High-throughput high density genotyping arrays continue to be a fast, accurate, and cost-effective method for genotyping thousands of polymorphisms in high numbers of individuals. Here we have developed a new high-density SNP genotyping array (103 270 SNPs) for honey bees, one of the most ecologically and economically important pollinators worldwide. SNPs were detected by conducting whole genome resequencing of 61 honey bee drones (haploid males) from throughout Europe. Selection of SNPs for the chip was done in multiple steps using several criteria. The majority of SNPs were selected based on their location within known candidate regions or genes underlying a range of honey bee traits, including hygienic behaviour against pathogens, foraging and subspecies. Additionally, markers from a GWAS of hygienic behaviour against the major honey bee parasite Varroa destructor, were brought over. The chip also includes SNPs associated with each of three major breeding objectives - honey yield, gentleness and Varroa resistance. We validated the chip and make recommendations for its use by determining error rates in repeat genotypings, examining the genotyping performance of different tissues, and by testing how well different sample types represent the queen’s genotype. The latter is a key test because it is highly beneficial to be able to determine the queen’s genotype by non-lethal means. The array is now publicly available and we suggest it will be a useful tool in genomic selection and honey bee breeding, as well as for GWAS of different traits, and for population genomic, adaptation and conservation questions.

SNP_Info_HDHB_SNPAssay.xlsx

The file lists all 103'270 SNPs included on the HDHB chip. The individual columns state the SNP's local ID, linkage group, base position, flanking sequences, and the polymorphisms.

Supp_Table_2.xlsx

The file lists all 3'272 samples available for the publication. The data includes the Beebreed ID (www.beebreed.eu) of the colony whose queen was genotyped, as well as its location, and the tissue type of the sample.

Genotypes_for_Supp_Table_2.tsv

This is a large file to be opened with special editors (e.g. "vim" or "Notepad++") or custom scripts (e.g. in languages R or Python). The first line gives the local IDs of the SNPs. Each line starts with the sample number in Supp_Table_2.xlsx with an additional "S" in front of it. The row proceeds giving the sample's genotyping results. Genotypes "AA", "AB", and "BB" are coded as "0", "1", and "2", respectively, while "0" states that the location could not be called for this sample.