2008 Annual Report 1a.Objectives (from AD-416) 1. Using prior information, assemble a list of ~4,500 genes that are differentially expressed between MD resistant and susceptible birds. 2. Screen for SNPs in each gene by sequencing the parental lines. 3. Conduct allele-specific expression assays using multiple F1 RNAs obtained at each of six different time points that are uninfected and MDV-infected, and artificial F1 RNA pools. 4. Analyze the data to (1) eliminate any assay bias, (2) determine if there is imprinting or maternal effects, (3) identify genes with polymorphic cis-acting elements, (4) identify genes influenced by polymorphic trans-acting factors, and (5) identify genes and specific alleles that are influenced by MDV infection. 1b.Approach (from AD-416) Our primary objective is to identify genes with polymorphic cis-acting elements that control expression in response to MDV challenge. In addition, our experimental design should allow for the determination of imprinting or maternal effects, and evidence for specific genes whose expression is influenced by one or more polymorphic trans-acting factor. 3.Progress Report This project is also related to 3635-31320-008-13R entitled “Genome-Wide Screen For Polymorphic Genes With Cis-Acting Elements That Respond To Marek’s Disease Virus Challenge In Chicken.” This is a new agreement, thus, we have no results to report at this time. This project is monitored by weekly e-mail and telephone calls between the two parties and, when possible, direct interactions at scientific meetings.