2006 Annual Report 4d.Progress report. This report serves to document research conducted under a Reimbursable Cooperative Agreement #58-5438-5-413 between ARS and North Carolina State University. Additional details of research can be found in the report for the parent project 5438-31000-069-00D Identification and characterization of genetic variation for factors affecting fetal survival and litter size in swine. Funding was obtained for the proposal and animal tissue resources were generated during FY2005. The research has identified novel imprinted genes that are implicated in placental development. The North Carolina State collaborators generated the expression data comparing gynogenote and normal pig embryos to identify candidate genes for evaluation of imprinting. Scientists at USMARC have designed primers for candidate loci and a protocol for polymorphism discovery that can be used to establish which genes are imprinted in the pig placenta is in place and succeeding. During FY2006, more than 100 polymorphisms have been identified and genotyping assays have been designed. Genomic and expressed templates have been extracted and plates created to evaluate imprinting status for these assays. Genotypic data to test imprinting status will be generated over the next couple of months. Additionally, tissues obtained from the serial slaughter experiment from the parent CRIS project were used to generate unique temporal expression patterns throughout gestation for the transcriptome of the pig placenta using the Affymetrix porcine microarrays. Manuscripts have been developed to provide updated annotation information about the Affymetrix porcine arrays, and also a direct evaluation comparing currently available array platforms. These breed comparison data also are contributing to the rapid identification of coding region polymorphism by analyzing the array data in a gene by gene approach and identifying breed by probe interactions. This discovery approach has the potential application to rapidly generate a resource of coding region polymorphisms for any given breed or line comparison being made (i.e., the USMARC selection lines). Review Publications Tsai, S., Weir, B., Cassady, J., Freking, B.A., Nonneman, D.J., Rohrer, G.A., Piedrahita, J. 2006. Annotation of affymetrix porcine genome microarray chip. Plant and Animal Genome Conference Proceedings. Poster #P768. p. 292. Piedrahita, J.A., Bischoff, S.R., Estrada, J.L., Freking, B.A., Nonneman, D.J., Martin, A.C., Mir, B., Rohrer, G.A., Tsai, S. 2006. Use of porcine parthenotes and gene expression profiling using microarrays for identification of imprinted genes [abstract]. Proceedings of the 32nd International Conference of the International Embryo Transfer Society (IETS), January 8-10, 2006, Orlando, FL. Page 239. Tsai, S., Cassady, J.P., Freking, B.A., Nonneman, D.J., Rohrer, G.A., Piedrahita, J.A. 2006. Annotation of the affymetrix porcine genome microarray. Animal Genetics. 37:423-424.