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| Status |
Public on Mar 31, 2017 |
| Title |
Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Here, we integrated genome-wide genotype, gene expression and phenotype (viremia level (VL) and weight gain (WG)) data to identify genetic variations and genes that are associated with variation in pigs’ response to PRRSV infection. RNA-seq analysis of peripheral blood samples collected just prior to experimental challenge (day 0) and at 4, 7, 10 and 14 days post infection from 44 pigs revealed 6430 differentially expressed genes after infection. We mapped genetic variations that are associated with inter-individual differences in expression at each day and found evidence of cis expression quantitative trait loci (cis-eQTL) for 1201 genes. Associations between cis-eQTL markers and phenotypes using 383 pigs indicated that host genotype-dependent reduced expression of GBP5, CD1D, PAK1, and USP18 contribute to higher VL or lower WG in response to PRRSV infection. We also validated that cis-eQTLs of these candidate genes for host response to PRRSV infection generally acted by a mechanism involving allele-specific expression.
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| Overall design |
Sixteen pigs (8 AA and 8 AB individual at the WUR marker) were selected from the PHGC3 trial. Twenty-eight pigs (18 AA, 9 AB and 1 BB individuals at the WUR marker) were selected from the PHGC5 trial. After a seven-day acclimation period, pigs were challenged orally with PRRSV isolate NVSL 97-7985 and followed for 42 days post infection (dpi). RNA-Seq was performed using Illumina HiSeq on whole blood samples obtained from each individual at 0, 4, 7, 10, and 14 dpi. For individuals from the PHGC5 trial, RNA-Seq was performed on whole blood samples collected at 2 additional time-points: 21 and 28 dpi. The PHGC5 RNA-Seq data is represented here.
Please note that the PHGC3 RNA-Seq data has been submitted directly to SRA [SRA accession: SRP069349].
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| Contributor(s) |
Bao H, Kommadath A, Choi I, Lunney JK, Reecy JM, Dekkers JC, Plastow GS, Stothard P |
| Citation(s) |
28393889 |
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| Submission date |
Feb 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Payam Vahmani |
| E-mail(s) |
[email protected]
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| Organization name |
University of California Davis
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| Department |
Department of Animal Science
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| Street address |
One Shields Avenue
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| City |
Davis |
| State/province |
California |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platforms (1) |
| GPL11429 |
Illumina HiSeq 2000 (Sus scrofa) |
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| Samples (179)
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| Relations |
| BioProject |
PRJNA313448 |
| SRA |
SRP070951 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE78762_RAW.tar |
17.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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