A Partnership for Improving Northeast Honey Bee Breeding Stock by Implementing Novel Selection Criteria

Progress report for ONE20-355

Project Type: Partnership
Funds awarded in 2020: $30,000.00
Projected End Date: 11/30/2023
Grant Recipient: University of Vermont
Region: Northeast
State: Vermont
Project Leader:
Dr. Samantha Alger
University of Vermont
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Project Information

Project Objectives:

This project seeks to leverage the capabilities and resources of the Vermont Bee Lab at the University of Vermont and French Hill Apiaries, the largest Vermont-based bee breeding operation in order to:

  1. Develop and implement improved metrics by which Northeast honey bee stock is selected, including pest/pathogen resistance,
  2. Improve the quality and availability of Northeast honey bee stock, and
  3. Spread awareness to beekeepers regarding the strengths of locally adapted bee stock.

By improving the quality and availability of locally raised bee stock, this project will improve honey production and reduce colony losses for Northeast beekeepers as well as reduce beekeepers’ reliance on imported bees, which are a potential source for pests and pathogens.


Since 2006, Vermont beekeepers have lost an average of 33% of their honey bee colonies each winter and in 2018-2019, Vermont’s average annual colony losses ranked third highest across the nation (Bee Informed Partnership, 2017). Colony losses are attributed to a multitude of interacting stressors which are often difficult to control by beekeepers. One sustainable mechanism whereby beekeepers can mitigate colony losses is through breeding programs that select for stock well-adapted to local environments and pest/pathogen resistance. To combat high colony losses, Vermont beekeepers need bees selected for the Northeast climate and resistant to pests/pathogens.

There are very few queen bee breeders in the Northeast who maintain stock locally bred and selected for high production, the ability to overwinter in the North, and pest/pathogen resistance. Selecting for traits such as colony longevity and overwintering success is accomplished over many years, even decades, of selective breeding. Selecting for pest and pathogen resistance requires scientific expertise and laboratory equipment to identify and quantify pathogen loads.

Thousands of colonies are imported each year to Vermont. Most are brought in by migratory commercial beekeeping operations that transport their bees out-of-state to warmer regions during the winter and participate in large pollination activities where the risk of disease transmission is significantly heightened. After providing pollination services, migratory colonies are split into smaller ‘nucleus’ or 'package' colonies and sold to beekeepers. Migratory honey bee colonies host novel pathogens (Runckel et al., 2011), have high virus loads (Welch et al., 2009; Alger et al., 2018) which can spillover into native bee populations (Alger et al., 2019), and are unlikely to be well adapted to the Northeast climate. Improving the availability and strength of locally adapted bee stock will reduce beekeepers’ reliance on imported bees which represent a risk to the health of both managed and wild bee populations.

Our proposed collaborative bee breeding initiative brings together one of the largest and longest-running bee breeding operations in the Northeast with the expertise and resources of bee disease experts at the University of Vermont- Vermont Bee Lab (VBL). The VBL is an important resource and presents an opportunity for collaboration towards improving current breeding programs. The VBL has the expertise and equipment to test for traits for incorporation into a breeding program to improve pest/pathogen resistance. We will build upon French Hill Apiaries’ existing breeding program and develop selection standards for Northeastern bees that are high producing, adapted to the local climate, and resistant to pests/pathogens.  In implementing these standards and selecting for a superior bee stock, we will improve the quality of bees available to regional beekeepers and bee breeders who may incorporate this stock in their own breeding programs. We will disseminate our research to beekeepers to spread awareness of the strengths of local bee stock. This work will improve the supply of locally adapted queens throughout the Northeast, and reduce beekeepers’ reliance on imported bees. In turn, our product will improve honey production while reducing colony losses and the risk of pathogen spread to pollinators.


Click linked name(s) to expand/collapse or show everyone's info
  • Adam Collins - Producer
  • Micheal Palmer - Producer


Materials and methods:

Field methods by beekeeping year:

Year 1: In 2020, we had aimed to identify 100 of the best performing production colonies based on honey and brood production as well as overwinter success. However, shut-downs due to the Covid-19 pandemic prohibited our UVM lab and personnel from working at the level we had anticipated. Our partnering beekeeper also experienced staffing shortages. Together, to maintain social distancing and keep everyone safe, we were unable to allow our (small) field teams to work hives together. Secondly, 2020 mite loads put too much pressure on the beekeeping operation, pushing activities well into late autumn. We aim to conduct the work planned for 2020 in 2021 during Year 2 of the grant.

Adam inspects a colony during the 2021 field season.

Year 2: In 2021, we used existing records of 500 colonies, to identify 64 of the best performing production colonies based on overwintering success, as well as honey and brood production. We tested these 64 colonies for the full suite of traits over the season (see ‘description of trait metrics and methodologies’ below), scored the colonies, and in early 2022, selected the 5 top ranking colonies to serve as our queen breeder colonies for the new breeding program (NBP). We used a reduced set of traits currently used by French Hill Apiaries (FHA) (honey and brood production and overwintering success) to select 5 colonies which serve   as queen breeders of the control group. Maintaining these two separate groups (NBP and control) enable us to compare the efficacy of the NBP with the existing program.

Year 3: In summer 2022, we assigned 50 colonies to the NBP group and 50 colonies to the control group. Colonies in the NBP group were requeened with NBP queens (full set of traits). Colonies in the control group were requeened with control queens  (reduced set of traits). The two treatment groups consisted of 10 daughter colonies produced from each of our 5 NBP queen breeders and 5 control queen breeders. The 10 daughter colonies descending from each of our 10 total queen breeders were divided across two separated yard locations in Vermont. All daughter colonies were established by July 1. Besides the origin of the queen, all management practices remained constant across all colonies. Once we requeened all colonies, we tested each throughout the remainder of the season for a reduced suite of metrics, including VSH behavior and pest/disease loads. Other metrics were not tested due to the small size of the nucleus colonies produced this season and the timeline of queen rearing. In 2022, we included one additional test which determines VSH behavior using an improved method of synthetic pheromone application (see ‘description of trait metrics and methodologies’ below).

To raise queens, we  use established queen rearing methods practiced by FHA. Queens are grafted from larvae in artificial queen cells. Upon emergence, queens are open mated in an isolated mating yard surrounded by colonies maintained by FHA. We harvest queens after it has been confirmed that the queen has successfully mated by the presence of eggs.

In early 2023, we will score the 2022 NBP colonies and select the 5 top-ranking colonies to serve as our second generation queen breeder colonies for the new breeding program (NBP) in 2023.

Year 4: In summer 2023, we will continue to test a the surviving colonies from 2022 for the full suite of traits. We will requeen weak colonies with queens from the appropriate lineage (either the NBP group or the control group). We will replace dead colonies with new colonies headed by queens of the appropriate lineage. To strengthen the presence of the NBP’s genetics within the mating yard, we will re-queen weak or dead colonies in the 'drone yards' or production yards surrounding the mating yard. We will only do this after all control colonies have been requeened to reduce the introduction of the NBP’s genetics on the control group.

We will also produce a set of daughter colonies from each of our 5 top-ranking 2022 NBP queen breeders, in addition to a set of daughter colonies from 5 control queen breeders, to serve as the next generation of our breeding program.

Once all data are collected, we will compare the two treatment groups on the full suite of metrics to determine the efficacy of the new breeding program in producing high-quality bees with hygienic behavior and pest/pathogen resistance.

Sydney collects bee samples for Varroa and Nosema testing in 2021.

Description of trait metrics and methodologies.

Brood production: Brood production is indicative of the colony population and strength. This metric is measured in the number of frames that contain brood (eggs, larvae, pupae). We will measure brood production once per season.

Honey production: We will measure honey production once at the time of honey harvest. We will weigh the honey harvested from each colony on a scale to derive the pounds of honey produced.

Overwintering success: We will measure overwintering success as the ability of a colony to survive the winter and remain healthy and viable as a production colony the following spring.

Varroa mite load: Varroa mites are ectoparasites that feed on the fat bodies and hemolymph of bees, suppress the immune system, and vector viruses. Introduced to North America from Asia in the 1980s, Varroa mites are considered the most damaging pest to modern beekeeping. Methods to control mites include chemical treatments, practices that interrupt the mite’s life cycle and utilizing mite resistant honey bee genetics. We will measure mite loads in all colonies once a month using the alcohol wash method (Lee et al., 2010). For any colonies that host mite loads above a treatment threshold (Honey Bee Health Coalition, 2018), we will treat them with approved mite treatments.

Varroa Sensitive Hygienics (VSH) behavior: VSH behavior is an indication of mite resistance (Spivak & Downey, 1998; Wagoner, Spivak & Rueppell, 2018). Honey bees that detect mites under pupal cappings will uncap pupae and remove the pupae and mites, disrupting the mite’s life cycle. We can test for VSH behavior by sacrificing a selected area of brood with liquid nitrogen and replacing it back into the colony for 24 hours. After 24 hours, a colony exhibiting VSH behavior will remove all the sacrificed dead pupae from the cells. VSH behavior may be quantified by counting the number of cells with pupae removed. We will conduct this test once per season.

Hygienic behavior by Unhealthy Brood Odor Assay: We can also test for hygienic behavior by conducting Unhealthy Brood Odor Assays (UBO) by applying a synthetic pheromone solution to an isolated section of capped brood and replacing it back into the colony for 2 hours. After 2 hours, a colony exhibiting VSH behavior will have damaged the wax cappings of the treated pupae. VSH behavior may be quantified by counting the number of cells with damage to the wax capping (Wagoner et al., 2021). We will conduct this test once per season, starting summer 2022.

Virus load: Varroa mites transmit a number of viruses to honey bees that cause a multitude of symptoms such as deformed wings, paralysis, and death. Once per year, we will test colonies for virus loads. We will use established molecular protocols to test samples for 1-3 virus targets known to be present in the apiaries based on National Honey Bee Survey data 2015-2020 (e.g.: deformed wing virus, Varroa destructor virus, chronic bee paralysis virus, etc.) and a housekeeping gene (Actin) (Alger et al., 2018)

Nosema load: Nosema is a microsporidian parasite that resides in the gut of honey bees that causes dysentery, poor survival, and reduced honey yield. We will test for Nosema once per season using established microscopy protocols on bee samples (Alger et al., 2018)

Data analysis:

To compare the performance of the two groups of colonies (NBP and control) on their performance across the suite of metrics, we will use generalized linear mixed-effects models with each metric as a dependent variable, time, group, and their interaction as predictor variables, and apiary as a random effect. To examine how the suite of metrics predict group membership, we will use multivariate statistical analyses.

Future work:

This project will take place over 3 beekeeping seasons and make great strides in improving bee stock quality. Additionally, this proposed work will provide the foundation for a long-term bee breeding initiative our team will continue beyond 2023.

Research results and discussion:

In 2021, we gathered data on a suite of metrics including overwintering success, honey/brood production, hygienic behavior, and pest/disease loads. Our results are as follows: Overwintering success was determined by the number of frames of bees or brood that were present in early May. Only colonies which exhibited 6 were selected for the study. Varroa mite and nosema loads were assessed on a monthly basis. Varroa mite counts increased consistently throughout the season, growing from an average of 0.14 mites/100 bees across all colonies in May to an average of 5.01 mites/100 bees in September when we treated any colonies above treatment threshold (2) with acaricide. Nosema peaked in late-May with an average of 825,000 spores/bee across all colonies (remaining under the treatment threshold), then the abundance decreased to a very tolerable level for the rest of the season. In most colonies, the fungus was completely eradicated by July. 16 colonies were considered to be ‘hygienic’ based on our lowered threshold, demonstrating 80% removal of freeze-killed pupae. Honey yield ranged from 55 lbs to 206lbs of honey stores. October weight ranged from 75 lbs to 195 lbs of fall nectar/honey stores. Using R-programming language, the top 15 colonies were identified to monitor for overwintering success in spring 2022, which informed the final 5 breeder queens.

In 2022, we gathered data on a reduced suite of metrics including hygienic behavior and pest/disease loads from our NBP and control colonies. Our results are as follows: Varroa mite counts increased consistently throughout the season, growing from an average of 0.24 mites/100 bees across all colonies in July to an average of 0.80 mites/100 bees in September when we treated any colonies above treatment threshold (2) with acaricide. Nosema abundance was highest in late-July when we began sampling, with an average of 162,000 spores/bee across all colonies (well below the treatment threshold). Minimal Nosema was found in September. 29 of the 50 colonies tested with our original method were considered to be ‘hygienic’ (with a threshold of 95%), while only nine colonies of the full 100 were considered to be ‘hygienic’ based on our improved UBO method (with a threshold of 60%).

Participation Summary

Education & Outreach Activities and Participation Summary

2 On-farm demonstrations
6 Webinars / talks / presentations

Participation Summary:

40 Farmers participated
20 Number of agricultural educator or service providers reached through education and outreach activities
Education/outreach description:

In 2021, Alger shared the progress of the research to date with two beekeeping clubs during virtual meetings (Franklin County Beekeepers and Southern Adirondack Beekeepers).

During the summer of 2021 and 2022, Alger taught an online and in-person beekeeping course. Participants included UVM students and community members.  In these courses, Alger shared the results of this study with beginner beekeepers and incorporated related hands-on activities to share how these procedures may be introduced to bee breeding programs that result in sustainable locally-raised stock. Activities included queen grafting/rearing, mite load testing, and VSH testing. Students in the summer course were also invited to French Hill Apiary ‘queen catch’ days where students participated in queen rearing and learn, first-hand, about local bee breeding efforts. Enrollment in 2021 was 11 for the online course and nine for the hands-on course. Enrollment in 2022 was 16 for the online course and eight for the hands-on course.

Alger and Palmer also aim to disseminate this research to broader audiences. Alger and Palmer both serve on the Vermont Beekeepers Association (VBA) board as advisors and are invited speakers to beekeeping events throughout the country. We will continue to present our findings to VBA members during annual summer and winter meetings, such as in 2021 and 2022. With nearly 646 members, these events will provide an opportunity to reach the majority of the state's beekeepers. To share our results with the broader beekeeping community, we will present our results at one national conference such as the American Beekeeping Federation Conference, Apimondia, Honey Producers of America, and Eastern Apicultural Society. 

Lastly, we plan to highlight our research on the Vermont Bee Lab and French Hill Apiaries websites: vermontbeelab.com, frenchhillapiaries.com.

Learning Outcomes

2 Farmers reported changes in knowledge, attitudes, skills and/or awareness as a result of their participation
Key areas in which farmers reported changes in knowledge, attitude, skills and/or awareness:
  • Freeze brood assay for hygienic behavior may not be as effective as other new methods.
  • Chemical treatments for Varroa should occur after mite testing shows the need.
Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.