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Goals & Objective: Goal 2
Objective 2.1

Obj 2.1: Identify genes that confer resistance to Varroa and pathogens, and genes that respond to biotic challenges

(Hunt, Spivak, Webster, Aronstein, Grozinger, Danka)

Phenotypic and genetic variation exists for virulent pathogens identified in Goal 1. Crosses to produce a segregating family challenged by these pathogens can be used to identify quantitative trait loci associated with resistance and genes that respond to infection.

Rationale and significance 
Breeding for host resistance is a cornerstone of IPM. In the 20+ years since the arrival of Varroa, breeding progress has been hampered by lack of economic incentives, insufficient knowledge of the traits involved in resistance, erosion of genetic diversity, and poor mating control. 

Mapping genes for disease resistance 
We will use genomic approaches that complement traditional breeding: mapping chromosomal regions that confer resistance to parasites and pathogens using the quantitative trait locus (QTL) method, and globally analyzing changes in gene expression in response to pathogens and mites. We will first identify QTL conferring resistance to Varroa because resistance mechanisms are known and stocks are available. Stocks resistant to the most virulent pathogens identified in cage studies will be used in breeding programs and genomic studies. We will fine-scale map QTL that confer resistance to Varroa and to at least one pathogen, and couple both of these studies with analysis of gene expression on microarrays. The pathogens chosen will depend on results of cage studies, but likely candidates are N. ceranae, IAPV and DWV. 

The two traits found to be most important for Varroa resistance are behavioral: Varroa-sensitive hygiene (VSH) and grooming (Harbo and Harris 2005; Mondragón et al. 2005). USDA/NRI has already funded G. Hunt to map QTL influencing grooming behavior. Mapping QTL that influence VSH in this CAP would complement that study. A line of honey bees expressing VSH has been developed by the Baton Rouge ARS bee lab and another expressing general hygienic behavior by M. Spivak at the University of Minnesota. It is not clear whether VSH and general hygienic behavior are regulated by the same genes (Ibrahim and Spivak, 2006). Previous studies have shown that even with maps based on DNA markers of mostly unknown sequences, QTL mapping narrowed the search to an average of about 40 candidate genes for six behavioral-trait QTL in bees (reviewed by Hunt et al. 2007). High-throughput genotyping platforms are now available capable of analyzing thousands of single-nucleotide polymorphisms (SNPs) in individual honey bees (Whitfield et al. 2006). 

Combining QTL mapping with gene expression 
Full-genome microarrays will be probed with the RNA of bees used for QTL mapping to leverage maximum information from these studies. The expression level of each gene can be considered as a quantitative trait (an “e-Trait”), enabling us to map genes that influence its expression. Combining expression data with genetic data (such as SNPs) permits study of gene networks involved in disease (Beyer et al. 2007, Sieberts and Schadt 2007, West et al. 2007). QTL that confer resistance may regulate unlinked genes (ie, a specific candidate gene identified from the QTL analysis may regulate expression of immune response genes). On the other hand, QTL conferring resistance may show cis-regulation, in which alternative alleles have different expression levels. The latter case would provide strong evidence for the role of specific candidate genes in the resistance phenotype by demonstrating altered gene expression within a QTL region that coincides with resistance. The SNPs in genes identified could be used for diagnostic tests for resistance alleles in populations and for marker-assisted selection in breeding programs.


Expected outcomes

  1. To identify genes that respond to bee infection by virulent pathogens,
  2. to identify small sets of candidate genes involved in resistance to Varroa and to pathogens,
  3. to identify potential gene regulatory networks that respond to disease, and
  4. to develop diagnostic SNP markers for alleles of candidate genes involved in resistance.

Timetable for deliverables

  1. identify genes that respond to biotic challenges 14 July 2010,
  2. identify genes that confer resistance to Varroa 14 July 2011, and
  3. identify genes that confer resistance to disease 14 July 2012 

Summary Statement for Goal 2
Workers in this goal have focused on improving breeding methods, identifying bee stocks with measurable resistance to Varroa mites, Nosema ceranae, and the virus IAPV, and improving the genetic diversity of bee stocks available to U.S. beekeepers. Greg Hunt’s lab developed an assay that correlates the proportion of mites removed from adult bees to the proportion of mites on bottom screens showing bite marks. Lab assays to screen bees for genetic resistance to N. ceranae were terminated following logistical difficulties and mounting evidence from this CAP that pathogenicity of N. ceranae is comparably low. Similar assays screening bees for resistance to IAPV showed only slight improvements in survivorship in a comparably resistant line. The return on effort has been much greater in the sub-objectives focused on identifying genes that confer resistance to Varroa mite. One putative quantitative trait locus (QTL) influencing grooming behavior and several putative QTLs influencing Varroa Sensitive Hygiene have been found, and work for year 4 will focus on confirming these QTLs for mite resistance and performing expression studies and RNAi experiments on the candidate genes identified.


Methodology, data and analysis of results to date are shared in an annual report to USDA. Papers generated by team members during the time of the CAP are listed and periodically updated below. Beyond the citation of published papers, the consensus of the group is that it would otherwise be unhelpful or possibly misleading to state preliminary results within the context on this web site.


Publications of objective 2.1 principal investigators (Aronstein, Danka, Grozinger, Hunt, Spivak, Webster) to date during the CAP

Andino, G.K. and G.J. Hunt. 2010. A new assay to measure mite grooming behavior, pp
497-511. In Proceedings, 2010 American bee research conference, 14-15 January
2010, Orlando FL. Am. Bee J.150:5. Also, Apidologie DOI: 10.1007/s13592-011-0004-1

Aronstein K.A, and J. Adamczyk. 2011. Influence of Genomics: The Post Genomic Era in the Honey Bee Research. The Journal of the Texas Beekeepers Association. 11(1): 12-17

Aronstein, K.A., H.E. Cabanillas. (ed. Samataro) Book: ”Honey Bee Colony Health: Challenges and Sustainable solutions” Book chapter 11: Chalkbrood Re-examined . Taylor and Francis, LLC, (accepted, 2011)

Aronstein, K.A. 2009. Detect Nosema Parasite in Time to Save Bee Colonies. Am. Bee J.150 (1): 63-65

Aronstein, K.A., Eduardo Saldivar, T.C. Webster. 2011. Evaluation of Nosema ceranae Spore-specific polyclonal antibodies. Journal of Apicultural Research 50(2): 145-151

Aronstein, K. A., B. Oppert, and M.D. Lorenzen. (ed. Paula Grabowski) 2011. Book: “RNA Processing,” Chapter “RNAi in the Agriculturally Important Arthropods.” ISBN 978-953-307-332-3, InTech.

Cornman, R. S., M.C. Schatz, J.S. Johnston, Y.P. Chen, J.S. Pettis, G. Hunt; B. Lanie, C. Elsik, D. Anderson, C.M. Grozinger, and J.D. Evans. 2010. Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera, BMC Genomics 11:602

Eitzer, B., F. Drummond, J.D. Ellis, N. Ostiguy, K. Aronstein, W.S. Sheppard, K. Visscher, D. Cox-Foster, & A. Averill. 2010. Pesticide analysis at the stationary apiaries, American Bee Journal, 150(5):500

Evans, J.D., M. Spivak. 2010. Socialized Medicine: Individual and communal disease
barriers in honey bees, Journal Invert. Pathol. 103, S62-S72

Holt, H.L., K.A. Aronstein, and C.M. Grozinger.  Genomic analysis of effects of Nosema parasites on honey bee workers (in prep.)

Hunt, G.J. 2010. Breeding bees for resistance to parasites and diseases. American Bee
Journal, 150(7):667-669

Krupke, C., B. Eitzer, & G.J. Hunt. 2011. Potential routes of exposure to honey bees from
neonicotinoid corn seed treatments. (Abstract) American Bee Journal (in Press)

Lee, K, Reuter GS, M. Spivak. 2010. Standardized sampling plan to detect Varroa densities in colonies and apiaries. Am. Bee J. 149(12):1151-1155

Mader, E., M. Spivak, E. Evans. 2010.  Managing Alternative Pollinators: A Handbook for Growers, Beekeepers and Conservationists”  NRAES/ SARE Publication.  250pp., ISBN 978-1-933395-20-3

Oxley, P., M. Spivak, & B.P. Oldroyd. 2010. Six quantitative trait loci influence task thresholds for hygienic behaviour in honeybees (Apis mellifera). Molecular Ecology 19: 1452–1461

Richard, FJ, H.L. Holt, and C.M. Grozinger.  Behavioral, chemical, and genomic effects of immunostimulation on honey bee workers  (in prep.)

Spivak, M., G.S. Reuter. 2008. New direction for the Minnesota hygienic line of bees. American Bee Journal 148(12):1085-1086

Spivak, M., G.S. Reuter, & B. Ranum. 2009. The future of the MN hygienic stock of bees
is in good hands! American Bee Journal, 149(10): 965-967

Spivak M. 2010. Honey bee “Medial records”: The stationary apiary project. Managed
Pollinator CAP Update. Bee Culture.150(3): 270-274

Spivak, M. 2010. Honey bee “medical records”: the stationary apiary monitoring project.
American Bee Journal, 149(3):271-274

Spivak, M., Y. Le Conte. 2010. Special issue on bee health. Apidologie, DOI:

Spivak M, E. Mader, M. Vaughan, N.H., Jr. Euliss. 2011. The plight of bees. Environ.
Sci. & Technol.45: 34-38. *Editor’s Choice Award, ES&T Best Feature Paper

Spivak, M. 2011. Laying groundwork for a sustainable market of genetically-improved
queens: The bee team. Managed pollinator CAP Update. Am. Bee J. 151(5): 483- 385

Tsuruda, J.M. J.W. Harris, L. Bourgeois, R.G. Danka & G.J. Hunt et al. 2011. Using single-nucleotide polymorphisms and genetic mapping to find candidate genes that influence varroa-specific hygiene. Am Bee J, 151(5): 507-518

Webster, T and K.A. Aronstein. Nosema ceranae Detection by Microscopy and Antibody
Tests. (ed. Samataro) Honey bee Colony Health: Challenges and Sustainable solutions (ed. Diana Samataro): Book chapter 10: Taylor and Francis, LLC. (accepted, 2011)

Further Background Information
Documentation of CAP progress in general, and of this objective in particular, is available through the following sources:

  1. Bee Health, an eXention initiative for peer-reviewed scientific recommendations
  2. Colony Collapse Disorder Progress Report for 2009
  3. When Varroacides Interact
  4. Detect Nosema Parasite in Time to Save Bee Colonies
  5. Nosema ceranae - The Inside Story
  6. Breeding Bees for Resistance to Parasites and Diseases
  7. Genetic Toolkits for Bee Health
  8. Laying Groundwork for a Sustainable Market of Genetically-Improved Queens

Updated July 22, 2011.