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. (April 2018) Construction of the third generation Zea mays haplotype map. Gigascience, 7 (4). pp. 1-12. ISSN 2047-217x

URL: https://www.ncbi.nlm.nih.gov/pubmed/29300887
DOI: 10.1093/gigascience/gix134

Abstract

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
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
Investigative techniques and equipment
organism description > plant > maize
Investigative techniques and equipment > assays
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism > haplotype
organism description > plant
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date: 1 April 2018
Date Deposited: 10 Jan 2018 17:40
Last Modified: 07 Feb 2024 18:35
PMCID: PMC5890452
Related URLs:
URI: https://repository.cshl.edu/id/eprint/35797

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