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

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.