Data from: Identification of genomic regions associated with sex in Pacific halibut
Understanding and identifying the genetic mechanisms responsible for sex-determination are important for species management, particularly in exploited fishes where sex biased harvest could have implications on population dynamics and long-term persistence. The Pacific halibut (Hippoglossus stenolepi...
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Online Access: | https://doi.org/10.5061/dryad.ff072 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::00f3692d8219536556278a2d9c5b062d 2023-05-15T18:15:53+02:00 Data from: Identification of genomic regions associated with sex in Pacific halibut Drinan, Daniel P. Loher, Timothy Hauser, Lorenz Drinan, Daniel P 2017-11-06 https://doi.org/10.5061/dryad.ff072 en eng Dryad http://dx.doi.org/10.5061/dryad.ff072 https://dx.doi.org/10.5061/dryad.ff072 lic_creative-commons 10.5061/dryad.ff072 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:99675 oai:easy.dans.knaw.nl:easy-dataset:99675 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 RAD Conservation genetics and biodiversity fisheries Pacific halibut genomics and gene mapping Comparative genomics sex determination Sex Identification Life sciences medicine and health care envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2017 fttriple https://doi.org/10.5061/dryad.ff072 2023-01-22T17:23:15Z Understanding and identifying the genetic mechanisms responsible for sex-determination are important for species management, particularly in exploited fishes where sex biased harvest could have implications on population dynamics and long-term persistence. The Pacific halibut (Hippoglossus stenolepis) supports important fisheries in the North Pacific Ocean. The proportion of each sex in the annual harvest is currently estimated using growth curves, but genetic techniques may provide a more accurate method. We used restriction-site associated DNA (RAD) sequencing to identify RAD-tags that were linked to genetic sex, based on differentiation (FST) between the sexes. Identified RAD-tags were aligned to the Atlantic halibut (Hippoglossus hippoglossus) linkage map, the turbot (Scophthalmus maximus) genome, and the half-smooth tongue sole (Cynoglossus semilaevis) genome to identify genomic regions that may be involved in sex determination. In total, 56 RAD-tags (70 single nucleotide polymorphisms) were linked to sex, and three RAD-tags were identified in only females. Sex-linked loci aligned to three linkage groups in the Atlantic halibut (LG07: 7 loci, LG15: 1 locus, and LG24: 1 locus), three chromosomes in the turbot (LG12: 13 loci, LG01: 1 locus, and LG05: 1 locus), and one chromosome in the half-smooth tongue sole (ChrZ: 9 loci). Results add support to the hypothesis that Pacific halibut genetic sex is determined in a ZW system. Two sex-linked loci were further developed into sex identification assays, and their efficacy was tested on individuals that had been morphologically sexed. The accuracy of each assay on its own was 97.5% compared to morphological sex. halibut_genepopFile containing all genotypes. File in Genepop format. Locus names are formatted with an underscore between the RADtag name and SNP position.supplemental_material_199_sex_assaysResults of two TaqMan assays linked to sex.supplemental_material_primers_and_probesPrimer and probe sequences for TaqMan ... Dataset Scophthalmus maximus Turbot Unknown Pacific |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
RAD Conservation genetics and biodiversity fisheries Pacific halibut genomics and gene mapping Comparative genomics sex determination Sex Identification Life sciences medicine and health care envir geo |
spellingShingle |
RAD Conservation genetics and biodiversity fisheries Pacific halibut genomics and gene mapping Comparative genomics sex determination Sex Identification Life sciences medicine and health care envir geo Drinan, Daniel P. Loher, Timothy Hauser, Lorenz Drinan, Daniel P Data from: Identification of genomic regions associated with sex in Pacific halibut |
topic_facet |
RAD Conservation genetics and biodiversity fisheries Pacific halibut genomics and gene mapping Comparative genomics sex determination Sex Identification Life sciences medicine and health care envir geo |
description |
Understanding and identifying the genetic mechanisms responsible for sex-determination are important for species management, particularly in exploited fishes where sex biased harvest could have implications on population dynamics and long-term persistence. The Pacific halibut (Hippoglossus stenolepis) supports important fisheries in the North Pacific Ocean. The proportion of each sex in the annual harvest is currently estimated using growth curves, but genetic techniques may provide a more accurate method. We used restriction-site associated DNA (RAD) sequencing to identify RAD-tags that were linked to genetic sex, based on differentiation (FST) between the sexes. Identified RAD-tags were aligned to the Atlantic halibut (Hippoglossus hippoglossus) linkage map, the turbot (Scophthalmus maximus) genome, and the half-smooth tongue sole (Cynoglossus semilaevis) genome to identify genomic regions that may be involved in sex determination. In total, 56 RAD-tags (70 single nucleotide polymorphisms) were linked to sex, and three RAD-tags were identified in only females. Sex-linked loci aligned to three linkage groups in the Atlantic halibut (LG07: 7 loci, LG15: 1 locus, and LG24: 1 locus), three chromosomes in the turbot (LG12: 13 loci, LG01: 1 locus, and LG05: 1 locus), and one chromosome in the half-smooth tongue sole (ChrZ: 9 loci). Results add support to the hypothesis that Pacific halibut genetic sex is determined in a ZW system. Two sex-linked loci were further developed into sex identification assays, and their efficacy was tested on individuals that had been morphologically sexed. The accuracy of each assay on its own was 97.5% compared to morphological sex. halibut_genepopFile containing all genotypes. File in Genepop format. Locus names are formatted with an underscore between the RADtag name and SNP position.supplemental_material_199_sex_assaysResults of two TaqMan assays linked to sex.supplemental_material_primers_and_probesPrimer and probe sequences for TaqMan ... |
format |
Dataset |
author |
Drinan, Daniel P. Loher, Timothy Hauser, Lorenz Drinan, Daniel P |
author_facet |
Drinan, Daniel P. Loher, Timothy Hauser, Lorenz Drinan, Daniel P |
author_sort |
Drinan, Daniel P. |
title |
Data from: Identification of genomic regions associated with sex in Pacific halibut |
title_short |
Data from: Identification of genomic regions associated with sex in Pacific halibut |
title_full |
Data from: Identification of genomic regions associated with sex in Pacific halibut |
title_fullStr |
Data from: Identification of genomic regions associated with sex in Pacific halibut |
title_full_unstemmed |
Data from: Identification of genomic regions associated with sex in Pacific halibut |
title_sort |
data from: identification of genomic regions associated with sex in pacific halibut |
publisher |
Dryad |
publishDate |
2017 |
url |
https://doi.org/10.5061/dryad.ff072 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_source |
10.5061/dryad.ff072 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:99675 oai:easy.dans.knaw.nl:easy-dataset:99675 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
http://dx.doi.org/10.5061/dryad.ff072 https://dx.doi.org/10.5061/dryad.ff072 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.ff072 |
_version_ |
1766189139182485504 |