Construction of the third-generation Zea mays haplotype map

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 F. Doebley, Jeffrey Ross-Ibarra, Anne Lorant, Vince BuffaloM. Cinta Romay, Edward S. Buckler, Doreen Ware, Jinsheng Lai, Qi Sun, Yunbi Xu

Research output: Contribution to journalArticlepeer-review

157 Scopus citations


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.

Original languageEnglish
Article numbergix134
Issue number4
StatePublished - Apr 1 2018


  • Genotyping
  • Haplotype map
  • Identity by descent
  • Imputation
  • Linkage disequilibrium
  • Sequencing
  • Variant discovery
  • Zea may


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