Population genomics from a food matrix: estimating csd variability using next generation sequencing on Apis mellifera DNA present in honey

The complementary sex determiner (csd) gene is a crucial genetic factor in the sex determination of Apis mellifera L. Females only develop if fertilized eggs have functional heterozygous genotypes at this gene. Males, being haploids, are emizygous. Two identical csd alleles result in non-viable males. Given the recent decline in honey bee populations, it is imperative to monitor allele variability at this gene to prevent negative effects of high inbreeding levels. In this study, we evaluated the use of next generation sequencing in conjunction with environmental honey DNA as a source of honey bee genomic information to obtain extensive sequencing data for analysing variability at the hypervariable region (HVR) of the csd gene. DNA was extracted from several honey samples directly collected from oneycombs of various colonies. A bioinformatic pipeline was utilised to analyse approx. 1.5 million reads, identifying a total of 160 different csd alleles, 55% of which were novel. The average number of alleles per sample corresponded with the expected number of patrilines per colony, based on queen mating behaviour. The diversity of alleles at the csd gene could also offer valuable information for reconstructing the honey bee population genetic history.