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Construction of the third-generation Zea mays haplotype map

By: Bukowski, R.
Contributor(s): Xiaosen Guo | Yanli Lu | Cheng Zou | Bing He | Zhengqin Rong | Bo Wang | Dawen Xu | Bicheng Yang | Chuanxiao Xie | Longjiang Fan | Shibin Gao | Xun Xu | Gengyun Zhang | Yingrui Li | Yinping Jiao | Doebley, J.F | Ross-Ibarra, J | Lorant, A | Buffalo, V | Romay, C | Buckler, E.S | Doreen Ware | Jinsheng Lai | Qi Sun | Yunbi Xu.
Material type: materialTypeLabelArticlePublisher: United Kingdom : Oxford University Press, 2018Subject(s): Zea mays | Genetic variation | GenomicsOnline resources: Open Access through Dspace In: GigaScience v. 7, no. 4, p. 1–12Summary: 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.
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Article CIMMYT Knowledge Center: John Woolston Library

Lic. Jose Juan Caballero Flores

 

CIMMYT Staff Publications Collection Available
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Open Access

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.

Maize CRP FP2 - Novel tools, technologies and traits for improving genetic gains and breeding efficiency FP3 - Stress resilient and nutritious maize

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