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
282set_CML264381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML264
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML277381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML277
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML281381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML281
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML287381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML287
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML311381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML311
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML314381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML314
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML321381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML321
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML322381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML322
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML323381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML323
Alternative accession-BioProject:PRJNA389800
...
+
282set_CML328381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML328
Alternative accession-BioProject:PRJNA389800
...
+
Displaying 81-90 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