Database dump
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
Germplasm
All germplasm passport data as a tab-delimited text file: [download]
Phenotypes
- 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):
- NEW: Flowering times (mean, min, max) for NAM families summarized within and across 8 summer environments [download]
Sequences
Genotypes
- All SNP data as a tab-delimited text file:
- All SSR data as a tab-delimited text file:
- 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]
SNP marker context sequences
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]
NAM map and genotypes
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.
|