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
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.
Keywords:
Additional details
Read the peer-reviewed publication(s):
(PubMed: 29300887)
Accessions (data generated as part of this study):
BioProject:
PRJNA389800
BioProject:
PRJNA260788
BioProject:
PRJNA399729
BioProject:
PRJNA82843
SRA:
SRA051245
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
282set_33-16 | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_33-16 Alternative accession-BioProject:PRJNA389800 ... + | |
282set_38-11Goodman-Buckler | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_38-11Goodman-Buckler Alternative accession-BioProject:PRJNA389800 ... + | |
282set_4226 | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_4226 Alternative accession-BioProject:PRJNA389800 ... + | |
282set_4722 | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_4722 Alternative accession-BioProject:PRJNA389800 ... + | |
282set_A188 | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_A188 Alternative accession-BioProject:PRJNA389800 ... + | |
282set_A214NGoodman-Buckler | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_A214NGoodman-Buckler Alternative accession-BioProject:PRJNA389800 ... + | |
282set_A239 | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_A239 Alternative accession-BioProject:PRJNA389800 ... + | |
282set_A441-5 | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_A441-5 Alternative accession-BioProject:PRJNA389800 ... + | |
282set_A554 | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_A554 Alternative accession-BioProject:PRJNA389800 ... + | |
282set_A556 | 381124 | mays | Zea mays sub sp. Mays | Description:DNA extracted from Mays cultivar 282se... Cultivar:282set_A556 Alternative accession-BioProject:PRJNA389800 ... + |