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]
  
  
• Flowering times (mean, min, max) for NAM families summarized within and across 8 summer environments [download]


• NEW: Flowering data and imputed genotypic data from the paper:

  Buckler ES et al. 2009. The genetic architecture of maize flowering time. Science 325: 714-718. [download data]   

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


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

• 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]

  Association panel genotypes at a set of 13 SSR markers (useful for quality control purposes) are available here.

• Data files (genotypes, phenotypes, plant information, kinship matrix and principle components describing population structure) from our first teosinte association mapping study:

  Weber, A., R.M. Clark, L. Vaughn, J. Sanchez-Gonzalez, J. Yu, B.S. Yandell, P. Bradbury and J. Doebley. 2007. Major regulatory genes in maize contribute to standing variation in teosinte (Zea mays ssp. parviglumis). Genetics 177: 2349-2359. [download zip archive of data]   

• Data files (genotypes, phenotypes, plant information, kinship matrix and principle components describing population structure) from our second teosinte association mapping study:

  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 180: 1221-1232. [download zip archive of data]   

• SSR genotypes (in PowerMarker format) from the following paper:

  Vigouroux, Y., J.C. Glaubitz, Y. Matsuoka, M.M. Goodman, J. Sanchez-G. and J. Doebley. 2008. Population structure and genetic diversity of New World maize races assessed by DNA microsatellites. American Journal of Botany 95: 1240-1253. [download data]   

• SNP genotypes (in PowerMarker format) from the following paper:

  Hamblin MT, Warburton ML, Buckler ES, 2007. Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS ONE 2: e1367. [download data]   

• SNP genotypes (in PowerMarker format) from the following paper:

  Nelson PT, Coles ND, Holland JB, Bubeck DM, Smith S, Goodman MM, 2008. Molecular characterization of maize inbreds with expired US plant variety protection. Crop Sci 48: 1673-1685. [download data]   

• NEW: Imputed genotypes and flowering data from the paper:

  Buckler ES et al. 2009. The genetic architecture of maize flowering time. Science 325: 714-718. [download data]   

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

• Context sequences for all of our functional SNPs to date with successful assays (4908 SNPs, including 145 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 (1144 SNPs): [download]


• Context sequences for our successfully genotyped "2007 candidate gene SNPs" (1363 SNPs, including 1 redundant SNP): [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]


• 33 bp context sequences for 126,683 SNPs discovered by our allied project "High density scoreable markers for maize trait dissection" (NSF DBI 0638566) by aligning 454 seqence from Mo17 against B73 MAGI4 reference sequences: [download zip archive].   The raw 454 sequencing data are available in the NCBI Short Read Archive with accession number SRA008616.

• Complete set of first generation HapMap SNPs & indels, including paralogs. All genotypes are quantitative.    [download zip archive]


• Subset of first generation HapMap SNPs & indels that each align to a single AGPv1 position. All genotypes are quantitative.    [download zip archive]


• Highest quality, single copy first generation HapMap SNPs (& indels) with qualitative genotypes.    [download zip archive]


• Pi and Fst for first generation HapMap SNPs averaged over 100 SNP windows.    [download file]


• Pi for first generation HapMap SNPs averaged over NAM genetic map intervals.    [download file]


• For more information on the maize first generation HapMap study, see Gore, Chia et al. 2009. Science 326: 1115-1117.

We provide a zip archive containing files needed for QTL mapping of your own traits in our maize Nested Association Mapping population. Descriptions of the contents of each file are given in the file File_Descrips_20090921.txt, included in the archive.   [download zip archive]