A genome-wide association study of fetal response to type 2 porcine reproductive and respiratory syndrome virus challenge

Yang, Tong; Wilkinson, James; Wang, Zhiquan; Ladinig, Andrea; Harding, John C. S.; Plastow, Graham

doi:10.1038/srep20305

Cited by 24 publications

(27 citation statements)

References 78 publications

(96 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The number of SNPs on every chromosome varies from 1,403 on Chr.18 to 4,728 on Chr.1, and the adjacent distance ranges from 32.00 Kb on Chr.12 to 66.65 Kb on Chr.1. Compared with the common used Porcine SNP60 BeadChip in previous study [17,18], this porcine BeadChip has more usable, and evenly distributed SNPs.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide association study for intramuscular fat content in Chinese Lulai black pigs

Wang

Ning

Cheng

et al. 2019

Asian-Australas J Anim Sci

View full text Add to dashboard Cite

Objective Intramuscular fat (IMF) content plays an important role in meat quality. Identification of single nucleotide polymorphisms (SNPs) and genes related to pig IMF, especially using pig populations with high IMF content variation, can help to establish novel molecular breeding tools for optimizing IMF in pork and unveil the mechanisms that underlie fat metabolism. Methods We collected muscle samples of 453 Chinese Lulai black pigs, measured IMF content by Soxhlet petroleum-ether extraction method, and genotyped genome-wide SNPs using GeneSeek Genomic Profiler Porcine HD BeadChip. Then a genome-wide association study was performed using a linear mixed model implemented in the GEMMA software. Results A total of 43 SNPs were identified to be significantly associated with IMF content by the cutoff p<0.001. Among these significant SNPs, the greatest number of SNPs (n = 19) were detected on Chr.9, and two linkage disequilibrium blocks were formed among them. Additionally, 17 significant SNPs are mapped to previously reported quantitative trait loci (QTLs) of IMF and confirmed previous QTLs studies. Forty-two annotated genes centering these significant SNPs were obtained from Ensembl database. Overrepresentation test of pathways and gene ontology (GO) terms revealed some enriched reactome pathways and GO terms, which mainly involved regulation of basic material transport, energy metabolic process and signaling pathway. Conclusion These findings improve our understanding of the genetic architecture of IMF content in pork and facilitate the follow-up study of fine-mapping genes that influence fat deposition in muscle.

show abstract

Section: Resultsmentioning

confidence: 99%

Genome-wide association study for intramuscular fat content in Chinese Lulai black pigs

Wang

Ning

Cheng

et al. 2019

Asian-Australas J Anim Sci

View full text Add to dashboard Cite

show abstract

“…Genes downstream of type-I interferon signaling are heavily upregulated, and pro-inflammatory signaling through PRRs and cytokines, the complement pathway, acute phase response signaling, and antigen presentation are all activated in response to PRRSV infection. A number of these genes map to regions of the genome that are associated with fetal resistance to PRRSV, and could help to identify causative single nucleotide polymorphisms (SNPs) [ 61 ]. This is the first detailed study of the fetal response to PRRSV infection at the transcriptomic level, although a previous study did find an upregulation of the pro-inflammatory cytokines genes for IFN-γ and TNF-α, which is in agreement with our analyses [ 16 ].…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

et al. 2016

Self Cite

View full text Add to dashboard Cite

BackgroundPorcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection of pregnant pigs can result in congenital infection and ultimately fetal death. Little is known about immune responses to infection at the maternal-fetal interface and in the fetus itself, or the molecular events behind virus transmission and disease progression in the fetus. To investigate these processes, RNA-sequencing of two sites, uterine endothelium with adherent placental tissue and fetal thymus, was performed 21 days post-challenge on four groups of fetuses selected from a large PRRSV challenge experiment of pregnant gilts: control (CON), uninfected (UNINF), infected (INF), and meconium-stained (MEC) (n = 12/group). Transcriptional analyses consisted of multiple contrasts between groups using two approaches: differential gene expression analysis and weighted gene co-expression network analysis (WGCNA). Biological functions, pathways, and regulators enriched for differentially expressed genes or module members were identified through functional annotation analyses. Expression data were validated by reverse transcription quantitative polymerase chain reaction (RTqPCR) carried out for 16 genes of interest.ResultsThe immune response to infection in endometrium was mainly adaptive in nature, with the most upregulated genes functioning in either humoral or cell-mediated immunity. In contrast, the expression profile of infected fetal thymus revealed a predominantly innate immune response to infection, featuring the upregulation of genes regulated by type I interferon and pro-inflammatory cytokines. Fetal infection was associated with an increase in viral load coupled with a reduction in T cell signaling in the endometrium that could be due to PRRSV-controlled apoptosis of uninfected bystander cells. There was also evidence for a reduction in TWIST1 activity, a transcription factor involved in placental implantation and maturation, which could facilitate virus transmission or fetal pathology through dysregulation of placental function. Finally, results suggested that events within the fetus could also drive fetal pathology. Thymus samples of meconium-stained fetuses exhibited an increase in the expression of pro-inflammatory cytokine and granulocyte genes previously implicated in swine infectious disease pathology.ConclusionsThis study identified major differences in the response to PRRSV infection in the uterine endometrium and fetus at the gene expression level, and provides insight into the molecular basis of virus transmission and disease progression.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2720-4) contains supplementary material, which is available to authorized users.

show abstract

“…Although Bayesian phylodynamic methods became well established for rapidly evolving RNA viruses like PRRS 56,57 , past PRRSv studies continued using traditional phylogenetic methods (e.g. ML trees) to characterize new emerging strains, without accounting for their related evolutionary parameters, spatial or temporal information [58][59][60][61][62] . Furthermore, they continued to use the RFLP patterns to genotype the newly detected strains and made unrealistic and unsupported conclusions about their origins, transmission and evolution.…”

Section: Discussionmentioning

confidence: 99%

Novel approaches for Spatial and Molecular Surveillance of Porcine Reproductive and Respiratory Syndrome Virus (PRRSv) in the United States

Alkhamis

Arruda

Morrison

et al. 2017

Sci Rep

View full text Add to dashboard Cite

The US swine industry has been impaired over the last 25 years by the far-reaching financial losses caused by the porcine reproductive and respiratory syndrome (PRRS). Here, we explored the relations between the spatial risk of PRRS outbreaks and its phylodynamic history in the U.S during 1998–2016 using ORF5 sequences collected from swine farms in the Midwest region. We used maximum entropy and Bayesian phylodynamic models to generate risk maps for PRRS outbreaks and reconstructed the evolutionary history of three selected phylogenetic clades (A, B and C). High-risk areas for PRRS were best-predicted by pig density and climate seasonality and included Minnesota, Iowa and South Dakota. Phylodynamic models demonstrated that the geographical spread of the three clades followed a heterogeneous spatial diffusion process. Furthermore, PRRS viruses were characterized by typical seasonality in their population size. However, endemic strains were characterized by a substantially slower population growth and evolutionary rates, as well as smaller spatial dispersal rates when compared to emerging strains. We demonstrated the prospects of combining inferences derived from two unique analytical methods to inform decisions related to risk-based interventions of an important pathogen affecting one of the largest food animal industries in the world.

show abstract

A genome-wide association study of fetal response to type 2 porcine reproductive and respiratory syndrome virus challenge

Cited by 24 publications

References 78 publications

Genome-wide association study for intramuscular fat content in Chinese Lulai black pigs

Genome-wide association study for intramuscular fat content in Chinese Lulai black pigs

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

Novel approaches for Spatial and Molecular Surveillance of Porcine Reproductive and Respiratory Syndrome Virus (PRRSv) in the United States

Contact Info

Product

Resources

About