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Construction of the third-generation Zea mays haplotype map

2017; University of Oxford; Volume: 7; Issue: 4 Linguagem: Inglês

10.1093/gigascience/gix134

2047-217X

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 Doebley, Jeffrey Ross‐Ibarra, Anne Lorant, Vince Buffalo, M. Cinta Romay, Edward S. Buckler, Doreen Ware, Jinsheng Lai, Qi Sun, Yunbi Xu,

Wheat and Barley Genetics and Pathology

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.