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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ftdoajarticles:oai:doaj.org/article:9478f53588854556957269898bf101ad 2023-05-15T15:32:10+02:00 Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis José M. Yáñez Grazyella M. Yoshida Ángel Parra Katharina Correa Agustín Barría Liane N. Bassini Kris A. Christensen Maria E. López Roberto Carvalheiro Jean P. Lhorente Rodrigo Pulgar 2019-08-01T00:00:00Z https://doi.org/10.3389/fgene.2019.00665 https://doaj.org/article/9478f53588854556957269898bf101ad EN eng Frontiers Media S.A. https://www.frontiersin.org/article/10.3389/fgene.2019.00665/full https://doaj.org/toc/1664-8021 1664-8021 doi:10.3389/fgene.2019.00665 https://doaj.org/article/9478f53588854556957269898bf101ad Frontiers in Genetics, Vol 10 (2019) coho salmon rainbow trout Atlantic salmon Piscirickettsia salmonis genome-wide association study comparative genomics Genetics QH426-470 article 2019 ftdoajarticles https://doi.org/10.3389/fgene.2019.00665 2022-12-31T00:36:59Z 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 ... Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles Canada Norway Frontiers in Genetics 10 |
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Open Polar |
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op_collection_id |
ftdoajarticles |
language |
English |
topic |
coho salmon rainbow trout Atlantic salmon Piscirickettsia salmonis genome-wide association study comparative genomics Genetics QH426-470 |
spellingShingle |
coho salmon rainbow trout Atlantic salmon Piscirickettsia salmonis genome-wide association study comparative genomics Genetics QH426-470 José M. Yáñez Grazyella M. Yoshida Ángel Parra Katharina Correa Agustín Barría Liane N. Bassini Kris A. Christensen Maria E. López Roberto Carvalheiro Jean P. Lhorente Rodrigo Pulgar Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis |
topic_facet |
coho salmon rainbow trout Atlantic salmon Piscirickettsia salmonis genome-wide association study comparative genomics Genetics QH426-470 |
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 |
Article in Journal/Newspaper |
author |
José M. Yáñez Grazyella M. Yoshida Ángel Parra Katharina Correa Agustín Barría Liane N. Bassini Kris A. Christensen Maria E. López Roberto Carvalheiro Jean P. Lhorente Rodrigo Pulgar |
author_facet |
José M. Yáñez Grazyella M. Yoshida Ángel Parra Katharina Correa Agustín Barría Liane N. Bassini Kris A. Christensen Maria E. López Roberto Carvalheiro Jean P. Lhorente Rodrigo Pulgar |
author_sort |
José M. Yáñez |
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 |
https://doi.org/10.3389/fgene.2019.00665 https://doaj.org/article/9478f53588854556957269898bf101ad |
geographic |
Canada Norway |
geographic_facet |
Canada Norway |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Frontiers in Genetics, Vol 10 (2019) |
op_relation |
https://www.frontiersin.org/article/10.3389/fgene.2019.00665/full https://doaj.org/toc/1664-8021 1664-8021 doi:10.3389/fgene.2019.00665 https://doaj.org/article/9478f53588854556957269898bf101ad |
op_doi |
https://doi.org/10.3389/fgene.2019.00665 |
container_title |
Frontiers in Genetics |
container_volume |
10 |
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1766362667218370560 |