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Construction of the third-generation Zea mays haplotype map
Robert Bukowski1, Xiaosen Guo2,3, Yanli Lu4
1Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.
Gigascience
|January 5, 2018
Summary
Researchers developed the maize haplotype version 3 (HapMap 3) from whole-genome sequencing of 1218 maize lines. This study identified millions of genetic variant sites, advancing maize genetic variation studies.
Area of Science:
- Genomics
- Plant Science
- Bioinformatics
Background:
- Characterizing genetic variations in maize is difficult due to genome collinearity issues.
- An international consortium developed the maize haplotype version 3 (HapMap 3) using whole-genome sequencing data.
- The HapMap 3 dataset includes 1218 maize lines, encompassing pre-domestication and domesticated varieties globally.
Purpose of the Study:
- To overcome challenges in maize genetic variation characterization.
- To build a comprehensive maize haplotype map (HapMap 3).
- To identify a large number of genetic variant sites across diverse maize varieties.
Main Methods:
- Whole-genome sequencing of 1218 maize lines.
- Development of a new computational pipeline to process over 12 trillion base pairs of sequencing data.
- Application of population genetics filters to identify variant sites.
Main Results:
- Identification of over 83 million variant sites in the maize genome.
- Discovery of polymorphisms in regions with preserved collinearity.
- The B73 reference genome represents only a fraction of all existing haplotypes.
Conclusions:
- The maize haplotype version 3 (HapMap 3) provides a valuable resource for studying maize genetic diversity.
- Despite advancements, the limited representation of haplotypes by the B73 reference genome remains a significant challenge.
- Further research is needed to fully capture the extent of maize haplotype diversity.
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