Examining parent-of-origin effects on transcription and RNA methylation in mediating aggressive behavior in honey bees (Apis mellifera)

Abstract

Conflict between genes inherited from the mother (matrigenes) and the father (patrigenes) is predicted to arise during social interactions among offspring if these genes are not evenly distributed among offspring genotypes. This intragenomic conflict drives parent-specific transcription patterns in offspring resulting from parent-specific epigenetic modifications. Previous tests of the kinship theory of intragenomic conflict in honey bees (Apis mellifera) provided evidence in support of theoretical predictions for variation in worker reproduction, which is associated with extreme variation in morphology and behavior. However, more subtle behaviors – such as aggression – have not been extensively studied. Additionally, the canonical epigenetic mark (DNA methylation) associated with parent-specific transcription in plant and mammalian model species does not appear to play the same role as in honey bees, and thus the molecular mechanisms underlying intragenomic conflict in this species is an open area of investigation. Here, we examined the role of intragenomic conflict in shaping aggression in honey bee workers through a reciprocal cross design and Oxford Nanopore direct RNA sequencing. We attempted to probe the underlying regulatory basis of this conflict through analyses of parent-specific RNA m6A and alternative splicing patterns. We report evidence that intragenomic conflict occurs in the context of honey bee aggression, with increased paternal and maternal allele-biased transcription in aggressive compared to non-aggressive bees, and higher paternal allele-biased transcription overall. However, we found no evidence to suggest that RNA m6A or alternative splicing mediate intragenomic conflict in this species.

Beyond conflict: Kinship theory of intragenomic conflict predicts individual variation in altruistic behaviour

“…Our results provide support for the model of intragenomic conflict altering phenotypes by cascading impacts on downstream GRNs, versus directly altering expression of a single gene with major effects (Patten et al, 2016). As in previous studies in bees (Bresnahan et al, 2023;Galbraith et al, 2016Galbraith et al, , 2021Marshall et al, 2020), there was little overlap between genes that showed parent-biased expression and genes whose overall expression differences were associated with behavioural variation. However, our SVM and the combined set of genes showing parent-biased expression both showed overrepresentation for genes encoding proteins with DNA binding function, including several TFs.…”

“…The KTIC predicts that selection should favour a balance between the individual effects of matrigenes and patrigenes engaged in conflict (Haig, 2008;Patten et al, 2016). In support of this prediction, previous studies in honey bees-which demonstrated that patrigenes favour the selfish behaviours of worker ovary activation (Galbraith et al, 2016(Galbraith et al, , 2021 and aggression (Bresnahan et al, 2023)-found that genes showing differences in parent-specific transcript abundance do not show differences in overall transcript abundance, presumably because upregulation of one allele was balanced by downregulation of the other allele. If the total amount of transcript for a given gene is the same between two behavioural phenotypes, how do genes engaged in parent-of-origin conflicts contribute to variation in physiology or behaviour?…”

“…We utilized the Storer-Kim (SK) binomial exact test of two proportions (Storer & Kim, 1990;Wang & Clark, 2014) and a general linear mixed-effects model with interaction terms (GLIMMIX) to identify transcripts that exhibited parent-of-origin expression bias following methods described previously (Bresnahan et al, 2023;Galbraith et al, 2016Galbraith et al, , 2021Kocher et al, 2015). Briefly, WGS reads were aligned to the latest A. mellifera genome assembly (Wallberg et al, 2019) to identify SNPs, which were used to construct individual genomes for each parent.…”

“…Honey bees are an outstanding model system for studying the causes and consequences of intragenomic conflict (Bresnahan et al, 2023;Galbraith et al, 2016Galbraith et al, , 2021Gibson et al, 2015;Kocher et al, 2015;Smith et al, 2020). Due to their haplodiploid genetics, polyandrous mating system and large colony size, matrigenes and patrigenes are unevenly distributed across colony members, and multiple social interactions are predicted to be influenced by intragenomic conflict (Queller, 2003).…”

Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)

“…Thus, matrigenes and patrigenes are unevenly distributed among nestmates and should experience different selective pressures leading to POEs on transcription (Queller, 2003). Such parent-of-origin intragenomic conflicts have been demonstrated in association with behavioral variation in adult worker honey bees (Bresnahan et al, 2023a(Bresnahan et al, , 2023bGalbraith et al, 2016aGalbraith et al, , 2021Gibson et al, 2015;Kocher et al, 2015), and in the transcriptomes of diploid eggs laid by queens (Smith et al, 2020).…”