# Inheritance of DNA Methylation Patterns and Its Role in Modulating Allelic Expression in Camellia F1 Hybrids

## TL;DR

This study explores how DNA methylation is inherited in Camellia hybrids and how it affects gene expression, revealing that methylation patterns often balance rather than bias gene activity.

## Contribution

The study reveals that parent-specific methylation sites balance allelic expression in Camellia F1 hybrids, challenging the assumption that allele-specific methylation leads to biased expression.

## Key findings

- The F1 hybrid's methylation level was intermediate between the two parents.
- ASM was rare due to widespread, randomly distributed parent-specific methylation sites.
- ASM influenced biased expression of some flower development-related alleles.

## Abstract

DNA methylation, as an important epigenetic modification, plays a key role in shaping hybrid phenotypes. Studies have shown that DNA methylation—specifically, allele-specific methylation (ASM)—can mediate allelic expression imbalance (AEI) and participate in the regulation of plant growth and development. However, since this regulatory mechanism is often sequence-dependent, the prevalence of ASM and the extent to which it influences allelic expression remain poorly characterized. To address this challenge, the present study utilized Camellia azalea, C. amplexicaulis and their F1 hybrids [C. azalea (♀) × C. amplexicaulis (♂)] as research materials. By performing whole-genome bisulfite sequencing (WGBS), resequencing, and transcriptome sequencing, we assessed the inheritance of DNA methylation patterns and its role in shaping allelic expression in F1 hybrids. The results showed the following: (1) the overall cytosine methylation level in the F1 hybrid was intermediate between the two parents; (2) the methylation states of the parental genomes were partly transmitted to the next generation; (3) ASM was not prevalent in the F1 hybrids, primarily because biparental parent-specific methylation sites (PSMSs) were widespread and randomly distributed, which often act on the same allele pairs; (4) although ASM was not common, it led to biased expression of some alleles related to flower development. The results indicated that ASM was rare in F1 hybrids, mainly because PSMSs occurred randomly. Instead of causing AEI, the randomly distributed PSMSs played a more important role in balancing allelic expression in F1 hybrids. Therefore, most of the alleles in F1 were not biasedly expressed. ASM did not necessarily lead to allele-biased expression; however, its occurrence may hold significant biological implications in modulating AEI and transgressive phenotypes in the F1 hybrids. These findings elucidate the synergistic effects of genetic and epigenetic controls on transcriptional regulation in hybrid plants, substantially deepening the mechanistic understanding of hybridization at the molecular scale.