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

Dataset type: Genomic
Data released on December 27, 2017

Bukowski R; Guo X; Lu Y; Zou C; He B; Rong Z; Wang B; Xu DX; 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 MC; Buckler ES; YX; Ware D; Lai J; Sun Q (2017): Supporting data for "Construction of the third generation Zea mays haplotype map" GigaScience Database. http://dx.doi.org/10.5524/100339

DOI10.5524/100339

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.

Additional details

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





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
TDD391034563 gama grassTripsacum dactyloides Description:DNA extracted from gama grass cultivar...
Cultivar:TDD39103
Alternative accession-BioProject:SRA051245
...
+
hmp3_B7381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar B7
Cultivar:B7
Alternative accession-BioProject:PRJNA399729
...
+
hmp3_huangchangb381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar huang...
Cultivar:huangchangb
Alternative accession-BioProject:PRJNA399729
...
+
hmp3_B8381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar B8
Cultivar:B8
Alternative accession-BioProject:PRJNA399729
...
+
hmp3_H105W381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar H105W
Cultivar:H105W
Alternative accession-BioProject:PRJNA399729
...
+
hmp3_H21381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar H21
Cultivar:H21
Alternative accession-BioProject:PRJNA399729
...
+
hmp3_B76381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar B76
Cultivar:B76
Alternative accession-BioProject:PRJNA399729
...
+
hmp3_ji870381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar ji870
Cultivar:ji870
Alternative accession-BioProject:PRJNA399729
...
+
hmp3_Oh43381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar Oh43
Cultivar:Oh43
Alternative accession-BioProject:PRJNA399729
...
+
hmp3_LH143381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar LH143
Cultivar:LH143
Alternative accession-BioProject:PRJNA399729
...
+
Displaying 1-10 of 1282 Sample(s).




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).
Date Action
December 27, 2017 Dataset publish
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix134