Identification of quantitative trait loci associated with calmness and gentleness in honey bees using whole-genome sequences

An integrative genomic toolkit for studying the genetic, evolutionary, and molecular underpinnings of eusociality in insects

While genomic resources for social insects have vastly increased over the past two decades, we are still far from understanding the genetic and molecular basis of eusociality. Here, we briefly review three scientific advancements that, when integrated, can be highly synergistic for advancing our knowledge of the genetics and evolution of eusocial traits. Population genomics provides a natural way to quantify the strength of natural selection on coding and regulatory sequences, highlighting genes that have undergone adaptive evolution during the evolution or maintenance of eusociality. Genome-wide association studies (GWAS) can be used to characterize the complex genetic architecture underlying eusocial traits and identify candidate causal variants. Concurrently, CRISPR/Cas9 enables the precise manipulation of gene function to both validate genotype-phenotype associations and study the molecular biology underlying interesting traits. While each approach has its own advantages and disadvantages, which we discuss herein, we argue that their combination will ultimately help us better understand the genetics and evolution of eusocial behavior. Specifically, by triangulating across these three different approaches, researchers can directly identify and study loci that have a causal association with key phenotypes and have evidence of positive selection over the relevant timescales associated with the evolution and maintenance of eusociality in insects.

The Potential of Instrumental Insemination for Sustainable Honeybee Breeding

Mating control is crucial in honeybee breeding and commonly guaranteed by bringing virgin queens to isolated mating stations (IMS) for their nuptial flights. However, most breeding programs struggle to provide sufficiently many IMS. Research institutions routinely perform instrumental insemination of honeybees, but its potential to substitute IMS in breeding programs has not been sufficiently studied. We performed stochastic simulations to compare instrumental insemination strategies and mating on IMS in terms of genetic progress and inbreeding development. We focused on the role of paternal generation intervals, which can be shortened to two years with instrumental insemination in comparison to three years when using IMS. After 70 years, instrumental insemination yielded up to 42% higher genetic gain than IMS strategies-particularly with few available mating sites. Inbreeding rates with instrumental insemination and IMS were comparable. When the paternal generation interval in instrumental insemination was stretched to three years, the number of drone producers required for sustainable breeding was reduced substantially. In contrast, when shortening the interval to two years, it yielded the highest generational inbreeding rates (up to 2.28%). Overall, instrumental insemination with drones from a single colony appears as a viable strategy for honeybee breeding and a promising alternative to IMS.

AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap

Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen's alleles and none from the many drones she mated with. Thus the ordered combination or 'phase' of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.

Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole-genome sequencing data

Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent. The length and distribution of ROH segments provide insights into the genetic diversity of populations and can be associated with selection signatures. Here, we analyzed reconstructed whole-genome queen genotypes, from a pool-seq data experiment including 265 Western honeybee colonies from Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a dynamic population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well-defined substructures according to the genetic origin of the queens. Despite the current applied conservation efforts, we pinpointed 79 admixed queens. Genomic inbreeding (F ROH) strongly varied within and between the identified subpopulations. Conserved A. m. mellifera from Switzerland had the highest mean F ROH (3.39%), while queens originating from a conservation area in France, which were also highly admixed, showed significantly lower F ROH (0.45%). The majority of A. m. carnica queens were also highly admixed, except 12 purebred queens with a mean F ROH of 2.33%. Within the breed-specific ROH islands, we identified 14 coding genes for A. m. mellifera and five for A. m. carnica, respectively. Local adaption of A. m. mellifera could be suggested by the identification of genes involved in the response to ultraviolet light (Crh-BP, Uvop) and body size (Hex70a, Hex70b), while the A. m. carnica specific genes Cpr3 and Cpr4 are most likely associated with the lighter striping pattern, a morphological phenotype expected in this subspecies. We demonstrated that queen genotypes derived from pooled workers are useful tool to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees.

A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA

Awareness has been raised over the last years on the genetic integrity of autochthonous honey bee subspecies. Genomic tools available in Apis mellifera can make it possible to measure this information by targeting individual honey bee DNA. Honey contains DNA traces from all organisms that contributed or were involved in its production steps, including the honey bees of the colony. In this study, we designed and tested a genotyping by sequencing (GBS) assay to analyse single nucleotide polymorphisms (SNPs) of A. mellifera nuclear genome using environmental DNA extracted from honey. A total of 121 SNPs (97 SNPs informative for honey bee subspecies identification and 24 SNPs associated with relevant traits of the colonies) were used in the assay to genotype honey DNA, which derives from thousands of honey bees. Results were integrated with information derived from previous studies and whole genome resequencing datasets. This GBS method is highly reliable in estimating honey bee SNP allele frequencies of the whole colony from which the honey derived. This assay can be used to identify the honey bee subspecies of the colony that produced the honey and, in turn, to authenticate the entomological origin of the honey.

Two quantitative trait loci are associated with recapping of Varroa destructor-infested brood cells in Apis mellifera mellifera

Recapping of Varroa destructor-infested brood cells is a trait that has recently attracted interest in honey bee breeding to select mite-resistant Apis mellifera colonies. To investigate the genetic architecture of this trait, we evaluated a sample of A. mellifera mellifera colonies (N = 155) from Switzerland and France and performed a genome-wide association study, using a pool of 500 workers per colony for next-generation sequencing. The results revealed that two QTL were significantly (P < 0.05) associated with recapping of V. destructor-infested brood cells. The best-associated QTL is located on chromosome 5 in a region previously found to be associated with grooming behaviour, a resistance trait against V. destructor, in A. mellifera and Apis cerana. The second best-associated QTL is located on chromosome 4 in an intron of the Dscam gene, which is involved in neuronal wiring. Previous research demonstrated that genes involved in neuronal wiring are associated with recapping and varroa sensitive hygiene. Therefore, our study confirms the role of a gene region on chromosome 5 in social immunity and simultaneously provides novel insights into genetic interactions between common mite resistance traits in honey bees.