Abstract
We evaluated differences in gene expression in pigs from the Porcine Reproductive and Respiratory Syndrome (PRRS) Host Genetics Consortium initiative showing a range of responses to PRRS virus infection. Pigs were allocated into four phenotypic groups according to their serum viral level and weight gain. RNA obtained from blood at 0, 4, 7, 11, 14, 28, and 42 days post-infection (DPI) was hybridized to the 70-mer 20K Pigoligoarray. We used a blocked reference design for the microarray experiment. This allowed us to account for individual biological variation in gene expression, and to assess baseline effects before infection (0 DPI). Additionally, this design has the flexibility of incorporating future data for differential expression analysis. We focused on evaluating transcripts showing significant interaction of weight gain and serum viral level. We identified 491 significant comparisons [false discovery rate (FDR) = 10%] across all DPI and phenotypic groups. We corroborated the overall trend in direction and level of expression (measured as fold change) at 4 DPI using qPCR (r = 0.91, p ≤ 0.0007). At 4 and 7 DPI, network and functional analyses were performed to assess if immune related gene sets were enriched for genes differentially expressed (DE) across four phenotypic groups. We identified cell death function as being significantly associated (FDR ≤ 5%) with several networks enriched for DE transcripts. We found the genes interferon-alpha 1(IFNA1), major histocompatibility complex, class II, DQ alpha 1 (SLA-DQA1), and major histocompatibility complex, class II, DR alpha (SLA-DRA) to be DE (p ≤ 0.05) between phenotypic groups. Finally, we performed a power analysis to estimate sample size and sampling time-points for future experiments. We concluded the best scenario for investigation of early response to PRRSV infection consists of sampling at 0, 4, and 7 DPI using about 30 pigs per phenotypic group.
Highlights
Porcine Reproductive and Respiratory Syndrome (PRRS) was initially described in the US over 20 years ago (Done et al, 1996)
We evaluated whole-genome expression profile of pigs assigned to four reaction groups according to the pigs’ weight gain and viral load (VL) as part of the PRRS Host Genetics Consortium (PHGC) (Lunney et al, 2011)
Dye labeled cDNA prepared from blood samples from 12 PHGC pigs at seven different time points (0, 4, 7, 11, 14, 28, and 42 days post-infection (DPI)) were hybridized to the Pigoligoarray using a block reference design
Summary
Porcine Reproductive and Respiratory Syndrome (PRRS) was initially described in the US over 20 years ago (Done et al, 1996). While the molecular pathways involved in the protection against PRRS have not yet been entirely elucidated (Kimman et al, 2009), phenotypic variation between breed-lines has been observed in disease-related and production traits of experimentally infected pigs (Petry et al, 2005; Vincent et al, 2006; Doeschl-Wilson et al, 2009). These authors reported differences in clinical symptoms and lung pathology in response to PRRSV infection, as well as in virus levels in serum and/or respiratory tissues, such as lung and bronchial lymph nodes. Host genetic response to infection can be studied using currently available genomic tools (Lewis et al, 2007; Lunney and Chen, 2010)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
