Resistance to pathogens in North American Atlantic salmon: Genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia
Resistance to pathogens is an economically important trait to the Atlantic salmon aquaculture industry. Many diseases that are common at sea cages, where product is reared until harvest, can cause high levels of mortality or cause product downgrading due to reduced growth or appearance. This profit...
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University of Guelph
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ftunivguelph:oai:atrium.lib.uoguelph.ca:10214/15996 2024-09-09T19:30:19+00:00 Resistance to pathogens in North American Atlantic salmon: Genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia Holborn, Melissa Boulding, Elizabeth 2019-05-08 application/pdf http://hdl.handle.net/10214/15996 en eng University of Guelph http://hdl.handle.net/10214/15996 Attribution-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nd/4.0/ Atlantic salmon Genome wide association study Quantitative genetics Resistance to pathogens Aquaculture Thesis 2019 ftunivguelph 2024-08-20T23:47:41Z Resistance to pathogens is an economically important trait to the Atlantic salmon aquaculture industry. Many diseases that are common at sea cages, where product is reared until harvest, can cause high levels of mortality or cause product downgrading due to reduced growth or appearance. This profit loss has prompted many breeding programs in the industry to investigate methods to breed for pathogen resistance, taking advantage of the naturally existing genetic variation within their broodstock candidates. In this PhD thesis, I exposed Atlantic salmon from the Saint John River strain to three pathogens: Renibacterium salmoninarum causing bacterial kidney disease (BKD), the salmon louse, and infectious salmon anemia (ISA) virus. Each of these disease challenges allowed for the recording of disease phenotypes representing resistance such as survival, time to death, or lice load, to be recorded on siblings of the broodstock candidates from Kelly Cove Salmon Ltd.’s breeding nucleus. High density SNP genotyping was performed on representatives from all families challenged, where the phenotypic extremes from each family were selected. Using the combination of genotypes and phenotypes, I performed genome wide association analyses to determine the genetic architecture of the disease resistance traits and identify regions of the genome associated with disease resistance. Resistance to BKD and salmon lice showed a polygenic trait inheritance while ISA resistance appeared to have oligogenic inheritance, and the regions of the genomes associated with resistance mostly differed for these traits. The exception was Ssa14 where two SNPs were within 1 Mb of each other, one associated with ISA resistance and the other associated with salmon lice resistance. For each disease resistance trait, I detected chromosome wide and/or genome wide significant SNPs that each explained between 4-9% of the phenotypic variation in the trait. These SNPs can be implemented as a subset of SNPs into a genomic selection protocol to estimate genomic ... Thesis Atlantic salmon University of Guelph: DSpace digital archive |
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Open Polar |
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University of Guelph: DSpace digital archive |
op_collection_id |
ftunivguelph |
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English |
topic |
Atlantic salmon Genome wide association study Quantitative genetics Resistance to pathogens Aquaculture |
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Atlantic salmon Genome wide association study Quantitative genetics Resistance to pathogens Aquaculture Holborn, Melissa Resistance to pathogens in North American Atlantic salmon: Genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia |
topic_facet |
Atlantic salmon Genome wide association study Quantitative genetics Resistance to pathogens Aquaculture |
description |
Resistance to pathogens is an economically important trait to the Atlantic salmon aquaculture industry. Many diseases that are common at sea cages, where product is reared until harvest, can cause high levels of mortality or cause product downgrading due to reduced growth or appearance. This profit loss has prompted many breeding programs in the industry to investigate methods to breed for pathogen resistance, taking advantage of the naturally existing genetic variation within their broodstock candidates. In this PhD thesis, I exposed Atlantic salmon from the Saint John River strain to three pathogens: Renibacterium salmoninarum causing bacterial kidney disease (BKD), the salmon louse, and infectious salmon anemia (ISA) virus. Each of these disease challenges allowed for the recording of disease phenotypes representing resistance such as survival, time to death, or lice load, to be recorded on siblings of the broodstock candidates from Kelly Cove Salmon Ltd.’s breeding nucleus. High density SNP genotyping was performed on representatives from all families challenged, where the phenotypic extremes from each family were selected. Using the combination of genotypes and phenotypes, I performed genome wide association analyses to determine the genetic architecture of the disease resistance traits and identify regions of the genome associated with disease resistance. Resistance to BKD and salmon lice showed a polygenic trait inheritance while ISA resistance appeared to have oligogenic inheritance, and the regions of the genomes associated with resistance mostly differed for these traits. The exception was Ssa14 where two SNPs were within 1 Mb of each other, one associated with ISA resistance and the other associated with salmon lice resistance. For each disease resistance trait, I detected chromosome wide and/or genome wide significant SNPs that each explained between 4-9% of the phenotypic variation in the trait. These SNPs can be implemented as a subset of SNPs into a genomic selection protocol to estimate genomic ... |
author2 |
Boulding, Elizabeth |
format |
Thesis |
author |
Holborn, Melissa |
author_facet |
Holborn, Melissa |
author_sort |
Holborn, Melissa |
title |
Resistance to pathogens in North American Atlantic salmon: Genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia |
title_short |
Resistance to pathogens in North American Atlantic salmon: Genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia |
title_full |
Resistance to pathogens in North American Atlantic salmon: Genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia |
title_fullStr |
Resistance to pathogens in North American Atlantic salmon: Genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia |
title_full_unstemmed |
Resistance to pathogens in North American Atlantic salmon: Genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia |
title_sort |
resistance to pathogens in north american atlantic salmon: genome wide association analyses for bacterial kidney disease, salmon lice, and infectious salmon anemia |
publisher |
University of Guelph |
publishDate |
2019 |
url |
http://hdl.handle.net/10214/15996 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://hdl.handle.net/10214/15996 |
op_rights |
Attribution-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nd/4.0/ |
_version_ |
1809899310868856832 |