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Resistance to MD and disease risk have long been thought to be influenced both by genetic and environmental factors, the combination of which contributes to the observed outcome in an individual. We hypothesize that after MDV infection, genes related to MD-resistance or -susceptibility may exhibit different trends in transcriptional activity in chicken lines having a varying degree of resistance to MD.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In order to study the mechanisms of resistance and susceptibility to MD, we performed genome-wide temporal expression analysis in spleen tissues from MD-resistant line 6<jats:sub>3<\/jats:sub>, susceptible line 7<jats:sub>2<\/jats:sub>and recombinant congenic strain M (RCS-M) that has a phenotype intermediate between lines 6<jats:sub>3<\/jats:sub>and 7<jats:sub>2<\/jats:sub>after MDV infection. Three time points of the MDV life cycle in chicken were selected for study: 5 days post infection (dpi), 10dpi and 21dpi, representing the early cytolytic, latent and late cytolytic stages, respectively. We observed similar gene expression profiles at the three time points in line 6<jats:sub>3<\/jats:sub>and RCS-M chickens that are both different from line 7<jats:sub>2<\/jats:sub>. Pathway analysis using Ingenuity Pathway Analysis (IPA) showed that MDV can broadly influence the chickens irrespective of whether they are resistant or susceptible to MD. However, some pathways like cardiac arrhythmia and cardiovascular disease were found to be affected only in line 7<jats:sub>2<\/jats:sub>; while some networks related to cell-mediated immune response and antigen presentation were enriched only in line 6<jats:sub>3<\/jats:sub>and RCS-M. We identified 78 and 30 candidate genes associated with MD resistance, at 10 and 21dpi respectively, by considering genes having the same trend of expression change after MDV infection in lines 6<jats:sub>3<\/jats:sub>and RCS-M. On the other hand, by considering genes with the same trend of expression change after MDV infection in lines 7<jats:sub>2<\/jats:sub>and RCS-M, we identified 78 and 43 genes at 10 and 21dpi, respectively, which may be associated with MD-susceptibility.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>By testing temporal transcriptome changes using three representative chicken lines with different resistance to MD, we identified 108 candidate genes for MD-resistance and 121 candidate genes for MD-susceptibility over the three time points. Genes included in our resistance or susceptibility genes lists that are also involved in more than 5 biofunctions, such as<jats:italic>CD8\u03b1<\/jats:italic>,<jats:italic>IL8<\/jats:italic>,<jats:italic>USP18<\/jats:italic>, and<jats:italic>CTLA4<\/jats:italic>, are considered to be important genes involved in MD-resistance or -susceptibility. We were also able to identify several biofunctions related with immune response that we believe play an important role in MD-resistance.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-12-501","type":"journal-article","created":{"date-parts":[[2012,1,31]],"date-time":"2012-01-31T16:32:25Z","timestamp":1328027545000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Temporal transcriptome changes induced by MDV in marek's disease-resistant and -susceptible inbred chickens"],"prefix":"10.1186","volume":"12","author":[{"given":"Ying","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Apratim","family":"Mitra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuang","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanmin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaijun","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiuzhou","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,10,12]]},"reference":[{"issue":"2","key":"3828_CR1","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1080\/03079450500059255","volume":"34","author":"RL Witter","year":"2005","unstructured":"Witter RL, Calnek BW, Buscaglia C, Gimeno IM, Schat KA: Classification of Marek's disease viruses according to pathotype: philosophy and methodology. 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