Genome-wide patterns of genetic 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

Submitted to: Insects
Publication Type: Proceedings
Publication Acceptance Date: 6/9/2020
Publication Date: 6/11/2020
Citation: Saelao, P., Simone-Finstrom, M., Avalos, A., Bilodeau, A.L., Danka, R.G., De Guzman, L.I., Rinkevich Jr, F.D. 2020. Genome-wide patterns of genetic differentiation within and across U.S. commercial honey bee stocks. Insects. 11(6):362. https://doi.org/10.3390/insects11060362.
DOI: https://doi.org/10.3390/insects11060362

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 similar or different commercial stocks are. This study looks 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. 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. Overall, there is a limited amount of genetic diversity between the U.S. honey bee stocks. However, investigations into the loci associated with mite resistance may assist in furthering research into the genes involved with beneficial behaviors.

Technical Abstract: The genetics of U.S. honey bee stocks remain poorly characterized despite the importance of Apis mellifera as a crop pollinator. Several breeding programs have made significant improvements of favorable genetic traits. The variety of bees produced by artificial selection provides an exciting opportunity to explore the landscape of genetic diversity in commonly used stocks. Population genetic analyses found strong genetic similarity among seven stocks, while Pol-line, a stock with mite resistance, showed significant differentiation likely due to strong selective breeding. Juxtaposing the underlying genetic variation of stocks selected for disease-resistance behavior, we identified genes and candidate regions potentially associated with resistance regulated by hygiene. This provides additional evidence for future studies towards understanding the genetic architecture of hygienic behavior. This study provides important insights into the distinct genetic characteristics and population diversity of honey bee stocks used in the United States. Composite signatures of selection helped highlight regions putatively under selection and potentially associated with disease resistance behavior. This study presents the initial effort towards effectively cataloging the standing variation within widely used honey bee stocks.