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

Abstract

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 behavior against pathogens, foraging, and subspecies. Additionally, markers from a GWAS of hygienic behavior 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 nonlethal 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.

Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies

“…Furthermore, we see both potentials and risks in the emergence of genomic selection methods in the honeybee [ 96 , 97 , 98 ]. In practice, the introduction of genomic selection has led to increased inbreeding rates and loss of genetic variance in cattle populations [ 99 , 100 ].…”

Geographical Distribution and Selection of European Honey Bees Resistant to Varroa destructor

“…Recent scientific programs on this topic are presented in Text S2 . Jones et al [ 185 ] have recently published a single nucleotide polymorphism array for selection and breeding on different traits including varroa resistance.…”

Non-Destructive Genotyping of Honeybee Queens to Support Selection and Breeding

“…The queens’ genotype representation in drone brood has been studied by sampling drone eggs and compared the detected loci to the queen’s own with DNA obtained from the muscle tissue. Drone eggs as an alternative source were shown to be reliable [ 12 ], and even with thirty drone eggs, the difference in the call between queen muscle tissue and pooled eggs was 0.17% on average. A drawback is a “refractory” period before the queen’s offspring may be sampled and thus, immediate genotyping after the virgin queen emerges is not possible [ 12 ].…”

“…Drone eggs as an alternative source were shown to be reliable [ 12 ], and even with thirty drone eggs, the difference in the call between queen muscle tissue and pooled eggs was 0.17% on average. A drawback is a “refractory” period before the queen’s offspring may be sampled and thus, immediate genotyping after the virgin queen emerges is not possible [ 12 ]. This also increases the cost of operation by forming nucleus colonies to sustain them until genotyping via drones is possible.…”

“…Their work laid the foundation for an early genotyping of queens, assuring that only those queens possessing specific traits identified molecularly will be placed in a colony [ 14 ]. Most recently, queen exuviae were also successfully used as a starting material for genotyping honeybee queens using commercially available honeybee ChipSNP [ 12 ]. In another study, the patriline composition of honeybee workers exhibiting fanning behavior was determined using exuviae as a non-destructive genotyping source [ 22 ], demonstrating the utility of such starting material for observing behavioral and genotypic dynamics in natural honeybee colonies.…”