Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome‑wide information
Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection, known as selection signatures or selective sweeps, have been traced in the genomes of many animal livestock species by exploiting variation in linkage d...
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ftunivchile:oai:repositorio.uchile.cl:2250/182817 2023-05-15T15:32:41+02:00 Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome‑wide information López, M. E. Cádiz Escobar, María Ignacia Rondeau, E. B. Koop, B. F. Yáñez López, José Manuel 2021 application/pdf https://doi.org/10.1038/s41598-021-86154-w https://repositorio.uchile.cl/handle/2250/182817 en eng Nature Scientifc Reports (2021) 11:9685 doi:10.1038/s41598-021-86154-w https://repositorio.uchile.cl/handle/2250/182817 Attribution-NonCommercial-NoDerivs 3.0 United States http://creativecommons.org/licenses/by-nc-nd/3.0/us/ CC-BY-NC-ND Scientifc Reports Positive Selection Adaptation Artículo de revista 2021 ftunivchile https://doi.org/10.1038/s41598-021-86154-w 2021-11-28T00:49:53Z Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection, known as selection signatures or selective sweeps, have been traced in the genomes of many animal livestock species by exploiting variation in linkage disequilibrium patterns and/or reduction of genetic diversity. Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subjected to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn, which have been previously associated with body weight in Atlantic salmon, or sec24d and robo1, which have been associated with resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon. Government of Canada through EPIC4 (Enhanced Production in Coho: Culture, Community, Catch) from Genome Canada Genome British Columbia Genome Quebec Versión publicada - versión final del editor Article in Journal/Newspaper Atlantic salmon Universidad de Chile: Repositorio académico British Columbia ENVELOPE(-125.003,-125.003,54.000,54.000) Canada Scientific Reports 11 1 |
institution |
Open Polar |
collection |
Universidad de Chile: Repositorio académico |
op_collection_id |
ftunivchile |
language |
English |
topic |
Positive Selection Adaptation |
spellingShingle |
Positive Selection Adaptation López, M. E. Cádiz Escobar, María Ignacia Rondeau, E. B. Koop, B. F. Yáñez López, José Manuel Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome‑wide information |
topic_facet |
Positive Selection Adaptation |
description |
Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection, known as selection signatures or selective sweeps, have been traced in the genomes of many animal livestock species by exploiting variation in linkage disequilibrium patterns and/or reduction of genetic diversity. Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subjected to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn, which have been previously associated with body weight in Atlantic salmon, or sec24d and robo1, which have been associated with resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon. Government of Canada through EPIC4 (Enhanced Production in Coho: Culture, Community, Catch) from Genome Canada Genome British Columbia Genome Quebec Versión publicada - versión final del editor |
format |
Article in Journal/Newspaper |
author |
López, M. E. Cádiz Escobar, María Ignacia Rondeau, E. B. Koop, B. F. Yáñez López, José Manuel |
author_facet |
López, M. E. Cádiz Escobar, María Ignacia Rondeau, E. B. Koop, B. F. Yáñez López, José Manuel |
author_sort |
López, M. E. |
title |
Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome‑wide information |
title_short |
Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome‑wide information |
title_full |
Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome‑wide information |
title_fullStr |
Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome‑wide information |
title_full_unstemmed |
Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome‑wide information |
title_sort |
detection of selection signatures in farmed coho salmon (oncorhynchus kisutch) using dense genome‑wide information |
publisher |
Nature |
publishDate |
2021 |
url |
https://doi.org/10.1038/s41598-021-86154-w https://repositorio.uchile.cl/handle/2250/182817 |
long_lat |
ENVELOPE(-125.003,-125.003,54.000,54.000) |
geographic |
British Columbia Canada |
geographic_facet |
British Columbia Canada |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Scientifc Reports |
op_relation |
Scientifc Reports (2021) 11:9685 doi:10.1038/s41598-021-86154-w https://repositorio.uchile.cl/handle/2250/182817 |
op_rights |
Attribution-NonCommercial-NoDerivs 3.0 United States http://creativecommons.org/licenses/by-nc-nd/3.0/us/ |
op_rightsnorm |
CC-BY-NC-ND |
op_doi |
https://doi.org/10.1038/s41598-021-86154-w |
container_title |
Scientific Reports |
container_volume |
11 |
container_issue |
1 |
_version_ |
1766363170295775232 |