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A genome-wide survey of DNA methylation in hexaploid wheat

Gardiner, Laura-Jayne, Quinton-Tulloch, Mark, Olohan, Lisa, Price, Jonathan, Hall, Neil, Hall, Anthony
Genome biology 2015 v.16 no.1 pp. 273
Aegilops tauschii, DNA methylation, diploidy, epigenetics, gene expression, genes, hexaploidy, sodium bisulfite, surveys, temperature, wheat
BACKGROUND: DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat. RESULTS: While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome-specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii. CONCLUSIONS: We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome-specific methylation shows more variation.