Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing
Abstract 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...
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crspringernat:10.1186/s12864-020-6694-x 2023-05-15T15:31:30+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. Biotechnology and Biological Sciences Research Council Scottish Aquaculture Innovation Centre Biotechnology and Biological Sciences Research Council The Royal Society H2020 European Research Council 2020 http://dx.doi.org/10.1186/s12864-020-6694-x http://link.springer.com/content/pdf/10.1186/s12864-020-6694-x.pdf http://link.springer.com/article/10.1186/s12864-020-6694-x/fulltext.html en eng Springer Science and Business Media LLC http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/ CC-BY BMC Genomics volume 21, issue 1 ISSN 1471-2164 Genetics Biotechnology journal-article 2020 crspringernat https://doi.org/10.1186/s12864-020-6694-x 2022-01-04T14:33:51Z Abstract 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 highlights candidate genes for further functional studies that can further elucidate the genomic mechanisms leading to resistance and contribute to enhancing salmon health via improved genomic selection. Article in Journal/Newspaper Atlantic salmon Springer Nature (via Crossref) BMC Genomics 21 1 |
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Springer Nature (via Crossref) |
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crspringernat |
language |
English |
topic |
Genetics Biotechnology |
spellingShingle |
Genetics Biotechnology 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 |
Genetics Biotechnology |
description |
Abstract 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 highlights candidate genes for further functional studies that can further elucidate the genomic mechanisms leading to resistance and contribute to enhancing salmon health via improved genomic selection. |
author2 |
Biotechnology and Biological Sciences Research Council Scottish Aquaculture Innovation Centre Biotechnology and Biological Sciences Research Council The Royal Society H2020 European Research Council |
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://dx.doi.org/10.1186/s12864-020-6694-x http://link.springer.com/content/pdf/10.1186/s12864-020-6694-x.pdf http://link.springer.com/article/10.1186/s12864-020-6694-x/fulltext.html |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
BMC Genomics volume 21, issue 1 ISSN 1471-2164 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/s12864-020-6694-x |
container_title |
BMC Genomics |
container_volume |
21 |
container_issue |
1 |
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1766362015395217408 |