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Data released on December 27, 2017

Supporting data for "Construction of the third generation Zea mays haplotype map"

Bukowski, R; Guo, X; Lu, Y; Zou, C; He, B; Rong, Z; Wang, B; Xu, D, X; Yang, B; Xie, C; Fan, L; Gao, S; Xu, X; Zhang, G; Li, Y; Jiao, Y; Doebley, J; Ross-Ibarra, J; Lorant, A; Buffalo, V; Romay , M, C; Buckler , E, S; , Y, X; Ware, D; Lai, J; Sun, Q (2017): Supporting data for "Construction of the third generation Zea mays haplotype map" GigaScience Database. RIS BibTeX Text

Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole genome sequencing data from 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world. A new computational pipeline was set up to process over 12 trillion bp of sequencing data, and a set of population genetics filters were applied to identify over 83 million variant sites. We identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.

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Read the peer-reviewed publication(s):

Bukowski, R., Guo, X., Lu, Y., Zou, C., He, B., Rong, Z., … Xu, Y. (2017). Construction of the third-generation Zea mays haplotype map. GigaScience, 7(4). doi:10.1093/gigascience/gix134

Accessions (data included in GigaDB):

BioProject: PRJNA389800
BioProject: PRJNA260788
BioProject: PRJNA399729
BioProject: PRJNA82843
SRA: SRA051245


zea mays sequencing haplotype map genotyping variant discovery linkage disequilibrium identity by descent imputation 


Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
ZM_UH304381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar germa...
Alternative accession-BioProject:PRJNA260788
ZM_W117381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar germa...
Alternative accession-BioProject:PRJNA260788
Displaying 1281-1282 of 1282 Sample(s).

Files: (FTP site) Table Settings


File Description
Sample ID
Data Type
File Format
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
archivezip187.13 MB2017-12-22
SNPsVCF2.01 GB2017-11-03
SNPsVCF4.25 GB2017-11-03
SNPsVCF4.07 GB2017-11-03
SNPsVCF4.21 GB2017-11-03
SNPsVCF9.03 GB2017-11-03
SNPsVCF8.62 GB2017-11-03
SNPsVCF3.22 GB2017-11-03
SNPsVCF6.87 GB2017-11-03
SNPsVCF6.41 GB2017-11-03
Displaying 1-10 of 52 File(s).



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