Lineage and parent-of-origin effects in DNA methylation of honey bees (Apis mellifera) revealed by reciprocal crosses and whole-genome bisulfite sequencing.

Parent-of-origin methylation arises when the methylation patterns of a particular allele is dependent on the parent it was inherited from. Previous work in honey bees has shown evidence of parent-of-origin specific expression, yet the mechanisms regulating such pattern remains unknown in honey bees. In mammals and plants, DNA methylation is known to regulate parent-of-origin effects such as genomic imprinting. Here, we utilize genotyping of reciprocal European and Africanized honey bee crosses to study genome-wide allele-specific methylation patterns in sterile and reproductive individuals. Our data confirms the presence of allele-specific methylation in honey bees in lineage-specific contexts but also importantly, though to a lesser degree, parent-of-origin contexts. We show that the majority of allele-specific methylation occur due to lineage rather than parent-of-origin factors, regardless of reproductive state. Interestingly, genes affected by allele-specific DNA methylation often exhibit both lineage and parent-of-origin effects, indicating that they are particularly labile in terms of DNA methylation patterns. Additionally, we re-analyzed our previous study on parent-of-origin specific expression in honey bees and found little association with parent-of-origin specific methylation. These results indicate strong genetic background effects on allelic DNA methylation, and suggest that while parent-of-origin effects are manifested in both DNA methylation and gene expression, they are not directly associated with each other.