Genome-wide patterns of differentiation within and across U.S. commercial honey bee stocks

The population genetics of U.S. honey bee stocks remain poorly characterized despite the agricultural importance of Apis mellifera as the major crop pollinator. Commercial and research-based breeding programs have made significant improvements of favorable genetic traits (e.g. production and disease resistance). The variety of bees produced by artificial selection provides an opportunity to characterize the genetic diversity and regions of the genome undergoing selection in commonly managed stocks. Pooled sequencing of eight honey bee stocks found strong genetic similarity among six of the stocks. Two stocks, Pol-line and Hilo, showed significant differentiation likely due to their intense and largely closed breeding for resistance to the parasitic Varroa mite. Few SNPs were identified as being specific to any one stock, indicating potential admixture among the sequenced stocks. Juxtaposing the underlying genetic variation of stocks selected for disease- and parasite-resistance behaviors, we identified genes and candidate regions putatively associated with resistance regulated by hygienic behavior. This study provides important insights into the distinct genetic characteristics and population diversity of honey bee stocks used in the United States, and provides further evidence of high levels of admixture in commercially managed honey bee stocks. Furthermore, breeding efforts to enhance parasite resistance in honey bees may have created unique genetic profiles. Genomic regions of interest have been highlighted for future work related to developing genetic markers for selection of disease and parasite resistance traits. Due to the vast genomic similarities found across stocks in general, our findings suggest that additional data regarding gene expression, epigenetic and regulatory information is needed to more fully determine how stock phenotypic diversity is regulated. Overall this work is an important step forward in characterizing the genetic structure of honey bee stocks commonly used in the U.S.