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Gigascience. 2018 Apr 1;7(4):1-12. doi: 10.1093/gigascience/gix134.

Construction of the third-generation Zea mays haplotype map.

Author information

1
Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.
2
BGI-Shenzhen, Shenzhen 518083, China.
3
Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
4
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.
5
Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facilities for Crop Gene Resource and Genetic Improvement, Beijing 100081, China.
6
Institute of Crop Science and Institute of Bioinformatics, Department of Agronomy, Zhejiang University, Hangzhou 310058, China.
7
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
8
Department of Genetics, University of Wisconsin, Madison, WI 53706, USA.
9
Department of Plant Sciences, University of California, Davis, CA 95616, USA.
10
Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.
11
US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA.
12
National Maize Improvement Center, China Agricultural University, Beijing 100193, China.
13
International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130, Texcoco, Mexico.

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 1218 maize lines, covering predomestication and domesticated Zea mays varieties across the world.

Results:

A new computational pipeline was set up to process more than 12 trillion bp of sequencing data, and a set of population genetics filters was applied to identify more than 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.

PMID:
29300887
PMCID:
PMC5890452
DOI:
10.1093/gigascience/gix134
[Indexed for MEDLINE]
Free PMC Article

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