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United States Department of Agriculture

Agricultural Research Service

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2011 Annual Report

1a. Objectives (from AD-416)
The long-term goal of this project is to develop an improved understanding of genetic resistance and vaccinal responses to Marek’s disease (MD) in order to increase productivity and safety of poultry products. Over the next 5 years, we will focus on the following specific objectives: Objective 1: Curate and enhance the chicken genetic map and its integration with the genome sequence. Objective 2: Identify and characterize chicken genes and pathways that confer resistance to MD. Sub-objective 2A: Validate, fine-map, and identify positional candidate genes for quantitative trait loci (QTL) that confer resistance to MD. Sub-objective 2B: Evaluate non-major histocompatibility complex (MHC) host genomic effects on MD vaccine efficacy. Objective 3: Functional characterization of the chicken MHC in response to tumor-virus infection or vaccination. Sub-objective 3A: Determine the relationship between in vivo passage of Marek’s disease virus (MDV) and the emergence of MDV strains with increased virulence. Sub-objective 3B: Determine the relationship between chicken MHC genetics and virus evolution. Sub-objective 3C: Determine the molecular basis for differential levels of cell surface MHC class I glycoprotein expression.

1b. Approach (from AD-416)
We define three interrelated approaches to help achieve our goals. First, we continue to enhance and curate the East Lansing (EL) chicken genetic map, which provides the foundation for molecular genetic studies and the chicken genome assembly. Second, we use an integrative genomics approach to identify QTL and candidate genes that confer genetic resistance or vaccinal immunity to MD. Our efforts are greatly enhanced by the availability of characterized inbred and recombinant congenic strains (RCS), genetic markers from our map, comprehensive DNA microarrays, as well as infectious MDV-BAC clones that we can manipulate to query and characterize specific virus-host protein interactions. And third, we evaluate an in vivo model for MDV virulence evolution and if successful, ask the question whether increased virulence is restricted to specific major histocompatibility (MHC) haplotypes.

3. Progress Report
Substantial progress was made on all three objectives and their subobjectives. Under Objective 1, in a collaborative effort with investigators from the Washington University School of Medicine in St. Louis, Michigan State University, and Wageningen University in The Netherlands, a new build of the chicken genome assembly was developed. This update includes the finished-quality Z chromosome (one of two chicken sex chromosomes) and many finished bacterial artificial chromosome (BAC) sequences (large regions that have been molecularly cloned). Our main contribution was generation of a “60K SNP chip” that added 54,293 genetic markers, which included 405 SNPs derived from unmapped sequence contigs. As a result, the latest genome assembly removed approximately 17 Mb of erroneous duplications. The improved genetic map, genome assembly, and 60K SNP chip provides the basis and tools for chicken biology including genetics and immunology of disease and disease resistance. For Objective 2, in collaborative efforts with investigators from the University of Maryland, significant progress was made to identify genomic regions and candidate genes that confer either genetic resistant to Marek’s disease (MD), a T cell lymphoma of chickens caused by the Marek’s disease virus (MDV), or confer differentiated MD vaccinal immunity. Specific genes were characterized that reveal the underlying biological pathways for host-pathogen interactions. Furthermore, epigenetic factors (do not alter the DNA sequence) including DNA methylation and microRNA were identified with differentiated patterns or expression levels between MD resistant and highly susceptible chicken lines suggesting epigenetic factors may also be involved in disease resistance. In another collaborative effort with investigators from Michigan State University, we addressed how the MDV Meq protein, a transcription factor and the likely viral oncogene, contributes to disease and tumor induction. Using a combination of molecular genetic techniques, we identified 351 specific genes that are directly regulated. These results are further supported by previous data that showed 319 of these genes were differentially expressed between chicken lines that are resistant or susceptible to MD. In collaboration with investigators at University of California at Davis, we determined that the majority of viral-induced tumors were clonal and, most interestingly, MDV preferentially integrates at the telomeres or ends of chromosomes. Substantial progress on Objective 3 was also made that advances our understanding of the chicken immune response when it encounters the virus. Of particular note is the role of genetic resistance and MHC (the major regulator of the immune response) haplotypes on viral evolution to higher virulence, which may provide alternative methods to inhibit MDV evolution to higher virulence. Finally, several MDV genes including UL49.5 and MDV012 have been identified that suppress the chicken immune system, thus, providing clues on how the virus evades the immune response as well as targets for disease control.

4. Accomplishments
1. Improved chicken genome sequence assembly. An ARS scientist in East Lansing, MI, in collaboration with other scientists at Washington University School of Medicine n St. Louis, Michigan State University, and Wageningen University in The Netherlands developed a new assembly of the chicken genome. This assembly is more accurate and contains less duplications compared to the previous version. This assembly and the accompanying genetic map are powerful tools for helping scientists around the world understand chicken biology including agronomically important traits such as production and disease resistance.

2. Gut microbes influence the health of chickens. Marek’s disease, a T cell lymphoma of chickens caused by an oncogenic herpesvirus, is one of the most serious and chronic infectious disease problems facing the poultry industry. Understanding factors that influence the susceptibility of chickens to Marek’s disease is of biological and economic importance. Using a model system, an ARS scientist in East Lansing, Michigan found that the microbial population in the intestinal tract is an important factor that alters disease incidence. This finding could lead to alternative methods besides vaccines for disease control in chickens.

3. Vaccination is the most cost-effective method for preventing diseases in both humans and livestock species. With regards to Marek’s disease, vaccines have been employed since the 1970s yet our understanding about the protective mechanisms is very limited. Additionally, earlier work by ARS scientists in East Lansing, MI, showed that the major histocompatibility complex (MHC), the key regulator of the immune response, was a major genetic contributor towards vaccinal protection against tumors in chickens induced by Marek’s disease viruses. Our recent studies show that genes outside the MHC also play an important role in vaccinal protection. This finding advances our understanding on host genetics influence over vaccine efficacy and lays a foundation for improvements in vaccine selection and administration.

Review Publications
Cheng, H.H. 2010. Viral diseases in chickens. In: Bishop S.C., Axford, R.F.E., Nicholas, F.W., Owen, J.B., editors. Breeding for Disease Resistance in Farm Animals. 3rd edition. Oxfordshire, United Kingdom: CAB International. p. 70-87.

Chang, S., Dunn, J.R., Heidari, M., Lee, L.F., Song, J., Ernst, C.W., Ding, Z., Bacon, L.D., Zhang, H. 2010. Genetics and Vaccine Efficacy: Host Genetic Variation Affecting Marek's Disease Vaccine Efficacy in White Leghorn Chickens. Poultry Science. 89(10):2083-2091.

Dodgson, J.B., Delany, M.E., Cheng, H.H. 2011. Poultry genome sequences: progress and outstanding challenges. Cytogenetics and Genome Research. p. 1-8. Available:

Niikura, M., Kim, T., Silva, R.F., Dodgson, J., Cheng, H.H. 2011. Virulent Marek's disease virus generated from infectious bacterial artificial chromosome clones with complete DNA sequence and implication of viral genetic homogeneity in pathogenesis. Journal of General Virology. 92:598-607.

Robinson, C.M., Hunt, H.D., Cheng, H.H., Delany, M.E. 2010. Chromosomal integration of an avian oncogenic herpesvirus reveals telomeric preferences and evidence for lymphoma clonality. BioMed Central (BMC) Herpesviridae. 1:5.

Robb, E.A., Gitter, C.L., Cheng, H.H., Delany, M.E. 2011. Chromosomal mapping and candidate gene discovery of chicken developmental mutants and genome-wide variation analysis of MHC congenics. Journal of Heredity. 102(2):141-156.

Megens, H., Crooijmans, R., Bastiaansen, J., Kerstens, H., Coster, A., Jalving, R., Vereijken, A., Silva, P., Muir, W., Cheng, H.H., Hanotte, O., Groenen, M. 2009. Comparison of Linkage Disequilibrium and Haplotype Diversity on Macro- and Microchromosomes in Chicken. BioMed Central (BMC) Genetics. Available:

Jarosinski, K.W., Hunt, H.D., Osterrieder, N. 2010. Down-regulation of MHC class I by the Marek's disease virus (MDV) UL49.5 gene product mildly affects virulence in a haplotype-specific fashion. Virology. 405(2):457-463. Available on-line at:

Hunt, H.D., Dunn, J.R. 2011. Serial transfer of a transplantable tumor: implications for Marek's vaccine mechanisms. Avian Diseases. 55(2):293-301.

Meydan, H., Yildiz, M.A., Dodgson, J.B., Cheng, H.H. 2011. Allele-specific expression analysis reveals CD79B has a cis-acting regulatory element that responds to Marek's disease virus infection in chicken. Poultry Science. 90(6):1206-1211.

Groenen, M., Megens, H., Zare, Y., Warren, W.C., Hillier, L.W., Crooijmans, R., Vereijken, A., Okimoto, R., Muir, W., Cheng, H.H. 2011. The development and characterization of a 60K SNP chip for chicken. Biomed Central (BMC) Genomics. 12:274. Available:

Maceachern, S., Muir, W.M., Crosby, S.D., Cheng, H.H. 2012. Genome-wide identification and quantification of cis- and trans-regulated genes responding to Marek's disease virus infection via analysis of allele-specific expression. Frontiers in Genetics. 2(113):1-11.

Last Modified: 05/27/2017
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