Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee

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, ge...