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Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss)
One of the main pathogens affecting rainbow trout (Oncorhynchus mykiss) farming is the facultative intracellular bacteria Piscirickettsia salmonis. Current treatments, such as antibiotics and vaccines, have not had the expected effectiveness in field conditions. Genetic improvement by means of selec...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829148/ https://www.ncbi.nlm.nih.gov/pubmed/31690599 http://dx.doi.org/10.1534/g3.119.400204 |
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author | Barria, Agustin Marín-Nahuelpi, Rodrigo Cáceres, Pablo López, María E. Bassini, Liane N. Lhorente, Jean P. Yáñez, José M. |
author_facet | Barria, Agustin Marín-Nahuelpi, Rodrigo Cáceres, Pablo López, María E. Bassini, Liane N. Lhorente, Jean P. Yáñez, José M. |
author_sort | Barria, Agustin |
collection | PubMed |
description | One of the main pathogens affecting rainbow trout (Oncorhynchus mykiss) farming is the facultative intracellular bacteria Piscirickettsia salmonis. Current treatments, such as antibiotics and vaccines, have not had the expected effectiveness in field conditions. Genetic improvement by means of selection for resistance is proposed as a viable alternative for control. Genomic information can be used to identify the genomic regions associated with resistance and enhance the genetic evaluation methods to speed up the genetic improvement for the trait. The objectives of this study were to i) identify the genomic regions associated with resistance to P. salmonis; and ii) identify candidate genes associated with the trait in rainbow trout. We experimentally challenged 2,130 rainbow trout with P. salmonis and genotyped them with a 57 K single nucleotide polymorphism (SNP) array. Resistance to P. salmonis was defined as time to death (TD) and as binary survival (BS). Significant heritabilities were estimated for TD and BS (0.48 ± 0.04 and 0.34 ± 0.04, respectively). A total of 2,047 fish and 26,068 SNPs passed quality control for samples and genotypes. Using a single-step genome wide association analysis (ssGWAS) we identified four genomic regions explaining over 1% of the genetic variance for TD and three for BS. Interestingly, the same genomic region located on Omy27 was found to explain the highest proportion of genetic variance for both traits (2.4 and 1.5% for TD and BS, respectively). The identified SNP in this region is located within an exon of a gene related with actin cytoskeletal organization, a protein exploited by P. salmonis during infection. Other important candidate genes identified are related with innate immune response and oxidative stress. The moderate heritability values estimated in the present study show it is possible to improve resistance to P. salmonis through artificial selection in the rainbow trout population studied here. Furthermore, our results suggest a polygenic genetic architecture for the trait and provide novel insights into the candidate genes underpinning resistance to P. salmonis in O. mykiss. |
format | Online Article Text |
id | pubmed-6829148 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-68291482019-11-06 Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss) Barria, Agustin Marín-Nahuelpi, Rodrigo Cáceres, Pablo López, María E. Bassini, Liane N. Lhorente, Jean P. Yáñez, José M. G3 (Bethesda) Investigations One of the main pathogens affecting rainbow trout (Oncorhynchus mykiss) farming is the facultative intracellular bacteria Piscirickettsia salmonis. Current treatments, such as antibiotics and vaccines, have not had the expected effectiveness in field conditions. Genetic improvement by means of selection for resistance is proposed as a viable alternative for control. Genomic information can be used to identify the genomic regions associated with resistance and enhance the genetic evaluation methods to speed up the genetic improvement for the trait. The objectives of this study were to i) identify the genomic regions associated with resistance to P. salmonis; and ii) identify candidate genes associated with the trait in rainbow trout. We experimentally challenged 2,130 rainbow trout with P. salmonis and genotyped them with a 57 K single nucleotide polymorphism (SNP) array. Resistance to P. salmonis was defined as time to death (TD) and as binary survival (BS). Significant heritabilities were estimated for TD and BS (0.48 ± 0.04 and 0.34 ± 0.04, respectively). A total of 2,047 fish and 26,068 SNPs passed quality control for samples and genotypes. Using a single-step genome wide association analysis (ssGWAS) we identified four genomic regions explaining over 1% of the genetic variance for TD and three for BS. Interestingly, the same genomic region located on Omy27 was found to explain the highest proportion of genetic variance for both traits (2.4 and 1.5% for TD and BS, respectively). The identified SNP in this region is located within an exon of a gene related with actin cytoskeletal organization, a protein exploited by P. salmonis during infection. Other important candidate genes identified are related with innate immune response and oxidative stress. The moderate heritability values estimated in the present study show it is possible to improve resistance to P. salmonis through artificial selection in the rainbow trout population studied here. Furthermore, our results suggest a polygenic genetic architecture for the trait and provide novel insights into the candidate genes underpinning resistance to P. salmonis in O. mykiss. Genetics Society of America 2019-09-19 /pmc/articles/PMC6829148/ /pubmed/31690599 http://dx.doi.org/10.1534/g3.119.400204 Text en Copyright © 2019 Barria et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Barria, Agustin Marín-Nahuelpi, Rodrigo Cáceres, Pablo López, María E. Bassini, Liane N. Lhorente, Jean P. Yáñez, José M. Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss) |
title | Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss) |
title_full | Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss) |
title_fullStr | Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss) |
title_full_unstemmed | Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss) |
title_short | Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss) |
title_sort | single-step genome-wide association study for resistance to piscirickettsia salmonis in rainbow trout (oncorhynchus mykiss) |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829148/ https://www.ncbi.nlm.nih.gov/pubmed/31690599 http://dx.doi.org/10.1534/g3.119.400204 |
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