RT Journal Article
SR Electronic
T1 Construction of the third generation <em>Zea mays</em> haplotype map
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 026963
DO 10.1101/026963
A1 Robert Bukowski
A1 Xiaosen Guo
A1 Yanli Lu
A1 Cheng Zou
A1 Bing He
A1 Zhengqin Rong
A1 Bo Wang
A1 Dawen Xu
A1 Bicheng Yang
A1 Chuanxiao Xie
A1 Longjiang Fan
A1 Shibin Gao
A1 Xun Xu
A1 Gengyun Zhang
A1 Yingrui Li
A1 Yinping Jiao
A1 John Doebley
A1 Jeffrey Ross-Ibarra
A1 Vince Buffalo
A1 M. Cinta Romay
A1 Edward S. Buckler
A1 Yunbi Xu
A1 Jinsheng Lai
A1 Doreen Ware
A1 Qi Sun
YR 2016
UL http://biorxiv.org/content/early/2016/09/16/026963.abstract
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.