Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

Authors

Gen Xu, University of Nebraska-LincolnFollow
Jing Lyu, University of Nebraska-LincolnFollow
Qing Li, University of MinnesotaFollow
Han Liu, Institute of Botany, Chinese Academy of Sciences
Dafang Wang, Delta State University, Cleveland, MSFollow
Mei Zhang, Institute of Botany, Chinese Academy of Sciences
Nathan M. Springer, University of Minnesota - Twin CitiesFollow
Jeffrey Ross-Ibarra, University of California, DavisFollow
Jinliang Yang, University of Nebraska - LincolnFollow

ORCID IDs

Nathan M. Springer http://orcid.org/0000-0002-7301-4759

Jeffrey Ross-Ibarra http://orcid.org/0000-0003-1656-4954

Jinliang Yang http://orcid.org/0000-0002-0999-3518

Document Type

Article

Date of this Version

2020

Citation

NATURE COMMUNICATIONS (2020) 11:5539

doi:10.1038/s41467-020-19333-4

Comments

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License

Abstract

DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.

Supplementary files attached below.