Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data
Background: A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs to the family Salmonidae of fishes and represents a species of great commercial...
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BMC Genomics
2019
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ftunivvigo:oai:www.investigo.biblioteca.uvigo.es:11093/4157 2023-05-15T15:30:42+02:00 Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data Gabián Álvarez, María Morán Martínez, Maria Paloma Fernández Ávila, Ana Isabel Villanueva, Beatriz Chtioui, Amel Kent, Matthew P Covelo Soto, Lara Fernández Muñoz, Almudena Saura Álvarez, María 2019-10-22 http://hdl.handle.net/11093/4157 https://doi.org/10.1186/s12864-019-6104-4 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6104-4 eng eng BMC Genomics Bioquímica, xenética e inmunoloxía Xenética de Poboacións e Citoxenética info:eu-repo/grantAgreement/MICINN//JCI-2011-10896/ES info:eu-repo/grantAgreement/MINECO//RZ2012–00011-C02–00/ES BMC Genomics, 20(1): 764 (2019) 14712164 http://hdl.handle.net/11093/4157 doi:10.1186/s12864-019-6104-4 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6104-4 Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ openAccess 2409.03 Genética de Poblaciones 2401.19 Zoología Marina 2409.90 Citogenética Animal article 2019 ftunivvigo https://doi.org/10.1186/s12864-019-6104-4 2023-04-11T23:23:49Z Background: A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs to the family Salmonidae of fishes and represents a species of great commercial value. Although the species is assumed to be male heterogametic with XY sex determination, the precise genetic basis of sexual development remains unclear. The complexity is likely associated to the relatively recent salmonid specific whole genome duplication that may be responsible for certain genome instability. This instability together with the capacity of the sex-determining gene to move across the genome as reported by previous studies, may explain that sexual development genes are not circumscribed to the same chromosomes in all members of the species. In this study, we have used a 220 K SNP panel developed for Atlantic salmon to identify the chromosomes explaining the highest proportion of the genetic variance for sex as well as candidate regions and genes associated to sexual development in this species. Results: Results from regional heritability analysis showed that the chromosomes explaining the highest proportion of variance in these populations were Ssa02 (heritability = 0.42, SE = 0.12) and Ssa21 (heritability = 0.26, SE = 0.11). After pruning by linkage disequilibrium, genome-wide association analyses revealed 114 SNPs that were significantly associated with sex, being Ssa02 the chromosome containing a greatest number of regions. Close examination of the candidate regions evidenced important genes related to sex in other species of Class Actinopterygii, including SDY, genes from family SOX, RSPO1, ESR1, U2AF2A, LMO7, GNRH-R, DND and FIGLA. Conclusions: The combined results from regional heritability analysis and genome-wide association have provided new advances in the knowledge of the genetic regulation of sex determination in Atlantic salmon, supporting that Ssa02 is the candidate chromosome for sex ... Article in Journal/Newspaper Atlantic salmon University of Vigo: Investigo (Repositorio Institucional de la Universidade de Vigo) BMC Genomics 20 1 |
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Open Polar |
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University of Vigo: Investigo (Repositorio Institucional de la Universidade de Vigo) |
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ftunivvigo |
language |
English |
topic |
2409.03 Genética de Poblaciones 2401.19 Zoología Marina 2409.90 Citogenética Animal |
spellingShingle |
2409.03 Genética de Poblaciones 2401.19 Zoología Marina 2409.90 Citogenética Animal Gabián Álvarez, María Morán Martínez, Maria Paloma Fernández Ávila, Ana Isabel Villanueva, Beatriz Chtioui, Amel Kent, Matthew P Covelo Soto, Lara Fernández Muñoz, Almudena Saura Álvarez, María Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data |
topic_facet |
2409.03 Genética de Poblaciones 2401.19 Zoología Marina 2409.90 Citogenética Animal |
description |
Background: A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs to the family Salmonidae of fishes and represents a species of great commercial value. Although the species is assumed to be male heterogametic with XY sex determination, the precise genetic basis of sexual development remains unclear. The complexity is likely associated to the relatively recent salmonid specific whole genome duplication that may be responsible for certain genome instability. This instability together with the capacity of the sex-determining gene to move across the genome as reported by previous studies, may explain that sexual development genes are not circumscribed to the same chromosomes in all members of the species. In this study, we have used a 220 K SNP panel developed for Atlantic salmon to identify the chromosomes explaining the highest proportion of the genetic variance for sex as well as candidate regions and genes associated to sexual development in this species. Results: Results from regional heritability analysis showed that the chromosomes explaining the highest proportion of variance in these populations were Ssa02 (heritability = 0.42, SE = 0.12) and Ssa21 (heritability = 0.26, SE = 0.11). After pruning by linkage disequilibrium, genome-wide association analyses revealed 114 SNPs that were significantly associated with sex, being Ssa02 the chromosome containing a greatest number of regions. Close examination of the candidate regions evidenced important genes related to sex in other species of Class Actinopterygii, including SDY, genes from family SOX, RSPO1, ESR1, U2AF2A, LMO7, GNRH-R, DND and FIGLA. Conclusions: The combined results from regional heritability analysis and genome-wide association have provided new advances in the knowledge of the genetic regulation of sex determination in Atlantic salmon, supporting that Ssa02 is the candidate chromosome for sex ... |
format |
Article in Journal/Newspaper |
author |
Gabián Álvarez, María Morán Martínez, Maria Paloma Fernández Ávila, Ana Isabel Villanueva, Beatriz Chtioui, Amel Kent, Matthew P Covelo Soto, Lara Fernández Muñoz, Almudena Saura Álvarez, María |
author_facet |
Gabián Álvarez, María Morán Martínez, Maria Paloma Fernández Ávila, Ana Isabel Villanueva, Beatriz Chtioui, Amel Kent, Matthew P Covelo Soto, Lara Fernández Muñoz, Almudena Saura Álvarez, María |
author_sort |
Gabián Álvarez, María |
title |
Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data |
title_short |
Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data |
title_full |
Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data |
title_fullStr |
Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data |
title_full_unstemmed |
Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data |
title_sort |
identification of genomic regions regulating sex determination in atlantic salmon using high density snp data |
publisher |
BMC Genomics |
publishDate |
2019 |
url |
http://hdl.handle.net/11093/4157 https://doi.org/10.1186/s12864-019-6104-4 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6104-4 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
info:eu-repo/grantAgreement/MICINN//JCI-2011-10896/ES info:eu-repo/grantAgreement/MINECO//RZ2012–00011-C02–00/ES BMC Genomics, 20(1): 764 (2019) 14712164 http://hdl.handle.net/11093/4157 doi:10.1186/s12864-019-6104-4 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6104-4 |
op_rights |
Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/ openAccess |
op_doi |
https://doi.org/10.1186/s12864-019-6104-4 |
container_title |
BMC Genomics |
container_volume |
20 |
container_issue |
1 |
_version_ |
1766361146910048256 |