Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing
Background Gill health is one of the main concerns for Atlantic salmon aquaculture, and Amoebic Gill Disease (AGD), attributable to infection by the amoeba Neoparamoeba perurans, is a frequent cause of morbidity. In the absence of preventive measures, increasing genetic resistance of salmon to AGD v...
Published in: | BMC Genomics |
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Main Authors: | , , , , |
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Format: | Article in Journal/Newspaper |
Language: | English |
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Springer Science and Business Media LLC
2020
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Online Access: | http://hdl.handle.net/1893/30957 https://doi.org/10.1186/s12864-020-6694-x http://dspace.stir.ac.uk/bitstream/1893/30957/1/s12864-020-6694-x.pdf |
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ftunivstirling:oai:dspace.stir.ac.uk:1893/30957 |
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openpolar |
institution |
Open Polar |
collection |
University of Stirling: Stirling Digital Research Repository |
op_collection_id |
ftunivstirling |
language |
English |
topic |
AGD Genomics Amoeba Gene expression RNA-seq Transcriptome Salmo salar Disease resistance Allelic specific expression |
spellingShingle |
AGD Genomics Amoeba Gene expression RNA-seq Transcriptome Salmo salar Disease resistance Allelic specific expression Robledo, Diego Hamilton, Alastair Gutiérrez, Alejandro P Bron, James E Houston, Ross D Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing |
topic_facet |
AGD Genomics Amoeba Gene expression RNA-seq Transcriptome Salmo salar Disease resistance Allelic specific expression |
description |
Background Gill health is one of the main concerns for Atlantic salmon aquaculture, and Amoebic Gill Disease (AGD), attributable to infection by the amoeba Neoparamoeba perurans, is a frequent cause of morbidity. In the absence of preventive measures, increasing genetic resistance of salmon to AGD via selective breeding can reduce the incidence of the disease and mitigate gill damage. Understanding the mechanisms leading to AGD resistance and the underlying causative genomic features can aid in this effort, while also providing critical information for the development of other control strategies. AGD resistance is considered to be moderately heritable, and several putative QTL have been identified. The aim of the current study was to improve understanding of the mechanisms underlying AGD resistance, and to identify putative causative genomic factors underlying the QTL. To achieve this, RNA was extracted from the gill and head kidney of AGD resistant and susceptible animals following a challenge with N. perurans, and sequenced. Results Comparison between resistant and susceptible animals primarily highlighted differences mainly in the local immune response in the gill, involving red blood cell genes and genes related to immune function and cell adhesion. Differentially expressed immune genes pointed to a contrast in Th2 and Th17 responses, which is consistent with the increased heritability observed after successive challenges with the amoeba. Five QTL-region candidate genes showed differential expression, including a gene connected to interferon responses (GVINP1), a gene involved in systemic inflammation (MAP4K4), and a positive regulator of apoptosis (TRIM39). Analyses of allele-specific expression highlighted a gene in the QTL region on chromosome 17, cellular repressor of E1A-stimulated genes 1 (CREG1), showing allelic differential expression suggestive of a cis-acting regulatory variant. Conclusions In summary, this study provides new insights into the mechanisms of resistance to AGD in Atlantic salmon, and ... |
author2 |
Scottish Aquaculture Innovation Centre Biotechnology and Biological Sciences Research Council Royal Society H2020 European Research Council University of Edinburgh Institute of Aquaculture orcid:0000-0002-9616-5912 orcid:0000-0003-3544-0519 |
format |
Article in Journal/Newspaper |
author |
Robledo, Diego Hamilton, Alastair Gutiérrez, Alejandro P Bron, James E Houston, Ross D |
author_facet |
Robledo, Diego Hamilton, Alastair Gutiérrez, Alejandro P Bron, James E Houston, Ross D |
author_sort |
Robledo, Diego |
title |
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing |
title_short |
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing |
title_full |
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing |
title_fullStr |
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing |
title_full_unstemmed |
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing |
title_sort |
characterising the mechanisms underlying genetic resistance to amoebic gill disease in atlantic salmon using rna sequencing |
publisher |
Springer Science and Business Media LLC |
publishDate |
2020 |
url |
http://hdl.handle.net/1893/30957 https://doi.org/10.1186/s12864-020-6694-x http://dspace.stir.ac.uk/bitstream/1893/30957/1/s12864-020-6694-x.pdf |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
Robledo D, Hamilton A, Gutiérrez AP, Bron JE & Houston RD (2020) Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing. BMC Genomics, 21 (1), Art. No.: 271. https://doi.org/10.1186/s12864-020-6694-x 271 http://hdl.handle.net/1893/30957 doi:10.1186/s12864-020-6694-x 32228433 WOS:000524213000005 2-s2.0-85082748543 1598146 http://dspace.stir.ac.uk/bitstream/1893/30957/1/s12864-020-6694-x.pdf |
op_rights |
This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. http://creativecommons.org/licenses/by/4.0/ |
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CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s12864-020-6694-x |
container_title |
BMC Genomics |
container_volume |
21 |
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ftunivstirling:oai:dspace.stir.ac.uk:1893/30957 2023-05-15T15:31:14+02:00 Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing Robledo, Diego Hamilton, Alastair Gutiérrez, Alejandro P Bron, James E Houston, Ross D Scottish Aquaculture Innovation Centre Biotechnology and Biological Sciences Research Council Royal Society H2020 European Research Council University of Edinburgh Institute of Aquaculture orcid:0000-0002-9616-5912 orcid:0000-0003-3544-0519 2020 application/pdf http://hdl.handle.net/1893/30957 https://doi.org/10.1186/s12864-020-6694-x http://dspace.stir.ac.uk/bitstream/1893/30957/1/s12864-020-6694-x.pdf en eng Springer Science and Business Media LLC Robledo D, Hamilton A, Gutiérrez AP, Bron JE & Houston RD (2020) Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing. BMC Genomics, 21 (1), Art. No.: 271. https://doi.org/10.1186/s12864-020-6694-x 271 http://hdl.handle.net/1893/30957 doi:10.1186/s12864-020-6694-x 32228433 WOS:000524213000005 2-s2.0-85082748543 1598146 http://dspace.stir.ac.uk/bitstream/1893/30957/1/s12864-020-6694-x.pdf This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. http://creativecommons.org/licenses/by/4.0/ CC0 PDM CC-BY AGD Genomics Amoeba Gene expression RNA-seq Transcriptome Salmo salar Disease resistance Allelic specific expression Journal Article VoR - Version of Record 2020 ftunivstirling https://doi.org/10.1186/s12864-020-6694-x 2022-06-13T18:43:33Z Background Gill health is one of the main concerns for Atlantic salmon aquaculture, and Amoebic Gill Disease (AGD), attributable to infection by the amoeba Neoparamoeba perurans, is a frequent cause of morbidity. In the absence of preventive measures, increasing genetic resistance of salmon to AGD via selective breeding can reduce the incidence of the disease and mitigate gill damage. Understanding the mechanisms leading to AGD resistance and the underlying causative genomic features can aid in this effort, while also providing critical information for the development of other control strategies. AGD resistance is considered to be moderately heritable, and several putative QTL have been identified. The aim of the current study was to improve understanding of the mechanisms underlying AGD resistance, and to identify putative causative genomic factors underlying the QTL. To achieve this, RNA was extracted from the gill and head kidney of AGD resistant and susceptible animals following a challenge with N. perurans, and sequenced. Results Comparison between resistant and susceptible animals primarily highlighted differences mainly in the local immune response in the gill, involving red blood cell genes and genes related to immune function and cell adhesion. Differentially expressed immune genes pointed to a contrast in Th2 and Th17 responses, which is consistent with the increased heritability observed after successive challenges with the amoeba. Five QTL-region candidate genes showed differential expression, including a gene connected to interferon responses (GVINP1), a gene involved in systemic inflammation (MAP4K4), and a positive regulator of apoptosis (TRIM39). Analyses of allele-specific expression highlighted a gene in the QTL region on chromosome 17, cellular repressor of E1A-stimulated genes 1 (CREG1), showing allelic differential expression suggestive of a cis-acting regulatory variant. Conclusions In summary, this study provides new insights into the mechanisms of resistance to AGD in Atlantic salmon, and ... Article in Journal/Newspaper Atlantic salmon Salmo salar University of Stirling: Stirling Digital Research Repository BMC Genomics 21 1 |