TY - JOUR T1 - Construction of the third generation <em>Zea mays</em> haplotype map JF - bioRxiv DO - 10.1101/026963 SP - 026963 AU - Robert Bukowski AU - Xiaosen Guo AU - Yanli Lu AU - Cheng Zou AU - Bing He AU - Zhengqin Rong AU - Bo Wang AU - Dawen Xu AU - Bicheng Yang AU - Chuanxiao Xie AU - Longjiang Fan AU - Shibin Gao AU - Xun Xu AU - Gengyun Zhang AU - Yingrui Li AU - Yinping Jiao AU - John Doebley AU - Jeffrey Ross-Ibarra AU - Vince Buffalo AU - Edward S. Buckler AU - Yunbi Xu AU - Jinsheng Lai AU - Doreen Ware AU - Qi Sun Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/09/16/026963.abstract N2 - Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species and the fact the B73 genome used as the reference only represents a fraction of all haplotypes. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap3), built from whole genome sequencing data from 916 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world. A new computational pipeline was set up to process over 7 trillion bp of sequencing data, and a set of population genetics filters were applied to identify over 60 million variant sites in regions where collinearity is largely preserved in the maize species. ER -