Location: Honey Bee Breeding, Genetics, and Physiology Research
2025 Annual Report
Objectives
Meaningful contributions towards enhancing the economic value of the nation’s commercially managed honey bee populations can be achieved through identifying, characterizing and breeding more robust bees. The proposed 5-year plan focuses on synergistic projects (Fig.1) that capitalize on genetic and breeding approaches with the following objectives:
Objective 1: Identify and evaluate traits, strains and stocks for improved honey bee health.
Sub-objective 1A: Understand the mechanisms of viral transmission and resistance or tolerance to reduce impacts of infection through selective breeding.
Sub-objective 1B: Evaluate genotype-dependent nutrient efficiency in commercial honey bee stocks.
Sub-objective 1C: Evaluate genotype-dependent nutritional stress resistance in commercial honey bee stocks.
Sub-objective 1D: Characterize the impact of genetically based variation in vitellogenin -- the primary honey bee storage protein with roles in immune function, oxidative stress resistance and lifespan -- on colony and reproductive (queen and drone) health and productivity.
Sub-objective 1E: Identify and characterize genetic and physiological mechanisms of pesticide resistance in honey bees.
Objective 2: Characterize genetic, physiological and behavioral aspects of important traits, strains and stocks.
Sub-objective 2A: Examine patterns of genetic diversity and loci under selection in United States honey bee breeding populations, with a focus on stocks exhibiting high VSH activity.
Sub-objective 2B: Elucidate the interaction between individual and social immune defenses.
Sub-objective 2C: Improve understanding of the biology of the VSH trait.
Objective 3: Conduct traditional breeding or marker-assisted selection of honey bees.
Sub-objective 3A: Ascertain the effect of inbreeding on genetic diversity across the honey bee genome to support breeding and maintaining health of breeding populations.
Sub-objective 3B. Assess genetic diversity at the sex locus of commercial breeding populations of honey bee stocks developed by USDA, ARS HBBGPL.
Sub-objective 3C: Determine the potential usefulness of a simple hygiene assay as a selection tool to predict VSH-based mite resistance in honey bee colonies.
Objective 4: Develop management tools for improving honey bee health.
Sub-objective 4A: Identify and characterize genetic differences in honey bee response to introduced dsRNA, and test for correlations with viral infection and resistance.
Sub-objective 4B: Improve understanding of the flight activity of Russian honey bees during almond pollination.
Sub-objective 4C: Evaluate the efficacy of a microalgae platform to improve honey bee colony performance and health.
Sub-objective 4D: Determine the sublethal effects of fungicides on honey bee health.
Sub-objective 4E: Assess sustainability of Varroa control methods.
Approach
Honey bee health is threatened by parasites, pathogens, poor nutrition and pesticides. Breeding robust bees with improved resistance (or tolerance) to threats could mitigate these problems. The project combines diverse approaches and techniques to seek and exploit genotype-dependent responses of honey bees to biotic-, nutrition- and pesticide-related stressors.
The project improves understanding of genetic diversity across U.S. commercial stocks, enabling both marker-assisted selection and conservation of genetic resources. This will enhance the effectiveness of contemporary breeding programs.
Varroa destructor (hereafter, Varroa) is the greatest threat to bee health worldwide. The project builds on past successes by improving selection efficiency for resistance to Varroa and for elevated colony performance, promoting adoption by beekeepers. Investigations target relationships between genetic diversity across stocks, immune responses, and treatment effectiveness against Varroa, viruses, and other related biotic threats. This is critical because of recent beekeeper reports of miticide- (amitraz-) resistant Varroa. Given the threat from Varroa, the plan outlines novel (Sub-objectives 2B, 4A) and continuing (Sub-objectives 2C, 3C, 4B) research on breeding and management related to Varroa-resistant honey bees.
In addition, we also initiate a suite of new studies addressing the negative impact of stressors whose prevalence has increased across managed honey bees in the past decade. These studies will assess differences in genotype-dependent responses to viruses and other pathogens (Sub-objectives 1A, 2B), poor nutrition (Sub-objectives 1B, 1C, 1D, 4C), and pesticides (Sub-objectives 1E, 4D, 4E). The project seeks to improve nutrient assimilation efficiency through breeding. Similarly, genotype-dependent differences in bee responses to pesticides will be targeted for breeding less susceptible bees and reducing queen failures. Biomarkers identified as useful for signaling emerging health threats will be verified, benefitting beekeepers by allowing for rapid corrective intervention. These approaches will capitalize on novel sequencing technologies to examine many of these issues at a higher level of resolution across the honey bee genome (Sub-objectives 2A, 3A, 3B).
Progress Report
This report documents progress of five-year period of project 6050-21000-016-00D (Using Genetics to Improve the Breeding and Health of Honey Bees), which began in March 2020. Progress was made in research objectives that fall under National Program 305, Component 2, Bees and Pollination. The goal of this research is to enhance the economic value of the nation’s commercially managed honey bee populations through identifying, characterizing and breeding more robust bees while informing management practices.
For research related to identifying and evaluating traits, strains, and stocks for improved bee health (Objective 1), developments across several projects highlighted the continued need to include honey bee genetic background across all studies. Viral infection experiments found repeated evidence that bee genetic background, life stage, type of virus, and environmental factors interact to influence viral susceptibility (1A). Genomic sequencing of virus in bee samples collected from five geographically distinct, commercial beekeeping operations provided insight into viral dynamics in mite-resistant versus mite-susceptible honey bee colonies. Malnutrition is another factor underlying honey bee colony declines. Research tested the effect of honey bee genetics on physiological responses to natural and artificial bee diets (1B). Results showed that stock-based responses to diet are present in honey bees, which has implications for tailored approaches to diet and health. Additional work, in collaboration with the Tucson unit examined food consumption and thermoregulatory capabilities across different environmental conditions, finding differences between commercially standard Italian colonies and mite-resistant Pol-line stock (developed in Baton Rouge). Additional research testing how colonies respond to a pollen (protein) dearth (1C), found that colonies became more aggressive than colonies that had access to pollen resources. Temperament is used to select breeding stock, so these findings are industry relevant.
Progress was also made in the characterization of the impact of genetically based variation in vitellogenin (Vg)—the primary honey bee storage protein with roles in colony health and productivity (1D). We identified age and task-based expression patterns of three Vg-like genes, and discovered a link between Vg expression and swarming behavior in collaboration with the University of Minnesota. This information further informs the use of Vg as an indicator of colony health and bee behavior.
Another project aimed to evaluate the potential of susceptibility to pesticide exposure as a possible trait for breeding selection in honey bees (1E). Sensitivity to pesticide exposure was evaluated from 11 honey bee genetic lines. Overall, there was little variation in sensitivity to chlorpyrifos (<1.3 fold), phenothrin (<3-fold), or clothianidin (<5.3-fold). This low level of variation in pesticide sensitivity across stocks prevented the initiation of a breeding program for pesticide resistant honey bees, but suggested that beekeepers do not need to change the stock that they use based on potential exposures to agrochemicals.
Research continued characterizing genetic, physiological and behavioral aspects of important traits, strains and stocks (Objective 2). Work investigating genetic diversity across the honey bee genome (2A) resulted in the first honey bee pangenome. This genomic tool unifies genetic variation from six key honey bee populations into a common reference allowing for characterization of honey bee genetic diversity and the ability to identify larger genomic structural variants. By creating this reference, honey bee breeding can be modernized to better incorporate genomic selection tools, allowing the beekeeping industry to more rapidly and effectively select for specific traits. Future work will focus on creating a global pangenome, and will provide a foundation for all future honey bee genomic work.
More specific assessments of different traits that could be selected for breeding programs, determined that there was no trade-off of among the individual and social defense measures (grooming, resin collection, hygienic behavior, larval immunity). However a colony’s level of hygienic behavior (tendency to remove dead or infected larvae and pupae) was positively associated with the immune response of larvae (2B). This finding provides further support for the hypothesis that larvae and pupae may be signaling to indicate their health status (2C). Research also identified that Russian honey bees exhibit, social apoptosis, where Varroa infested pupae die more quickly. This prevents mites from successfully producing offspring on pupae (2B). Collaborative work also began with Louisiana State University to determine how selection for mite resistance has affected behavioral development in Russian and Pol-line stocks. These results confirm importance of fully evaluating stocks to enhance resistance traits and also highlight need for multiple resistance traits to to ensure food security and promote successful rural agricultural production.
A case study on a stakeholder’s migratory commercial beekeeping operation using mite-resistant and susceptible stocks provided economic justification for adoption of mite resistant stock. Additional developments include establishment of a “working group” with members of the Russian Honey Bee Breeders Association to assess areas of success and improvements in the program to increase mite resistant bees in the US. This effort will improve livelihoods of US farmers and access to quality products by US consumers.
Work related to traditional breeding and marker-assisted selection of honey bees (Objective 3) continued to develop. We conducted research on semen storage and viability, a critical logistic limitation to the application of genomic-based marker assisted selection (MAS) (3A). Collaborative studies with Colorado State University included a proof of concept for MAS using metabolic rate since the trait is determined by a small set of markers. Two generations of queens were selected solely using genomic markers, providing one of the first examples of MAS in honey bees. Additional collaboration with Breeding Insight continues towards broader application of MAS in honey bees, which will modernize breeding strategies for commercial beekeepers and ultimately lead to improved colony health and reduced colony losses. Genetic analysis of csd of the mite resistant Russian honey bee, Hilo and Pol-line populations were completed, finding them comparable to other selected stocks (3B). In collaboration with University of Missouri, a standardized nomenclature system for honey bee csd alleles was developed and is used to inform breeding decisions. Modernization of the established stock identification assay for Russian honey bees progressed, identifying approximately 200 markers to be applied by the industry.
Development of management tools to improve bee health (Objective 4) progressed in several areas. A novel, RNA interference (RNAi)-based treatment was developed using edible blue-green algae that have been genetically engineered to deliver therapeutic double-stranded RNAs (dsRNAs) to honey bees. Once consumed, the dsRNAs trigger a sequence-specific RNAi response, targeting viral pathogens. Treatments targeting deformed wing virus suppressed viral infection and improved bee survival (4A). This design presents a versatile and sustainable therapeutic that can be directly incorporated into supplemental feeds to mitigate viruses and support global food security. A series of laboratory experiments and trials in commercial beekeeping operations have been completed showing that non-modified microalgae-based diets improve colony health (4C). The beekeeping industry has translated this research into commercial products.
For an examination of how different stocks may be managed differently for pollination services (4B), the foraging rates of Russian, Pol-Line, and unselected stocks were compared in almond orchards. Overall, colony size predicted foraging activity more than stock, however there were stock-specific differences that could lead to changes in how colonies are placed in fields for pollination services of agricultural crops. Research has completed on effects of chlorothalonil on colony performance(4D). Colonies treated with chlorothalonil experienced higher rates of colony losses due to higher Varroa infestation. This research is important to understand indirect impacts of fungicides for beekeepers to work with cooperating farmers to reduce exposure risks.
Progress on identification of resistance of Varroa control treatments has led to profound changes in the beekeeping industry and miticide use (4E). Annual monitoring of amitraz resistance levels in beekeeping operations across the US has shown a 5% annual increase in the level of amitraz resistance where the monitoring in 2024 revealed that high levels of amitraz resistance were widespread. A high prevalence of amitraz resistance in Varroa has been associated with high colony losses. Genetic testing has shown a single mutation in the ß2 octopamine receptor is highly associated with amitraz resistance in Varroa. This monitoring program allows beekeepers to make informed management decisions to reduce annual colony losses.
Another study was initiated on the effects of colony boxes that stimulate propolis deposition(antimicrobial plant resins collected by the bees) on Varroa infestation in honey bee colonies (4E). Results show that a propolis-enriched environment can significantly reduce mite infestation loads. Additionally, USDA Areawide Pest Management Program was awarded to the Unit to continue to monitor amitraz resistance monitoring, expand prevalence of Varroa resistant honey bee stocks, improve genomic tools to selectively breed Varroa resistant honey bees, and generate an economic impact analysis of Varroa resistant honey bee stocks.
Accomplishments
1. Genomic advances improve global understanding of honey bee genetics.. Using improved sequencing methods and genome assembly methods, the first honey bee (Apis mellifera) commercial and research pangenome has been developed. ARS researchers at Baton Rouge, Louisiana believe this tool unifies genetic variation from six key honey bee populations into a common reference. This novel tool represents a method by which to increase our understanding of genetic variation and improve breeding tools to allow the beekeeping industry to more rapidly and effectively select for specific traits. Results also provide a reference for the genetic health of honey bee populations and can be practically implemented in genetic monitoring programs to guarantee US honey bee populations are robust and resilient. Furthermore, the use of the pangenome and population genetic data has provided us with thousands of previously unknown genetic features, many tied to key traits of interest and which can be used to develop novel selection programs tailored to present and future demands from US agriculture at large. Future work will focus on expanding to develop a pangenome that includes worldwide honey bee genetic representation, and will provide the foundation for all genomic work in honey bees.
Review Publications
Shanahan, M., Simone-Finstrom, M., Spivak, M. 2024. Resin use and social immunity in honey bees and stingless bees. Book Chapter. https://doi.org/10.1007/978-3-031-43274-3_10.
Wizenberg, S.M., French, S.K., Newburn, L.R., Pepinelli, M., Conflitti, I.M., Mouboney, M., Ritchie, C., Jamieson, A., Achkanian, A., Travas, A., Imrit, M., Khusi, D., Chihata, M., Higo, H., Common, J., Walsh, E.M., Bixby, M., Guarna, M.M., Pernal, S.F., Hoover, S.E., Currie, R., Giovenazzo, P., Guzman-Novoa, E., Borges, D., Foster, L.J., Zayed, Z. 2024. Pollen foraging mediates exposure to dichotomous stressor syndromes in honey bee. Proceedings of the National Academy of Sciences-Nexus. https://doi.org/10.1093/pnasnexus/pgae440.
Tran, L., Lansing, L., Cunningham, M., Ho, J., Deckers, T., Newman, T., Wu, L., Gregoris, A., Zorz, J., Muntz, L., Walsh, E.M., Lee, K., Trépanier-Leroux, D., Conflitti, I., Pepinelli, M., Morfin, N., Powell, J., Moran, N., Hooves, S., Pernal, S., Currie, R., Giovenazzo, P., Guzman-Novoa, E., Jabbari, H., Foster, L., Zayed, A., Ortega, P. 2025. Gut microbiome metagenomic sequences of honey bees (Apis mellifera) exposed to crops. Microbiology Resource Announcements. https://doi.org/10.1128/mra.00731-24.
Mcafee, A., Alavi-Shoushtari, N., Tran, L., Labuschagne, R., Walsh, E.M., Foster, L., Common, J., Higo, H., Pernal, S.F., Giovenazzo, P., Hoover, S.E., Guzman-Novoa, E., Currie, R.W., Wolf Veiga, P., French, S.K., Conflitti, I.M., Pepinelli, M., Borges, D., Zayed, A., Bishop, C.A., Duffe, J., Guarna, M.M. 2025. Regional patterns and climatic predictors of viruses in honey bee (Apis mellifera) colonies over time. Scientific Reports. https://doi.org/10.1038/s41598-024-79675-7.
Ihle, K.E., Payne, A.N., Elsik, C., Bilodeau, A.L. 2025. Scientific note updating allelic nomenclature standards of the highly diverse complementary sex-determiner locus in honey bees. Apidologie. https://doi.org/10.1007/s13592-025-01161-4.