| Summary: | Growth and wood formation are crucial and complex biological processes during tree development. These biological regulatory processes are presumed to be controlled by DNA methylation. However, there is little direct evidence to show that genes taking part in wood regulation are affected by cytosine methylation, resulting in phenotypic variations. Here, we detected epimarkers using a methylation-sensitive amplification polymorphism (MSAP) method and performed epimarker–trait association analysis on the basis of nine growth and wood property traits within populations of 432 genotypes of <i>Populus tomentosa</i>. Tree height was positively correlated with relative full-methylation level, and 1101 out of 2393 polymorphic epimarkers were associated with phenotypic traits, explaining 1.1–7.8% of the phenotypic variation. In total, 116 epimarkers were successfully sequenced, and 96 out of these sequences were linked to putative genes. Among them, 13 candidate genes were randomly selected for verification using quantitative real-time PCR (qRT-PCR), and it also showed the expression of nine putative genes of <i>PtCYP450</i>, <i>PtCpn60</i>, <i>PtPME</i>, <i>PtSCP</i>, <i>PtGH</i>, <i>PtMYB</i>, <i>PtWRKY</i>, <i>PtSTP</i>, and <i>PtABC</i> were negatively correlated with DNA methylation level. Therefore, it suggested that changes in DNA methylation might contribute to regulating tree growth and wood property traits.
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