miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection
Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host mi...
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2020
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Online Access: | https://doi.org/10.3389/fimmu.2020.02113 https://doaj.org/article/89b743077d0d4c4ea17ff2f05b5bde1e |
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ftdoajarticles:oai:doaj.org/article:89b743077d0d4c4ea17ff2f05b5bde1e 2023-05-15T15:32:17+02:00 miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection Nardos Tesfaye Woldemariam Oleg Agafonov Hilde Sindre Bjørn Høyheim Ross D. Houston Diego Robledo James E. Bron Rune Andreassen 2020-09-01T00:00:00Z https://doi.org/10.3389/fimmu.2020.02113 https://doaj.org/article/89b743077d0d4c4ea17ff2f05b5bde1e EN eng Frontiers Media S.A. https://www.frontiersin.org/article/10.3389/fimmu.2020.02113/full https://doaj.org/toc/1664-3224 1664-3224 doi:10.3389/fimmu.2020.02113 https://doaj.org/article/89b743077d0d4c4ea17ff2f05b5bde1e Frontiers in Immunology, Vol 11 (2020) Atlantic salmon microRNA IPNV immune response host-virus interactions Immunologic diseases. Allergy RC581-607 article 2020 ftdoajarticles https://doi.org/10.3389/fimmu.2020.02113 2022-12-31T00:24:39Z Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host miRNAs that respond to IPNV challenge in salmon fry that were either homozygous resistant (RR) or homozygous susceptible (SS) for the IPN-QTL. Small RNA-sequenced control samples were compared to samples collected at 1, 7, and 20 days post challenge (dpc). This revealed 72 differentially expressed miRNAs (DE miRNAs). Viral load (VL) was lower in RR vs. SS individuals at 7 and 20 dpc. However, analysis of miRNA expression changes revealed no differences between RR vs. SS individuals in controls, at 1 or 7 dpc, while 38 “high viral load responding” miRNAs (HVL-DE miRNAs) were identified at 20 dpc. Most of the HVL-DE miRNAs showed changes that were more pronounced in the high VL SS group than in the low VL RR group when compared to the controls. The absence of differences between QTL groups in controls, 1 and 7 dpc indicates that the QTL genotype does not affect miRNA expression in healthy fish or their first response to viral infections. The miRNA differences at 20 dpc were associated with the QTL genotype and could, possibly, contribute to differences in resistance/susceptibility at the later stage of infection. In silico target gene predictions revealed that 180 immune genes were putative targets, and enrichment analysis indicated that the miRNAs may regulate several major immune system pathways. Among the targets of HVL-DE miRNAs were IRF3, STAT4, NFKB2, MYD88, and IKKA. Interestingly, TNF-alpha paralogs were targeted by different DE miRNAs. Most DE miRNAs were from conserved miRNA families that respond to viral infections in teleost (e.g., miR-21, miR-146, miR-181, miR-192, miR-221, miR-462, miR-731, and miR-8159), while eight were species specific. The miRNAs showed dynamic temporal changes implying they would affect ... Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles Ikka ENVELOPE(-48.100,-48.100,61.150,61.150) Frontiers in Immunology 11 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Atlantic salmon microRNA IPNV immune response host-virus interactions Immunologic diseases. Allergy RC581-607 |
spellingShingle |
Atlantic salmon microRNA IPNV immune response host-virus interactions Immunologic diseases. Allergy RC581-607 Nardos Tesfaye Woldemariam Oleg Agafonov Hilde Sindre Bjørn Høyheim Ross D. Houston Diego Robledo James E. Bron Rune Andreassen miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
topic_facet |
Atlantic salmon microRNA IPNV immune response host-virus interactions Immunologic diseases. Allergy RC581-607 |
description |
Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host miRNAs that respond to IPNV challenge in salmon fry that were either homozygous resistant (RR) or homozygous susceptible (SS) for the IPN-QTL. Small RNA-sequenced control samples were compared to samples collected at 1, 7, and 20 days post challenge (dpc). This revealed 72 differentially expressed miRNAs (DE miRNAs). Viral load (VL) was lower in RR vs. SS individuals at 7 and 20 dpc. However, analysis of miRNA expression changes revealed no differences between RR vs. SS individuals in controls, at 1 or 7 dpc, while 38 “high viral load responding” miRNAs (HVL-DE miRNAs) were identified at 20 dpc. Most of the HVL-DE miRNAs showed changes that were more pronounced in the high VL SS group than in the low VL RR group when compared to the controls. The absence of differences between QTL groups in controls, 1 and 7 dpc indicates that the QTL genotype does not affect miRNA expression in healthy fish or their first response to viral infections. The miRNA differences at 20 dpc were associated with the QTL genotype and could, possibly, contribute to differences in resistance/susceptibility at the later stage of infection. In silico target gene predictions revealed that 180 immune genes were putative targets, and enrichment analysis indicated that the miRNAs may regulate several major immune system pathways. Among the targets of HVL-DE miRNAs were IRF3, STAT4, NFKB2, MYD88, and IKKA. Interestingly, TNF-alpha paralogs were targeted by different DE miRNAs. Most DE miRNAs were from conserved miRNA families that respond to viral infections in teleost (e.g., miR-21, miR-146, miR-181, miR-192, miR-221, miR-462, miR-731, and miR-8159), while eight were species specific. The miRNAs showed dynamic temporal changes implying they would affect ... |
format |
Article in Journal/Newspaper |
author |
Nardos Tesfaye Woldemariam Oleg Agafonov Hilde Sindre Bjørn Høyheim Ross D. Houston Diego Robledo James E. Bron Rune Andreassen |
author_facet |
Nardos Tesfaye Woldemariam Oleg Agafonov Hilde Sindre Bjørn Høyheim Ross D. Houston Diego Robledo James E. Bron Rune Andreassen |
author_sort |
Nardos Tesfaye Woldemariam |
title |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_short |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_full |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_fullStr |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_full_unstemmed |
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection |
title_sort |
mirnas predicted to regulate host anti-viral gene pathways in ipnv-challenged atlantic salmon fry are affected by viral load, and associated with the major ipn resistance qtl genotypes in late infection |
publisher |
Frontiers Media S.A. |
publishDate |
2020 |
url |
https://doi.org/10.3389/fimmu.2020.02113 https://doaj.org/article/89b743077d0d4c4ea17ff2f05b5bde1e |
long_lat |
ENVELOPE(-48.100,-48.100,61.150,61.150) |
geographic |
Ikka |
geographic_facet |
Ikka |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Frontiers in Immunology, Vol 11 (2020) |
op_relation |
https://www.frontiersin.org/article/10.3389/fimmu.2020.02113/full https://doaj.org/toc/1664-3224 1664-3224 doi:10.3389/fimmu.2020.02113 https://doaj.org/article/89b743077d0d4c4ea17ff2f05b5bde1e |
op_doi |
https://doi.org/10.3389/fimmu.2020.02113 |
container_title |
Frontiers in Immunology |
container_volume |
11 |
_version_ |
1766362792185561088 |