Table_1_Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.).DOCX
Amoebic gill disease (AGD) is one of the most important parasitic diseases of farmed Atlantic salmon. It is a source of major economic loss to the industry and poses significant threats to animal welfare. Previous studies have shown that resistance against this disease has a moderate, heritable gene...
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ftfrontimediafig:oai:figshare.com:article/7774559 2023-05-15T15:30:53+02:00 Table_1_Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.).DOCX Solomon Antwi Boison Bjarne Gjerde Borghild Hillestad Shokouh Makvandi-Nejad Hooman K. Moghadam 2019-02-27T04:21:19Z https://doi.org/10.3389/fgene.2019.00068.s009 https://figshare.com/articles/Table_1_Genomic_and_Transcriptomic_Analysis_of_Amoebic_Gill_Disease_Resistance_in_Atlantic_Salmon_Salmo_salar_L_DOCX/7774559 unknown doi:10.3389/fgene.2019.00068.s009 https://figshare.com/articles/Table_1_Genomic_and_Transcriptomic_Analysis_of_Amoebic_Gill_Disease_Resistance_in_Atlantic_Salmon_Salmo_salar_L_DOCX/7774559 CC BY 4.0 CC-BY Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy Atlantic salmon amoebic gill disease AGD transcriptome genome-wide association study GWAS genomic predictions Dataset 2019 ftfrontimediafig https://doi.org/10.3389/fgene.2019.00068.s009 2019-02-27T23:58:16Z Amoebic gill disease (AGD) is one of the most important parasitic diseases of farmed Atlantic salmon. It is a source of major economic loss to the industry and poses significant threats to animal welfare. Previous studies have shown that resistance against this disease has a moderate, heritable genetic component, although the genes and the genetic pathways that contribute to this process have yet to be elucidated. In this study, to identify the genetic mechanisms of AGD resistance, we first investigated the molecular signatures of AGD infection in Atlantic salmon through a challenge model, where we compared the transcriptome profiles of the naïve and infected animals. We then conducted a genome-wide association analysis with 1,333 challenged tested fish to map the AGD resistance genomic regions, supported by the results from the transcriptomic data. Further, we investigated the potential of incorporating gene expression analysis results in genomic prediction to improve prediction accuracy. Our data suggest thousands of genes have modified their expression following infection, with a significant increase in the transcription of genes with functional properties in cell adhesion and a sharp decline in the abundance of various components of the immune system genes. From the genome-wide association analysis, QTL regions on chromosomes ssa04, ssa09, and ssa13 were detected to be linked with AGD resistance. In particular, we found that QTL region on ssa04 harbors members of the cadherin gene family. These genes play a critical role in target recognition and cell adhesion. The QTL region on ssa09 also is associated with another member of the cadherin gene family, protocadherin Fat 4. The associated genetic markers on ssa13 span a large genomic region that includes interleukin-18-binding protein, a gene with function essential in inhibiting the proinflammatory effect of cytokine IL18. Incorporating gene expression information through a weighted genomic relationship matrix approach decreased genomic prediction accuracy ... Dataset Atlantic salmon Salmo salar Frontiers: Figshare |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy Atlantic salmon amoebic gill disease AGD transcriptome genome-wide association study GWAS genomic predictions |
spellingShingle |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy Atlantic salmon amoebic gill disease AGD transcriptome genome-wide association study GWAS genomic predictions Solomon Antwi Boison Bjarne Gjerde Borghild Hillestad Shokouh Makvandi-Nejad Hooman K. Moghadam Table_1_Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.).DOCX |
topic_facet |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy Atlantic salmon amoebic gill disease AGD transcriptome genome-wide association study GWAS genomic predictions |
description |
Amoebic gill disease (AGD) is one of the most important parasitic diseases of farmed Atlantic salmon. It is a source of major economic loss to the industry and poses significant threats to animal welfare. Previous studies have shown that resistance against this disease has a moderate, heritable genetic component, although the genes and the genetic pathways that contribute to this process have yet to be elucidated. In this study, to identify the genetic mechanisms of AGD resistance, we first investigated the molecular signatures of AGD infection in Atlantic salmon through a challenge model, where we compared the transcriptome profiles of the naïve and infected animals. We then conducted a genome-wide association analysis with 1,333 challenged tested fish to map the AGD resistance genomic regions, supported by the results from the transcriptomic data. Further, we investigated the potential of incorporating gene expression analysis results in genomic prediction to improve prediction accuracy. Our data suggest thousands of genes have modified their expression following infection, with a significant increase in the transcription of genes with functional properties in cell adhesion and a sharp decline in the abundance of various components of the immune system genes. From the genome-wide association analysis, QTL regions on chromosomes ssa04, ssa09, and ssa13 were detected to be linked with AGD resistance. In particular, we found that QTL region on ssa04 harbors members of the cadherin gene family. These genes play a critical role in target recognition and cell adhesion. The QTL region on ssa09 also is associated with another member of the cadherin gene family, protocadherin Fat 4. The associated genetic markers on ssa13 span a large genomic region that includes interleukin-18-binding protein, a gene with function essential in inhibiting the proinflammatory effect of cytokine IL18. Incorporating gene expression information through a weighted genomic relationship matrix approach decreased genomic prediction accuracy ... |
format |
Dataset |
author |
Solomon Antwi Boison Bjarne Gjerde Borghild Hillestad Shokouh Makvandi-Nejad Hooman K. Moghadam |
author_facet |
Solomon Antwi Boison Bjarne Gjerde Borghild Hillestad Shokouh Makvandi-Nejad Hooman K. Moghadam |
author_sort |
Solomon Antwi Boison |
title |
Table_1_Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.).DOCX |
title_short |
Table_1_Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.).DOCX |
title_full |
Table_1_Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.).DOCX |
title_fullStr |
Table_1_Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.).DOCX |
title_full_unstemmed |
Table_1_Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.).DOCX |
title_sort |
table_1_genomic and transcriptomic analysis of amoebic gill disease resistance in atlantic salmon (salmo salar l.).docx |
publishDate |
2019 |
url |
https://doi.org/10.3389/fgene.2019.00068.s009 https://figshare.com/articles/Table_1_Genomic_and_Transcriptomic_Analysis_of_Amoebic_Gill_Disease_Resistance_in_Atlantic_Salmon_Salmo_salar_L_DOCX/7774559 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.3389/fgene.2019.00068.s009 https://figshare.com/articles/Table_1_Genomic_and_Transcriptomic_Analysis_of_Amoebic_Gill_Disease_Resistance_in_Atlantic_Salmon_Salmo_salar_L_DOCX/7774559 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2019.00068.s009 |
_version_ |
1766361346810576896 |