Construction of the third-generation <i>Zea mays</i> haplotype map

TLDR

Characterizing genetic variation in maize is difficult because collinearity between genomes deteriorates, and the B73 reference represents only a fraction of all haplotypes, limiting analyses. An international consortium built HapMap 3 from whole‑genome sequencing of 1,218 maize lines worldwide, using a new computational pipeline that processed over 12 trillion base pairs and applied population‑genetics filters to identify more than 83 million variant sites. The study identified polymorphisms in genomic regions where collinearity is largely preserved across maize varieties.

Abstract

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.