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- W3100190346 abstract "DNA methylation is a ubiquitous chromatin feature — in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte ( Zea mays ssp. parviglumis ) to investigate the adaptive and phenotypic consequences of methylation variations in maize. By using a novel estimation approach, we inferred the methylome site frequency spectrum (mSFS) to estimate forward and backward epimutation rates and selection coefficients. We found weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) were identified in population-wide that are correlated with recent selection. Further investigation revealed that DMRs are enriched in 5’ untranslated regions, and that maize hypomethylated DMRs likely helped rewire distal gene regulation. For two trait-associated DMRs, vgt1 -DMR and tb1 -DMR, our HiChIP data indicated that the interactive loops between DMRs and respective downstream genes were present in B73, a modern maize line, but absent in teosinte. Functional analyses suggested that these DMRs likely served as cis -acting elements that modulated gene regulation after domestication. 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." @default.
- W3100190346 created "2020-11-23" @default.
- W3100190346 creator A5006569282 @default.
- W3100190346 creator A5019708503 @default.
- W3100190346 creator A5023378154 @default.
- W3100190346 creator A5051993838 @default.
- W3100190346 creator A5053780153 @default.
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- W3100190346 creator A5085102532 @default.
- W3100190346 creator A5087046049 @default.
- W3100190346 creator A5089438704 @default.
- W3100190346 date "2020-03-15" @default.
- W3100190346 modified "2023-09-23" @default.
- W3100190346 title "Evolutionary and functional genomics of DNA methylation in maize domestication and improvement" @default.
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