Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis
Piscirickettsia salmonis is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; Oncorhynchus kisutch), Atlantic salmon (AS; Salmo salar), and rainbow trout (RT; Oncorhynchus mykiss)...
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ftpubmed:oai:pubmedcentral.nih.gov:6690157 2023-05-15T15:32:59+02:00 Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis Yáñez, José M. Yoshida, Grazyella M. Parra, Ángel Correa, Katharina Barría, Agustín Bassini, Liane N. Christensen, Kris A. López, Maria E. Carvalheiro, Roberto Lhorente, Jean P. Pulgar, Rodrigo 2019-08-05 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690157/ http://www.ncbi.nlm.nih.gov/pubmed/31428125 https://doi.org/10.3389/fgene.2019.00665 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690157/ http://www.ncbi.nlm.nih.gov/pubmed/31428125 http://dx.doi.org/10.3389/fgene.2019.00665 Copyright © 2019 Yáñez, Yoshida, Parra, Correa, Barría, Bassini, Christensen, López, Carvalheiro, Lhorente and Pulgar http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. CC-BY Genetics Text 2019 ftpubmed https://doi.org/10.3389/fgene.2019.00665 2019-08-25T00:22:35Z Piscirickettsia salmonis is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; Oncorhynchus kisutch), Atlantic salmon (AS; Salmo salar), and rainbow trout (RT; Oncorhynchus mykiss) in several countries, including Norway, Canada, Scotland, Ireland, and Chile. We used Bayesian genome-wide association study analyses to investigate the genetic architecture of resistance to P. salmonis in farmed populations of these species. Resistance to SRS was defined as the number of days to death and as binary survival (BS). A total of 828 CS, 2130 RT, and 2601 AS individuals were phenotyped and then genotyped using double-digest restriction site-associated DNA sequencing and 57K and 50K Affymetrix® Axiom® single nucleotide polymorphism (SNP) panels, respectively. Both traits of SRS resistance in CS and RT appeared to be under oligogenic control. In AS, there was evidence of polygenic control of SRS resistance. To identify candidate genes associated with resistance, we applied a comparative genomics approach in which we systematically explored the complete set of genes adjacent to SNPs, which explained more than 1% of the genetic variance of resistance in each salmonid species (533 genes in total). Thus, genes were classified based on the following criteria: i) shared function of their protein domains among species, ii) shared orthology among species, iii) proximity to the SNP explaining the highest proportion of the genetic variance, and iv) presence in more than one genomic region explaining more than 1% of the genetic variance within species. Our results allowed us to identify 120 candidate genes belonging to at least one of the four criteria described above. Of these, 21 of them were part of at least two of the criteria defined above and are suggested to be strong functional candidates influencing P. salmonis resistance. These genes are related to diverse biological processes, such as kinase activity, GTP ... Text Atlantic salmon Salmo salar PubMed Central (PMC) Canada Norway Frontiers in Genetics 10 |
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Genetics |
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Genetics Yáñez, José M. Yoshida, Grazyella M. Parra, Ángel Correa, Katharina Barría, Agustín Bassini, Liane N. Christensen, Kris A. López, Maria E. Carvalheiro, Roberto Lhorente, Jean P. Pulgar, Rodrigo Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis |
topic_facet |
Genetics |
description |
Piscirickettsia salmonis is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; Oncorhynchus kisutch), Atlantic salmon (AS; Salmo salar), and rainbow trout (RT; Oncorhynchus mykiss) in several countries, including Norway, Canada, Scotland, Ireland, and Chile. We used Bayesian genome-wide association study analyses to investigate the genetic architecture of resistance to P. salmonis in farmed populations of these species. Resistance to SRS was defined as the number of days to death and as binary survival (BS). A total of 828 CS, 2130 RT, and 2601 AS individuals were phenotyped and then genotyped using double-digest restriction site-associated DNA sequencing and 57K and 50K Affymetrix® Axiom® single nucleotide polymorphism (SNP) panels, respectively. Both traits of SRS resistance in CS and RT appeared to be under oligogenic control. In AS, there was evidence of polygenic control of SRS resistance. To identify candidate genes associated with resistance, we applied a comparative genomics approach in which we systematically explored the complete set of genes adjacent to SNPs, which explained more than 1% of the genetic variance of resistance in each salmonid species (533 genes in total). Thus, genes were classified based on the following criteria: i) shared function of their protein domains among species, ii) shared orthology among species, iii) proximity to the SNP explaining the highest proportion of the genetic variance, and iv) presence in more than one genomic region explaining more than 1% of the genetic variance within species. Our results allowed us to identify 120 candidate genes belonging to at least one of the four criteria described above. Of these, 21 of them were part of at least two of the criteria defined above and are suggested to be strong functional candidates influencing P. salmonis resistance. These genes are related to diverse biological processes, such as kinase activity, GTP ... |
format |
Text |
author |
Yáñez, José M. Yoshida, Grazyella M. Parra, Ángel Correa, Katharina Barría, Agustín Bassini, Liane N. Christensen, Kris A. López, Maria E. Carvalheiro, Roberto Lhorente, Jean P. Pulgar, Rodrigo |
author_facet |
Yáñez, José M. Yoshida, Grazyella M. Parra, Ángel Correa, Katharina Barría, Agustín Bassini, Liane N. Christensen, Kris A. López, Maria E. Carvalheiro, Roberto Lhorente, Jean P. Pulgar, Rodrigo |
author_sort |
Yáñez, José M. |
title |
Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis |
title_short |
Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis |
title_full |
Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis |
title_fullStr |
Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis |
title_full_unstemmed |
Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis |
title_sort |
comparative genomic analysis of three salmonid species identifies functional candidate genes involved in resistance to the intracellular bacterium piscirickettsia salmonis |
publisher |
Frontiers Media S.A. |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690157/ http://www.ncbi.nlm.nih.gov/pubmed/31428125 https://doi.org/10.3389/fgene.2019.00665 |
geographic |
Canada Norway |
geographic_facet |
Canada Norway |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690157/ http://www.ncbi.nlm.nih.gov/pubmed/31428125 http://dx.doi.org/10.3389/fgene.2019.00665 |
op_rights |
Copyright © 2019 Yáñez, Yoshida, Parra, Correa, Barría, Bassini, Christensen, López, Carvalheiro, Lhorente and Pulgar http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2019.00665 |
container_title |
Frontiers in Genetics |
container_volume |
10 |
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1766363457998815232 |