Construction of the third-generation Zea mays haplotype map

文献类型： 外文期刊

第一作者： Bukowski, Robert

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

作者机构：

关键词： Zea may; sequencing; haplotype map; genotyping; variant discovery; linkage disequilibrium; identity by descent; imputation

期刊名称：GIGASCIENCE （ 影响因子：6.524； 五年影响因子：8.702 ）

ISSN： 2047-217X

年卷期： 2017 年 7 卷 4 期

页码：

收录情况： SCI

摘要： 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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