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

Authors: Saelao, Perot; Simone-Finstrom, Michael; Avalos, Arian; Bilodeau, Lanie; Danka, Robert; De Guzman, Lilia; Rinkevich, Frank; Tokarz, Philip

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2020
Publication Date: 10/9/2020
Citation: Saelao, P., Simone-Finstrom, M., Avalos, A., Bilodeau, A.L., Danka, R.G., De Guzman, L.I., Rinkevich Jr, F.D., Tokarz, P.G. 2020. Genome-wide patterns of differentiation within and across U.S. commercial honey bee stocks. BMC Genomics. 21:1-12. https://doi.org/10.1186/s12864-020-07111-x.
DOI: https://doi.org/10.1186/s12864-020-07111-x

Interpretive Summary: Honey bee stocks are a very important agricultural resource due to their role as a crop pollinator. Unfortunately, little is known about the genetic make-up of these bees and how different commercial stocks are from one another. This study aimed to quantify the differences between the mostly commonly used varieties of honey bees in order to identify regions of the genome that may be associated with favorable traits or unique genes that could be used for stock certification. Genomic sequencing was conducted of colonies for Italian, Carniolan, Russian, MN Hygienic, Pol-line and Hilo stocks. We found that a research stock highly bred for mite resistant behavior (Pol-line), and a commercial stock derived from this stock (Hilo), were the most genetically distinct from the other honey bee stocks. This potentially highlights similarities between these two stocks associated with mite resistance. Investigations into the loci associated with mite resistance may assist in furthering research into the genes involved with parasite and disease resistance traits in an attempt to develop tools for marker assisted selection. Overall, we found a limited amount of genetic differentiation between the U.S. honey bee stocks, indicating similarities in focus for selection of specific breeding traits (e.g. productivity, colony size), potential mixing of genes from across different populations, or similar starting populations from the different breeding programs. This large sequencing effort is the first genomic description of these stocks and the novel insights presented will provide the basis for a host of future studies and serve as a crucial resource in future goals related to developing tools for marker assisted selection.

Technical Abstract: 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.