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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ftpubmed:oai:pubmedcentral.nih.gov:8102513 2023-05-15T15:32:34+02:00 Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information López, M. E. Cádiz, M. I. Rondeau, E. B. Koop, B. F. Yáñez, J. M. 2021-05-06 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8102513/ http://www.ncbi.nlm.nih.gov/pubmed/33958603 https://doi.org/10.1038/s41598-021-86154-w en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8102513/ http://www.ncbi.nlm.nih.gov/pubmed/33958603 http://dx.doi.org/10.1038/s41598-021-86154-w © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . CC-BY Sci Rep Article Text 2021 ftpubmed https://doi.org/10.1038/s41598-021-86154-w 2021-05-16T00:35:38Z 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. Text Atlantic salmon PubMed Central (PMC) Scientific Reports 11 1 |
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Article López, M. E. Cádiz, M. I. Rondeau, E. B. Koop, B. F. Yáñez, J. M. Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information |
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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. |
format |
Text |
author |
López, M. E. Cádiz, M. I. Rondeau, E. B. Koop, B. F. Yáñez, J. M. |
author_facet |
López, M. E. Cádiz, M. I. Rondeau, E. B. Koop, B. F. Yáñez, J. M. |
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 Publishing Group UK |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8102513/ http://www.ncbi.nlm.nih.gov/pubmed/33958603 https://doi.org/10.1038/s41598-021-86154-w |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Sci Rep |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8102513/ http://www.ncbi.nlm.nih.gov/pubmed/33958603 http://dx.doi.org/10.1038/s41598-021-86154-w |
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© The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
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CC-BY |
op_doi |
https://doi.org/10.1038/s41598-021-86154-w |
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