2011 Annual Report
Identifying PRRSV genotypes that confer fitness in macrophages, and host genes that respond to PRRSV fitness, to provide novel targets for intervention and control of PRRSV infections. These studies will use adapted isolates to identify viral genotypes that correlate with fitness of PRRSV in porcine alveolar macrophages and corresponding changes in macrophage transcriptional profiles.
Genetic variation in specific ovine genes influences predisposition to ovine lentivirus (OLV) and the associated disease, ovine progressive pneumonia (OPP). We will thoroughly evaluate the most obvious candidate genomic regions for effects on lentiviral disease, like that containing CCR5. Our aim is to evaluate important regions of the genome for allelic association with the OLV disease susceptibility and progression phenotypes. Selection of regions will be based on a variety of scientific observations including, but not limited to, comparative mammalian biology.
A selected set of 90 single nucleotide polymorphism (SNP) markers will be identified that are highly-informative in beef and dairy cattle. The development of this marker set represents non-hypothesis-driven research. The markers and genotyping assays for the markers will be readily available for any traceback needs. The same markers are also ideal for animal identification (i.e., sample matching) and routine parentage analysis. After ear tags and other physical identification devices have been removed, an animal’s DNA remains as a stable, accessible, integral, and identifiable component of its products and, thus, provides a gold standard for auditing the fidelity of physical labels and associated records.
Informatics for studying the transcriptome of swine infected with PRRSV. In April 2011, the Swine Genome Sequencing Consortium released Build 10 of the swine genome (Ssc10) with much improved transcript annotation (in quality and scope) over that which was available in 2010. During 2010, we analyzed the data generated by scientists at the USDA, ARS, National Animal Disease Center, Ames, IA, to investigate genes involved in the progression of PRSSV, pseudorabies virus (PRV), swine influenza virus (SIV), and porcine circovirus type 2 (PCV2) in infected swine as part of a National Pork Board grant (effective 11/01/2008 to 11/01/2010, entitled “Gene expression in lymph nodes of PRRSV-infected pigs,” Accession Number: 415042, Project Number: 3625-32000-088-28R). Next-generation sequencing was used to create libraries of 10 million “SAGE-like” 20-bp tags at days 1, 3, 7 and 14 post-infection in both infected and control groups of swine. These data were reanalyzed using Ssc10 as the reference, and have provided evidence of many more unambiguous tag to transcript to gene to pathway associations than what was possible in 2010.
Harhay, G.P., Smith, T.P.L., Alexander, L.J., Haudenschild, C.D., Keele, J.W., Matukumalli, L.K., Schroeder, S.G., Van Tassell, C.P., Gresham, C.R., Bridges, S.M., Burgess, S.C., Sonstegard, T.S. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology [online serial]. 11:R102.
Miller, L.C., Neill, J.D., Harhay, G.P., Lager, K.M., Laegreid, W.W., Kehrli, Jr., M.E. 2010. In-depth global analysis of transcript abundance levels in porcine alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus. Advances in Virology. 2010:Article 864181. Available: http://downloads.hindawi.com/journals/av/2010/864181.pdf.
Murdoch, B.M., Clawson, M.L., Yue, S., Basu, U., McKay, S., Settles, M., Capoferri, R., Laegreid, W.W., Williams, J.L., Moore, S.S. 2010. PRNP haplotype associated with classical BSE incidence in European Holstein cattle. PLoS One [serial online]. 5(9): e12786.
Durso, L.M., Harhay, G.P., Bono, J.L., Smith, T.P. 2011. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. Journal of Microbiological Methods. 84: 278-282.
Durso, L.M., Harhay, G.P., Smith, T.P., Bono, J.L., Desantis, T.Z., Clawson, M.L. 2011. Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces. Foodborne Pathogens and Disease. 8(5):647-649. Available: DOI: 10.1089/fpd.2010.0774.