Construction of the third-generation Zea mays haplotype map

Robert Bukowski; 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; John F. Doebley; Jeffrey Ross-Ibarra; Anne Lorant; Vince Buffalo; M. Cinta Romay; Edward S. Buckler; Doreen Ware; Jinsheng Lai; Qi Sun; Yunbi Xu

doi:10.1093/gigascience/gix134

Construction of the third-generation Zea mays haplotype map

Robert Bukowski, 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, John F. Doebley, Jeffrey Ross-Ibarra, Anne Lorant, Vince BuffaloM. Cinta Romay, Edward S. Buckler, Doreen Ware, Jinsheng Lai, Qi Sun, Yunbi Xu

Plant & Soil Science

Research output: Contribution to journal › Article › peer-review

163 Scopus citations

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.

Original language	English
Article number	gix134
Journal	GigaScience
Volume	7
Issue number	4
DOIs	https://doi.org/10.1093/gigascience/gix134
State	Published - Apr 1 2018

Keywords

Genotyping
Haplotype map
Identity by descent
Imputation
Linkage disequilibrium
Sequencing
Variant discovery
Zea may

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10.1093/gigascience/gix134

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title = "Construction of the third-generation Zea mays haplotype map",

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.",

keywords = "Genotyping, Haplotype map, Identity by descent, Imputation, Linkage disequilibrium, Sequencing, Variant discovery, Zea may",

author = "Robert Bukowski and Xiaosen Guo and Yanli Lu and Cheng Zou and Bing He and Zhengqin Rong and Bo Wang and Dawen Xu and Bicheng Yang and Chuanxiao Xie and Longjiang Fan and Shibin Gao and Xun Xu and Gengyun Zhang and Yingrui Li and Yinping Jiao and Doebley, {John F.} and Jeffrey Ross-Ibarra and Anne Lorant and Vince Buffalo and {Cinta Romay}, M. and Buckler, {Edward S.} and Doreen Ware and Jinsheng Lai and Qi Sun and Yunbi Xu",

year = "2018",

month = apr,

day = "1",

doi = "10.1093/gigascience/gix134",

language = "English",

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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, JF, Ross-Ibarra, J, Lorant, A, Buffalo, V, Cinta Romay, M, Buckler, ES, Ware, D, Lai, J, Sun, Q & Xu, Y 2018, 'Construction of the third-generation Zea mays haplotype map', GigaScience, vol. 7, no. 4, gix134. https://doi.org/10.1093/gigascience/gix134

TY - JOUR

T1 - Construction of the third-generation Zea mays haplotype map

AU - Bukowski, Robert

AU - Guo, Xiaosen

AU - Lu, Yanli

AU - Zou, Cheng

AU - He, Bing

AU - Rong, Zhengqin

AU - Wang, Bo

AU - Xu, Dawen

AU - Yang, Bicheng

AU - Xie, Chuanxiao

AU - Fan, Longjiang

AU - Gao, Shibin

AU - Xu, Xun

AU - Zhang, Gengyun

AU - Li, Yingrui

AU - Jiao, Yinping

AU - Doebley, John F.

AU - Ross-Ibarra, Jeffrey

AU - Lorant, Anne

AU - Buffalo, Vince

AU - Cinta Romay, M.

AU - Buckler, Edward S.

AU - Ware, Doreen

AU - Lai, Jinsheng

AU - Sun, Qi

AU - Xu, Yunbi

PY - 2018/4/1

Y1 - 2018/4/1

N2 - 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.

AB - 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.

KW - Genotyping

KW - Haplotype map

KW - Identity by descent

KW - Imputation

KW - Linkage disequilibrium

KW - Sequencing

KW - Variant discovery

KW - Zea may

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U2 - 10.1093/gigascience/gix134

DO - 10.1093/gigascience/gix134

M3 - Article

C2 - 29300887

AN - SCOPUS:85054300311

SN - 2047-217X

VL - 7

JO - GigaScience

JF - GigaScience

IS - 4

M1 - gix134

ER -

Construction of the third-generation Zea mays haplotype map

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