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 of our public phenotypic data for NAM and the maize 282 association population collected between 2006 & 2009 in a single text file formatted for TASSEL (57 traits; 285 trait/environment combinations): [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]

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


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

• A table of links to prepackaged genotypic data for various sets of germplasm is available here.
  
  
• Preliminary Genotyping by Sequencing (GBS) genotypes for NAM, IBM, the Maize282 association mapping population, and our teosinte/W22 BC₂S₃ population. By downloading these data you are agreeing to our data release conditions which can be read here (the file 'GBSGenosDataReleaseConditions.txt' is also included in each zip download). As we further refine our GBS bioinformatics pipeline, we will post new releases of these genotypes. Check here frequently for updated data.   (NAM, IBM, & 282 current version: AllZeaGBSv2.3;  Posted: 20121218)
  • NAM (raw genotypes):   [download zip archive]   (1.45 GB)
  • NAM (partially imputed genotypes):   [download zip archive]   (604 MB)
  • NAM (new: phased and fully imputed genotypes at 1 cM resolution):   [download zip archive]   (2 MB)  Posted 20130212
  • IBM (raw genotypes):   [download zip archive]   (117 MB)
  • IBM (partially imputed genotypes):   [download zip archive]   (62 MB)
  • Maize282 (raw genotypes):   [download zip archive]   (178 MB)
  • Maize282 (partially imputed genotypes):   [download zip archive]   (93 MB)
  • Teosinte/W22 BC₂S₃ RILs (phased and imputed genotypes; current version 20110423):   [download zip archive]   (3.3 MB)
  
  
• All traditional 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.

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 SNPs with successful assays (4908 SNPs, including 145 redundant 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]


• 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.

• The files available from the links below are in B73 RefGen_v1 coordinates. (Maize HapMap markers in B73 RefGen_v2 coordinates are available here)


• 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. (Note: "CML52R" is the "real" CML52, while "CML52:BC1" is a CML52/B73 RIL.)    [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.

The maize HapMapV2 study was a collaborative effort involving Panzea, CSHL, BGI, CAU, UC Davis, USDOE and several others. This study generated random-sheared, paired-end Illumina GAII reads from 103 maize, teosinte and maize landrace inbred lines at a depth ranging from 4-30X. High quality genotypes were obtained for 55 million SNPs and small indels. Two papers from this work have been published in Nature Genetics (see Chia et al. 2012 and Hufford et al. 2012 on our Project Publications page). The raw sequence reads are available in the NCBI Short Read Archive under the accession number SRA051245. The SNP genotype calls are available from the table below (be forewarned: the files are large!). A readme file (README_MaizeHapMapV2.txt) describing the content of these files is available here. The alignment of Hapmap2 sequencing reads have been deposited to iPlant Data Store(instruction for accessing the bam files on iPlant). PLEASE NOTE: the alleles in the "alleles" column are given in major/minor order (NOT ref/alt). An extended version of Supplemental Table 1 from Chia et al. 2012 (MaizeHapMapV2_SuppTable1_extended.xlsx) containing additional information about the teosinte and landrace inbred lines is availabe here.

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_20110218.txt, included in the archive.   [download zip archive]