Abstract
Runs of homozygosity (ROH) are continuous homozygous segments that arise
through the transmission of haplotypes that are identical by descent
(IBD). The length and distribution of ROH segments provide insight into
the genetic diversity of populations and are useful to detect selection
signatures. Here, we analysed pooled whole-genome sequencing data from
265 Western honey bee colonies from the two subspecies Apis
mellifera mellifera and Apis mellifera carnica . Integrating
individual ROH patterns and admixture levels in a high-resolution
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 colonies and a fair amount of admixed colonies, despite the
current applied conservation efforts. In contrast, A. m. carnicacolonies were more inbred and could not be differentiated according to
the geographical origin. We identified 29 coding genes in overlapping
ROH segments within the two subspecies. Genes embedded inA. m. carnica specific homozygosity islands suggested a strong
selection for production and behavioural traits, whilst the identified
cuticula protein-coding genes (CPR3 and CPR4) were
associated with their breed-specific stripe pattern. Local adaption of
the two subspecies could be confirmed by the identification of two genes
involved in the response to ultraviolet (UV) light. We demonstrated that
colony genotypes derived from pooled honey bee workers are reliable to
unravel the population dynamics in A. mellifera and provide
fundamental information to conserve native honey bees.