PT  - JOURNAL ARTICLE
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  - M. Cinta Romay
AU  - Edward S. Buckler
AU  - Yunbi Xu
AU  - Jinsheng Lai
AU  - Doreen Ware
AU  - Qi Sun
TI  - Construction of the third generation <em>Zea mays</em> haplotype map
AID  - 10.1101/026963
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 026963
4099  - http://biorxiv.org/content/early/2016/09/16/026963.short
4100  - http://biorxiv.org/content/early/2016/09/16/026963.full
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 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world.Results A new computational pipeline was set up to process over 12 trillion bp of sequencing data, and a set of population genetics filters were applied to identify over 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.