Evolutionary and functional genomics of DNA methylation in maize domestication and improvement.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
02 11 2020
02 11 2020
Historique:
received:
25
03
2020
accepted:
08
10
2020
entrez:
3
11
2020
pubmed:
4
11
2020
medline:
21
11
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 33139747
doi: 10.1038/s41467-020-19333-4
pii: 10.1038/s41467-020-19333-4
pmc: PMC7606521
doi:
Substances chimiques
DNA, Plant
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
5539Subventions
Organisme : NIGMS NIH HHS
ID : P20 GM103476
Pays : United States
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