Table_2_Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.xlsx
Sea lice (Caligus rogercresseyi) are ectoparasitic copepods which have a large negative economic and welfare impact in Atlantic salmon (Salmo salar) aquaculture, particularly in Chile. A multi-faceted prevention and control strategy is required to tackle lice, and selective breeding contributes via...
Main Authors: | , , , , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
2019
|
Subjects: | |
Online Access: | https://doi.org/10.3389/fgene.2019.00056.s005 https://figshare.com/articles/Table_2_Discovery_and_Functional_Annotation_of_Quantitative_Trait_Loci_Affecting_Resistance_to_Sea_Lice_in_Atlantic_Salmon_xlsx/7692764 |
id |
ftfrontimediafig:oai:figshare.com:article/7692764 |
---|---|
record_format |
openpolar |
spelling |
ftfrontimediafig:oai:figshare.com:article/7692764 2023-05-15T15:32:09+02:00 Table_2_Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.xlsx Diego Robledo Alejandro P. Gutiérrez Agustín Barría Jean P. Lhorente Ross D. Houston José M. Yáñez 2019-02-08T04:29:09Z https://doi.org/10.3389/fgene.2019.00056.s005 https://figshare.com/articles/Table_2_Discovery_and_Functional_Annotation_of_Quantitative_Trait_Loci_Affecting_Resistance_to_Sea_Lice_in_Atlantic_Salmon_xlsx/7692764 unknown doi:10.3389/fgene.2019.00056.s005 https://figshare.com/articles/Table_2_Discovery_and_Functional_Annotation_of_Quantitative_Trait_Loci_Affecting_Resistance_to_Sea_Lice_in_Atlantic_Salmon_xlsx/7692764 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 Caligus rogercresseyi Salmo salar aquaculture disease parasite GWAS heritability imputation Dataset 2019 ftfrontimediafig https://doi.org/10.3389/fgene.2019.00056.s005 2019-02-13T23:59:09Z Sea lice (Caligus rogercresseyi) are ectoparasitic copepods which have a large negative economic and welfare impact in Atlantic salmon (Salmo salar) aquaculture, particularly in Chile. A multi-faceted prevention and control strategy is required to tackle lice, and selective breeding contributes via cumulative improvement of host resistance to the parasite. While host resistance has been shown to be heritable, little is yet known about the individual loci that contribute to this resistance, the potential underlying genes, and their mechanisms of action. In this study we took a multifaceted approach to identify and characterize quantitative trait loci (QTL) affecting host resistance in a population of 2,688 Caligus-challenged Atlantic salmon post-smolts from a commercial breeding program. We used low and medium density genotyping with imputation to collect genome-wide SNP marker data for all animals. Moderate heritability estimates of 0.28 and 0.24 were obtained for lice density (as a measure of host resistance) and growth during infestation, respectively. Three QTL explaining between 7 and 13% of the genetic variation in resistance to sea lice (as represented by the traits of lice density) were detected on chromosomes 3, 18, and 21. Characterisation of these QTL regions was undertaken using RNA sequencing and pooled whole genome sequencing data. This resulted in the identification of a shortlist of potential underlying causative genes, and candidate functional mutations for further study. For example, candidates within the chromosome 3 QTL include a putative premature stop mutation in TOB1 (an anti-proliferative transcription factor involved in T cell regulation) and an uncharacterized protein which showed significant differential allelic expression (implying the existence of a cis-acting regulatory mutation). While host resistance to sea lice is polygenic in nature, the results of this study highlight significant QTL regions together explaining between 7 and 13 % of the heritability of the trait. Future ... Dataset Atlantic salmon Salmo salar Copepods 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 Caligus rogercresseyi Salmo salar aquaculture disease parasite GWAS heritability imputation |
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 Caligus rogercresseyi Salmo salar aquaculture disease parasite GWAS heritability imputation Diego Robledo Alejandro P. Gutiérrez Agustín Barría Jean P. Lhorente Ross D. Houston José M. Yáñez Table_2_Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.xlsx |
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 Caligus rogercresseyi Salmo salar aquaculture disease parasite GWAS heritability imputation |
description |
Sea lice (Caligus rogercresseyi) are ectoparasitic copepods which have a large negative economic and welfare impact in Atlantic salmon (Salmo salar) aquaculture, particularly in Chile. A multi-faceted prevention and control strategy is required to tackle lice, and selective breeding contributes via cumulative improvement of host resistance to the parasite. While host resistance has been shown to be heritable, little is yet known about the individual loci that contribute to this resistance, the potential underlying genes, and their mechanisms of action. In this study we took a multifaceted approach to identify and characterize quantitative trait loci (QTL) affecting host resistance in a population of 2,688 Caligus-challenged Atlantic salmon post-smolts from a commercial breeding program. We used low and medium density genotyping with imputation to collect genome-wide SNP marker data for all animals. Moderate heritability estimates of 0.28 and 0.24 were obtained for lice density (as a measure of host resistance) and growth during infestation, respectively. Three QTL explaining between 7 and 13% of the genetic variation in resistance to sea lice (as represented by the traits of lice density) were detected on chromosomes 3, 18, and 21. Characterisation of these QTL regions was undertaken using RNA sequencing and pooled whole genome sequencing data. This resulted in the identification of a shortlist of potential underlying causative genes, and candidate functional mutations for further study. For example, candidates within the chromosome 3 QTL include a putative premature stop mutation in TOB1 (an anti-proliferative transcription factor involved in T cell regulation) and an uncharacterized protein which showed significant differential allelic expression (implying the existence of a cis-acting regulatory mutation). While host resistance to sea lice is polygenic in nature, the results of this study highlight significant QTL regions together explaining between 7 and 13 % of the heritability of the trait. Future ... |
format |
Dataset |
author |
Diego Robledo Alejandro P. Gutiérrez Agustín Barría Jean P. Lhorente Ross D. Houston José M. Yáñez |
author_facet |
Diego Robledo Alejandro P. Gutiérrez Agustín Barría Jean P. Lhorente Ross D. Houston José M. Yáñez |
author_sort |
Diego Robledo |
title |
Table_2_Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.xlsx |
title_short |
Table_2_Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.xlsx |
title_full |
Table_2_Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.xlsx |
title_fullStr |
Table_2_Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.xlsx |
title_full_unstemmed |
Table_2_Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.xlsx |
title_sort |
table_2_discovery and functional annotation of quantitative trait loci affecting resistance to sea lice in atlantic salmon.xlsx |
publishDate |
2019 |
url |
https://doi.org/10.3389/fgene.2019.00056.s005 https://figshare.com/articles/Table_2_Discovery_and_Functional_Annotation_of_Quantitative_Trait_Loci_Affecting_Resistance_to_Sea_Lice_in_Atlantic_Salmon_xlsx/7692764 |
genre |
Atlantic salmon Salmo salar Copepods |
genre_facet |
Atlantic salmon Salmo salar Copepods |
op_relation |
doi:10.3389/fgene.2019.00056.s005 https://figshare.com/articles/Table_2_Discovery_and_Functional_Annotation_of_Quantitative_Trait_Loci_Affecting_Resistance_to_Sea_Lice_in_Atlantic_Salmon_xlsx/7692764 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2019.00056.s005 |
_version_ |
1766362660982489088 |