Identification of runs of homozygosity in Western honey bees () 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 and . Integrating individual ROH patterns and admixture levels in a dynamic population network visualization allowed us to ascertain major differences between the two subspecies. Within , 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 ( ) strongly varied within and between the identified subpopulations. Conserved from Switzerland had the highest mean (3.39%), while queens originating from a conservation area in France, which were also highly admixed, showed significantly lower (0.45%). The majority of queens were also highly admixed, except 12 purebred queens with a mean of 2.33%. Within the breed-specific ROH islands, we identified 14 coding genes for and five for , respectively. Local adaption of could be suggested by the identification of genes involved in the response to ultraviolet light (, ) and body size (, ), while the specific genes and 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 and provide fundamental information to conserve native honey bees.