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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ftslunivuppsala:oai:pub.epsilon.slu.se:24668 2023-05-15T15:32:38+02:00 Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information López, Maria-Eugenia Cadiz, M. Rondeau, E. B. Koop, B. F. Yanez, J. M. 2021 application/pdf https://pub.epsilon.slu.se/24668/ https://pub.epsilon.slu.se/24668/1/lopez_m_e_et_al_210623.pdf en eng eng https://pub.epsilon.slu.se/24668/1/lopez_m_e_et_al_210623.pdf López, Maria-Eugenia and Cadiz, M. and Rondeau, E. B. and Koop, B. F. and Yanez, J. M. (2021). Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information. Scientific Reports. 11 , 9685 [Research article] Evolutionary Biology Genetics (medical genetics to be 30107 and agricultural genetics to be 40402) Research article NonPeerReviewed info:eu-repo/semantics/article 2021 ftslunivuppsala 2022-01-09T19:16:28Z 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. Article in Journal/Newspaper Atlantic salmon Swedish University of Agricultural Sciences (SLU): Epsilon Open Archive |
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Open Polar |
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Swedish University of Agricultural Sciences (SLU): Epsilon Open Archive |
op_collection_id |
ftslunivuppsala |
language |
English |
topic |
Evolutionary Biology Genetics (medical genetics to be 30107 and agricultural genetics to be 40402) |
spellingShingle |
Evolutionary Biology Genetics (medical genetics to be 30107 and agricultural genetics to be 40402) López, Maria-Eugenia Cadiz, M. Rondeau, E. B. Koop, B. F. Yanez, J. M. Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information |
topic_facet |
Evolutionary Biology Genetics (medical genetics to be 30107 and agricultural genetics to be 40402) |
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. |
format |
Article in Journal/Newspaper |
author |
López, Maria-Eugenia Cadiz, M. Rondeau, E. B. Koop, B. F. Yanez, J. M. |
author_facet |
López, Maria-Eugenia Cadiz, M. Rondeau, E. B. Koop, B. F. Yanez, J. M. |
author_sort |
López, Maria-Eugenia |
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 |
publishDate |
2021 |
url |
https://pub.epsilon.slu.se/24668/ https://pub.epsilon.slu.se/24668/1/lopez_m_e_et_al_210623.pdf |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
https://pub.epsilon.slu.se/24668/1/lopez_m_e_et_al_210623.pdf López, Maria-Eugenia and Cadiz, M. and Rondeau, E. B. and Koop, B. F. and Yanez, J. M. (2021). Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information. Scientific Reports. 11 , 9685 [Research article] |
_version_ |
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