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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.
Variation and evolution of DNA methylation during maize domestication remain largely unknown. Here, the authors generate genome and methylome sequencing data as well as HiChIP-based interactome data to investigate the adaptive and phenotypic consequences of methylation variations in maize.
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1 University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, USA (GRID:grid.24434.35) (ISNI:0000 0004 1937 0060); University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, USA (GRID:grid.24434.35) (ISNI:0000 0004 1937 0060)
2 University of Minnesota, Department of Plant Biology, Microbial and Plant Genomics Institute, Saint Paul, USA (GRID:grid.17635.36) (ISNI:0000000419368657); Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement, Wuhan, China (GRID:grid.35155.37) (ISNI:0000 0004 1790 4137)
3 Chinese Academy of Sciences, Key Laboratory of Plant Molecular Physiology, Institute of Botany, Beijing, China (GRID:grid.9227.e) (ISNI:0000000119573309)
4 Delta State University, Division of Math and Sciences, Cleveland, USA (GRID:grid.255007.5) (ISNI:0000000403908866)
5 University of Minnesota, Department of Plant Biology, Microbial and Plant Genomics Institute, Saint Paul, USA (GRID:grid.17635.36) (ISNI:0000000419368657)
6 University of California, Department of Evolution and Ecology, Center for Population Biology and Genome Center, Davis, USA (GRID:grid.27860.3b) (ISNI:0000 0004 1936 9684)