007 candidate gene SNPs" (genotyping in progress) (1536 SNPs): [download]


• Context sequences and gene diversity for maize and teosinte for our initial set of 73 SNPs in 15 candidate genes controlling various plant phenotypes: [download]


• Context sequences and gene diversity for maize and teosinte for our initial set of 912 SNPs in 585 randomly chosen genes: [download]

We provide a zip archive containing files needed for QTL mapping of your own traits in our maize Nested Association Mapping population. Please be sure to read the text file Disclaimer_and_File_Descrips_20080419.txt first; this file is included in the archive, and includes descriptions of the contents of each file as well as the following disclaimer:

DISCLAIMER: NAM_map_20080419.xls is a preliminary map for the phenotypers of NAM. We are still correcting map errors as the maize physical map improves and errors are found in the map order and calling; however, this map is accurate enough to be useful for basic QTL mapping. Our group is currently working on two papers describing this data set: One on mapping flowering time and one on recombination and segregation distortion. Please check back monthly for updates.

Download the zip archive with the current NAM map and genotypes.