Table_3_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.XLSX
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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Online Access: | https://doi.org/10.3389/fimmu.2020.02113.s006 https://figshare.com/articles/dataset/Table_3_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_XLSX/12941360 |
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ftfrontimediafig:oai:figshare.com:article/12941360 2023-05-15T15:32:22+02:00 Table_3_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.XLSX Nardos Tesfaye Woldemariam Oleg Agafonov Hilde Sindre Bjørn Høyheim Ross D. Houston Diego Robledo James E. Bron Rune Andreassen 2020-09-11T04:25:46Z https://doi.org/10.3389/fimmu.2020.02113.s006 https://figshare.com/articles/dataset/Table_3_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_XLSX/12941360 unknown doi:10.3389/fimmu.2020.02113.s006 https://figshare.com/articles/dataset/Table_3_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_XLSX/12941360 Immunology Applied Immunology (incl. Antibody Engineering Xenotransplantation and T-cell Therapies) Autoimmunity Cellular Immunology Humoural Immunology and Immunochemistry Immunogenetics (incl. Genetic Immunology) Innate Immunity Transplantation Immunology Tumour Immunology Immunology not elsewhere classified Genetic Immunology Animal Immunology Veterinary Immunology Atlantic salmon microRNA IPNV immune response host-virus interactions Dataset 2020 ftfrontimediafig https://doi.org/10.3389/fimmu.2020.02113.s006 2020-09-16T22:56:23Z 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 ... Dataset Atlantic salmon Frontiers: Figshare Ikka ENVELOPE(-48.100,-48.100,61.150,61.150) |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Immunology Applied Immunology (incl. Antibody Engineering Xenotransplantation and T-cell Therapies) Autoimmunity Cellular Immunology Humoural Immunology and Immunochemistry Immunogenetics (incl. Genetic Immunology) Innate Immunity Transplantation Immunology Tumour Immunology Immunology not elsewhere classified Genetic Immunology Animal Immunology Veterinary Immunology Atlantic salmon microRNA IPNV immune response host-virus interactions |
spellingShingle |
Immunology Applied Immunology (incl. Antibody Engineering Xenotransplantation and T-cell Therapies) Autoimmunity Cellular Immunology Humoural Immunology and Immunochemistry Immunogenetics (incl. Genetic Immunology) Innate Immunity Transplantation Immunology Tumour Immunology Immunology not elsewhere classified Genetic Immunology Animal Immunology Veterinary Immunology Atlantic salmon microRNA IPNV immune response host-virus interactions Nardos Tesfaye Woldemariam Oleg Agafonov Hilde Sindre Bjørn Høyheim Ross D. Houston Diego Robledo James E. Bron Rune Andreassen Table_3_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.XLSX |
topic_facet |
Immunology Applied Immunology (incl. Antibody Engineering Xenotransplantation and T-cell Therapies) Autoimmunity Cellular Immunology Humoural Immunology and Immunochemistry Immunogenetics (incl. Genetic Immunology) Innate Immunity Transplantation Immunology Tumour Immunology Immunology not elsewhere classified Genetic Immunology Animal Immunology Veterinary Immunology Atlantic salmon microRNA IPNV immune response host-virus interactions |
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 |
Dataset |
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 |
Table_3_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.XLSX |
title_short |
Table_3_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.XLSX |
title_full |
Table_3_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.XLSX |
title_fullStr |
Table_3_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.XLSX |
title_full_unstemmed |
Table_3_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.XLSX |
title_sort |
table_3_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.xlsx |
publishDate |
2020 |
url |
https://doi.org/10.3389/fimmu.2020.02113.s006 https://figshare.com/articles/dataset/Table_3_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_XLSX/12941360 |
long_lat |
ENVELOPE(-48.100,-48.100,61.150,61.150) |
geographic |
Ikka |
geographic_facet |
Ikka |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
doi:10.3389/fimmu.2020.02113.s006 https://figshare.com/articles/dataset/Table_3_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_XLSX/12941360 |
op_doi |
https://doi.org/10.3389/fimmu.2020.02113.s006 |
_version_ |
1766362871976951808 |