Genome-Wide Differential DNA Methylation in Reproductive, Morphological, and Visual System Differences Between Queen Bee and Worker Bee (Apis mellifera)

Hongfang Wang,Zhenguo Liu,Lanting Ma,Weixing Zhang,Baohua Xu,Ying Wang

doi:10.3389/fgene.2020.00770

Abstract

There are many differences in external morphology and internal physiology between the Apis mellifera queen bee and worker bee, some of which are relevant to beekeeping production. These include reproductive traits, body size, royal jelly secreting properties, and visual system development, among others. The identification of candidate genes that control the differentiation of these traits is critical for selective honeybee breeding programs. In this study, we compared the genomic methylation of queen bee and worker bee larvae at 3, 4, and 5 days of age by whole-genome bisulfite sequencing, and found that the basic characteristics of genomic methylation in queen and worker larvae were the same. There were approximately 49 million cytosines in the Apis larvae genome, of which about 90,000 were methylated. Methylated CpG sites accounted for 99% of the methylated cytosines, and methylation mainly occurred in exons. However, methylation levels of queen and worker larvae showed different trends with age: the methylation level of queen larvae varied with age in an inverted parabola, while the corresponding trend for worker larvae with resembled an exponential curve with a platform. The methylation level of queen larvae was higher than that of worker larvae at 3 days of age, lower than that of worker larvae at 4 days of age, and similar to that of worker larvae at 5 days old. The top 10 differentially methylated genes (DMGs) and 13 caste-specific methylated genes were listed, and correlations with caste determination were speculated. We additionally screened 38 DMGs between queen larvae and worker larvae involved in specific organ differentiation as well as reproduction, morphology, and vision differentiation during caste determination. These genes are potential molecular markers for selective breeding of A. mellifera to improve fecundity, royal jelly production, body size, and foraging, and represent candidate genes for investigating specialized functional segregation during the process of caste differentiation.

Highlights

MATERIALS AND METHODSHoneybees are social insects which possess the ability to develop into two castes of organisms with different morphological and physiological features, with the same genome, in response to environmental cues (Winston, 1991; Groh and Rössler, 2008)
Published studies reveal methylation patterns in the adult brain (Lyko et al, 2010) and larval head (Foret et al, 2012): 70,000 methylated cytosines are reported in the adult brain, and 1,00,000 in the larval head
We found approximately 90,000 methylated cytosines in 3–5 day-old larvae; the majority of this methylation occurred in the exons, and over 99% methylated cytosines occurred in CpG dinucleotides

Summary

Introduction

Honeybees are social insects which possess the ability to develop into two castes of organisms with different morphological and physiological features, with the same genome, in response to environmental cues (Winston, 1991; Groh and Rössler, 2008). This fascinating biological phenomenon is referred to as caste differentiation. There are many differences in characteristics between worker bees and queen bees. The selection of candidate genes related to these traits should establish a strong theoretical foundation for bee selective breeding and beekeeping

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Results

Conclusion