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., Yang, B., Xie, C., Fan, L., Gao, S., Xu, X., Zhang, G., Li, Y., Jiao, Y., Doebley, J. F., Ross-Ibarra, J., Lorant, A., Buffalo, V., Romay, M. C., Buckler, E. S., Ware, D., Lai, J., Sun, Q., Xu, Y. (2017) Construction of the third generation Zea mays haplotype map. Gigascience. ISSN 2047-217x

DOI: 10.1093/gigascience/gix134


Background: 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. Results: 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. Conclusions: 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.

Item Type: Paper
Uncontrolled Keywords: Zea mays sequencing genotyping haplotype map identity by descent imputation linkage disequilibrium variant discovery
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism > haplotype
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date Deposited: 10 Jan 2018 17:40
Last Modified: 10 Jan 2018 17:40
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