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United States Department of Agriculture

Agricultural Research Service

Research Project: USING THE GENOME TO UNDERSTAND IMMUNOGENETICS OF POULTRY
2012 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:
This final report shows that substantial progress was made on all three objectives and their sub-objectives. Under Objective 1, with support from our national and international collaborators (Washington University School of Medicine in St. Louis, Michigan State University, and Wageningen University in the Netherlands) an improved chicken genetic map was generated with the aid of a custom 60K SNP chip, which in turn, was used to produce an update genome assembly (galGal3). The improved genetic map, genome assembly, and related resources provide the basis and tools for understanding chicken biology including genetics and immunology of disease and disease resistance. For Objective 2, using a combination of molecular genetics techniques and computational analyses, we were able to identify the sequence motifs that recruit Marek’s disease virus (MDV) protein Meq, a transcription factor and the viral oncogene as well as revealing host pathways that are altered by the expression of Meq. This information is being leveraged to explain genetic resistance to Marek’s disease (MD) via transcriptional differences. Specifically, we identified 6,142 SNPs in genes that showed allele-specific expression (ASE) in response to MDV infection. Thus, high confidence MD resistance genes have been identified as they exhibit ASE upon viral infection and have a SNP in their upstream promoter for a Meq-binding motif. In addition, a genome-wide association study was completed. A total of 172 SNPs distributed over chromosomes 1, 3, 15 and Z was determined to be potentially associated with MD. Further analyses revealed that one SNP located in LMBRD2 on chromosome Z is of considerable interest, which may be used to improve genetic resistance in chicken by marker-assisted selection. Finally, we demonstrated that non-MHC host genetics influences MD vaccine efficacy. For Objective 3, advances were made to enhance our understanding of the chicken immune response when it encounters MDV. Specifically, a new technique to isolate the MDV genome from chickens was developed that isolated viral DNA directly from birds, thereby, bypassing the need for in vitro culture and associated side effects including viral attenuation. Thus, sequencing the virus directly from chickens ensured the genomic sequence obtained reflects the virulent form of the virus.


4.Accomplishments
1. Breeding chickens using genetic markers is more accurate and faster than current breeding methods. Genomic selection, a new method that selects for animals based on their DNA content only, promises significant benefits over traditional breeding methods that rely on familial relationships and the collection of agronomic traits. To prove that genomic selection works, an ARS scientist in East Lansing, Michigan, in collaboration with other scientists at Purdue University, University of Georgia, University of Wisconsin, Wageningen University in The Netherlands, and Cobb Vantress, Inc. compared commercial chickens selected by genomic selection or traditional selection. Our results demonstrate that genomic selection improves breeding accuracies by up to 100% depending on the trait being measured. If costs for genetic testing continue to go down, then poultry breeders should be able to economically breed chickens faster using genomic selection and adapt more readily to changing consumer demands. The economic impact could be great since with 1 million meat-type birds processed per hour in the US alone, the net effect of even small improvements are large and worth millions of dollars.

2. Marek’s disease virus (MDV) evolved to greater virulence in the lab. MDV continues to evolve toward greater virulence in commercial production facilities. The factors influencing this increase in virulence is not well understood primarily because MDV consists of multiple genetic subsets that have evolved in commercial lines of chickens with varying genetic backgrounds. ARS Researchers at East Lansing, Michigan have developed a laboratory model to observe this increase in viral virulence using a cloned virus passed through highly defined genetic stocks of chickens. The results have provided insights that can be used to select lines of chicken for disease resistance while still reducing virus evolution toward greater virulence, which will benefit US consumers.

3. Host genetic resistance to Marek’s disease (MD) enhances vaccinal protection. Marek’s disease virus (MDV) continues to evolve to higher virulence, thus, it is important to develop new and improved control measures that augment current MD vaccines. An ARS scientist in East Lansing, Michigan has shown that herpesvirus of turkeys (HVT), a lower efficacy MD vaccine that conveys poor protection to chickens that are highly susceptible to MD, provided good protection to chickens that are genetically resistant to MD and its efficacy was comparable to that of known highly efficacious vaccines. This finding has important implications on customizing vaccine development and application. Since HVT is less expensive than other commercial MD vaccines, increasing use of HVT to successfully protect MD resistant populations of chickens should economically benefit both producers and consumers.


Review Publications
Yu, Y., Luo, J., Mitra, A., Chang, S., Tian, F., Zhang, H., Yuan, P., Zhou, H., Song, J. 2012. Temporal transcriptome changes induced by MDV in Marek's disease-resistant and -susceptible inbred chickens. Biomed Central (BMC) Genomics. 12:501. Available: http://www.biomedcentral.com/1471-2164/12/501.

Chang, S., Ding, Z., Dunn, J.R., Lee, L.F., Heidari, M., Song, J., Ernst, C.W., Zhang, H. 2011. A comparative evaluation of the protective efficacy of rMd5-delta-Meq and CV1988/Rispens against a vv+ strain of Marek's disease virus infection in a series of recombinant congenic strains of white leghorn chickens. Avian Diseases. 55(3):384-390.

Cheng, H.H., Maceachern, S., Subramaniam, S., Muir, W.M. 2012. Chicks and single-nucleotide polymorphisms: an entree into identifying genes conferring disease resistance in chicken. Animal Production Science. 52(3). Available: http://dx.doi.org/10.1071/AN11099.

Chang, S., Dunn, J.R., Heidari, M., Lee, L.F., Ernst, C.W., Song, J., Zhang, H. 2012. Vaccine by chicken line interaction alters the protective efficacy against challenge with a very virulent plus strain of Marek's disease virus in white leghorn chickens. World Journal of Vaccines. 2(1):1-11. Available: http://www.scirp.org/journal/wjv/.

Luo, J., Yu, Y., Chang, S., Tian, F., Zhang, H., Song, J. 2012. DNA methylation fluctuation induced by virus infection differs between MD-resistant and -susceptible chickens. Frontiers in Genetics. 3(20):1-15. Available: http://www.frontiersin.org/epigenomics/10.3389/fgene.2012.00020/full.

Ng, C., Wu, P., Foley, J., Foley, A., McDonald, M., Juan, W., Huang, C., Lai, Y., Lo, W., Chen, C., Leal, S.M., Zhang, H., Widelitz, R.B., Patel, P.I., Li, W., Chuong, C. 2012. The chicken frizzle feather is due to an a-keratin (KRT75) mutation that causes a defective rachis. PLoS Genetics. 8(7). Available: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002748.

Tian, F., Luo, J., Zhang, H., Chang, S., Song, J. 2012. MiRNA expression signatures induced by Marek disease virus infection in chickens. Genomics. 99(3):152-159. Available: http://www.sciencedirect.com/science/article/pii/S0888754311002618.

Last Modified: 12/22/2014
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