Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data
Abstract 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 co...
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ftsubgoettingen:oai:goescholar:1/16540 2023-05-15T15:30:39+02:00 Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data Gabián, María Morán, Paloma Fernández, Ana I Villanueva, Beatriz Chtioui, Amel Kent, Matthew P Covelo-Soto, Lara Fernández, Almudena Saura, María 2019 http://resolver.sub.uni-goettingen.de/purl?gs-1/16540 https://doi.org/10.1186/s12864-019-6104-4 en eng BioMed Central http://resolver.sub.uni-goettingen.de/purl?gs-1/16540 BMC Genomics. 2019 Oct 22;20(1):764 doi:10.1186/s12864-019-6104-4 openAccess The Author(s). journalArticle publishedVersion 2019 ftsubgoettingen https://doi.org/10.1186/s12864-019-6104-4 2022-11-02T09:29:18Z Abstract 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 ... Article in Journal/Newspaper Atlantic salmon Georg-August-Universität Göttingen: GoeScholar BMC Genomics 20 1 |
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Open Polar |
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Georg-August-Universität Göttingen: GoeScholar |
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ftsubgoettingen |
language |
English |
description |
Abstract 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 ... |
format |
Article in Journal/Newspaper |
author |
Gabián, María Morán, Paloma Fernández, Ana I Villanueva, Beatriz Chtioui, Amel Kent, Matthew P Covelo-Soto, Lara Fernández, Almudena Saura, María |
spellingShingle |
Gabián, María Morán, Paloma Fernández, Ana I Villanueva, Beatriz Chtioui, Amel Kent, Matthew P Covelo-Soto, Lara Fernández, Almudena Saura, María Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data |
author_facet |
Gabián, María Morán, Paloma Fernández, Ana I Villanueva, Beatriz Chtioui, Amel Kent, Matthew P Covelo-Soto, Lara Fernández, Almudena Saura, María |
author_sort |
Gabián, 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 |
BioMed Central |
publishDate |
2019 |
url |
http://resolver.sub.uni-goettingen.de/purl?gs-1/16540 https://doi.org/10.1186/s12864-019-6104-4 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://resolver.sub.uni-goettingen.de/purl?gs-1/16540 BMC Genomics. 2019 Oct 22;20(1):764 doi:10.1186/s12864-019-6104-4 |
op_rights |
openAccess The Author(s). |
op_doi |
https://doi.org/10.1186/s12864-019-6104-4 |
container_title |
BMC Genomics |
container_volume |
20 |
container_issue |
1 |
_version_ |
1766361113500319744 |