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

This is the authors' abstract. We don't add key points for this paper.

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 fromApis mellifera melliferaandApis 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. WithinA. 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 (FROH) strongly varied within and between the identified subpopulations. ConservedA. m. melliferafrom Switzerland had the highest meanFROH(3.39%), while queens originating from a conservation area in France, which were also highly admixed, showed significantly lowerFROH(0.45%). The majority ofA. m. carnicaqueens were also highly admixed, except 12 purebred queens with a meanFROHof 2.33%. Within the breed‐specific ROH islands, we identified 14 coding genes forA. m. melliferaand five forA. m. carnica, respectively. Local adaption ofA. m. melliferacould be suggested by the identification of genes involved in the response to ultraviolet light (Crh‐BP,Uvop) and body size (Hex70a,Hex70b), while theA. m. carnicaspecific genesCpr3andCpr4are 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 inA. melliferaand provide fundamental information to conserve native honey bees.