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Abstract
Simple SummaryHoney contains traces of the DNA of the honey bees that produced it. This environmental DNA can therefore be used to investigate the genome of the honey bees. In this study, we used a next generation sequencing technology to analyze the variability of a key gene of Apis mellifera L., the complementary sex determiner (csd) gene, using honey environmental DNA as a source of honey bee DNA. This gene determines the sex of the bees. Two different alleles at this locus are needed to produce females whereas males have only one copy of this gene as they are haploid. In case two identical alleles are present in a diploid individual, the larvae are not vital and are discarded by the workers. Therefore, there is an advantage in maintaining a large csd diversity in honey bee populations. In light of the recent decline in honey bee populations, it is important to monitor the allele variability at this gene. The applied methodology provided a new strategy to disclose the genetic diversity at the csd gene at the population-wide level and identify most, if not all, csd alleles present in the colonies in a single analysis.The complementary sex determiner (csd) gene plays an essential role in the sex determination of Apis mellifera L. Females develop only if fertilized eggs have functional heterozygous genotypes at this gene whereas males, being haploids, are hemizygous. Two identical csd alleles produce non vital males. In light of the recent decline in honey bee populations, it is therefore important to monitor the allele variability at this gene. In this study, we tested the application of next generation semiconductor-based sequencing technology (Ion Torrent) coupled with environmental honey DNA as a source of honey bee genome information to retrieve massive sequencing data for the analysis of variability at the hypervariable region (HVR) of the csd gene. DNA was extracted from 12 honey samples collected from honeycombs directly retrieved from 12 different colonies. A specifically designed bioinformatic pipeline, applied to analyze a total of about 1.5 million reads, identified a total of 160 different csd alleles, 55% of which were novel. The average number of alleles per sample was compatible with the number of expected patrilines per colony, according to the mating behavior of the queens. Allele diversity at the csd could also provide information useful to reconstruct the history of the honey.
Highlights
Honey bees (Apis mellifera L., 1758) are haplodiploid organisms like all species of the insect order Hymenoptera [1]
If two functional identical csd alleles are present, the condition results in being similar to hemizygosity and the honey bees develop into sterile diploid male forms [3,4,5]
We investigated the level of genetic diversity at the csd gene considering all of the analyzed samples together or considering only data within each sample separately
Summary
Honey bees (Apis mellifera L., 1758) are haplodiploid organisms like all species of the insect order Hymenoptera [1] In these organisms, females develop from fertilized oocytes, which form diploid embryos, whereas males develop from unfertilized eggs, which produce haploid embryos [1,2]. If two functional identical csd alleles are present (i.e., homozygosity), the condition results in being similar to hemizygosity and the honey bees develop into sterile diploid male forms [3,4,5] These diploid males are eliminated by the worker bees within three days of hatching as they would constitute a drain in colony resources and energy [6,7]. These eliminated larvae, cause decreased brood viability and, in turn, can affect colony growth and productivity due to the lack of worker bees [8,9,10]
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