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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ftdatacite:10.6084/m9.figshare.c.4708811 2023-05-15T15:30:54+02:00 Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data Gabián, María Morán, Paloma Fernández, Ana Villanueva, Beatriz Chtioui, Amel Kent, Matthew Covelo-Soto, Lara Fernández, Almudena Saura, María 2019 https://dx.doi.org/10.6084/m9.figshare.c.4708811 https://springernature.figshare.com/collections/Identification_of_genomic_regions_regulating_sex_determination_in_Atlantic_salmon_using_high_density_SNP_data/4708811 unknown figshare https://dx.doi.org/10.1186/s12864-019-6104-4 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences Collection article 2019 ftdatacite https://doi.org/10.6084/m9.figshare.c.4708811 https://doi.org/10.1186/s12864-019-6104-4 2021-11-05T12:55:41Z 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 for sex in this species and suggesting an alternative population lineage in Spanish wild populations according to the results from Ssa21. Article in Journal/Newspaper Atlantic salmon DataCite Metadata Store (German National Library of Science and Technology) |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences |
spellingShingle |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences Gabián, María Morán, Paloma Fernández, Ana Villanueva, Beatriz Chtioui, Amel Kent, Matthew Covelo-Soto, Lara Fernández, Almudena Saura, María Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data |
topic_facet |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified 110309 Infectious Diseases FOS Health sciences |
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 for sex in this species and suggesting an alternative population lineage in Spanish wild populations according to the results from Ssa21. |
format |
Article in Journal/Newspaper |
author |
Gabián, María Morán, Paloma Fernández, Ana Villanueva, Beatriz Chtioui, Amel Kent, Matthew Covelo-Soto, Lara Fernández, Almudena Saura, María |
author_facet |
Gabián, María Morán, Paloma Fernández, Ana Villanueva, Beatriz Chtioui, Amel Kent, Matthew 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 |
figshare |
publishDate |
2019 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.4708811 https://springernature.figshare.com/collections/Identification_of_genomic_regions_regulating_sex_determination_in_Atlantic_salmon_using_high_density_SNP_data/4708811 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
https://dx.doi.org/10.1186/s12864-019-6104-4 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.4708811 https://doi.org/10.1186/s12864-019-6104-4 |
_version_ |
1766361367122542592 |