Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata
WOS:000431009400014 International audience Selective breeding strategies require pedigree information over generations, but many species produced in aquaculture are too small to be physically tagged at early stages. Consequently, maintaining a sufficient number of separate families is often needed b...
Published in: | Aquaculture |
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Main Authors: | , , , , , , , |
Other Authors: | , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2018
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Subjects: | |
Online Access: | https://hal.science/hal-02626095 https://hal.science/hal-02626095/document https://hal.science/hal-02626095/file/Harney_etal_Aquaculture_2018.pdf https://doi.org/10.1016/j.aquaculture.2018.03.006 |
id |
ftinsu:oai:HAL:hal-02626095v1 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
Institut national des sciences de l'Univers: HAL-INSU |
op_collection_id |
ftinsu |
language |
English |
topic |
ACL Transcriptome pacific oyster Abalone atlantic salmon Selective breeding oyster crassostrea-gigas pecten-maximus reproductive success linkage disequilibrium effective population-size genetic diversity microsatellite markers Parentage assignment Pedigree single-nucleotide polymorphisms snp [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
spellingShingle |
ACL Transcriptome pacific oyster Abalone atlantic salmon Selective breeding oyster crassostrea-gigas pecten-maximus reproductive success linkage disequilibrium effective population-size genetic diversity microsatellite markers Parentage assignment Pedigree single-nucleotide polymorphisms snp [SDE.BE]Environmental Sciences/Biodiversity and Ecology Harney, Ewan Lachambre, Sebastien Roussel, Sabine Huchette, Sylvain Enez, Florian Morvezen, Romain Haffray, Pierrick Boudry, Pierre Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata |
topic_facet |
ACL Transcriptome pacific oyster Abalone atlantic salmon Selective breeding oyster crassostrea-gigas pecten-maximus reproductive success linkage disequilibrium effective population-size genetic diversity microsatellite markers Parentage assignment Pedigree single-nucleotide polymorphisms snp [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
description |
WOS:000431009400014 International audience Selective breeding strategies require pedigree information over generations, but many species produced in aquaculture are too small to be physically tagged at early stages. Consequently, maintaining a sufficient number of separate families is often needed but costly and logistically difficult. Alternatively, parentage assignment can be obtained using DNA markers. We developed a panel of single nucleotide polymorphism (SNP) markers for the European abalone Haliotis tuberculata using an existing transcriptomic resource. An initial set of 2,176,887 SNPs was filtered to select 500 for high throughput genotyping. Of these, 298 SNPs were amplified in at least 90% of our H. tuberculata samples, consisting of a mixed family cohort (945 offspring) generated by crossing 40 abalones, and 5 full-sib training families (70 offspring). Based on amplification success among parents, minimum allele frequency and checks carried out against the training families, a subset of 123 markers was used to carry out parentage assignment in our mixed family cohorts. Maximum likelihood and exclusion-based methods of parentage assignment yielded consistent results, allowing parentage to be assigned in 98.9% of the studied progeny. Optimization of markers suggests that the 60 most informative SNPs may be sufficient for 95% assignment success in these progeny. The panel was also used to estimate effective population size, and revealed a low N-e due to high variance of reproductive success between parents. Our panel could be used to estimate genetic parameters of traits in mixed family cohorts, an essential stage to initiate selective breeding in H. tuberculata. It could also be useful tool in the context of monitoring stock enhancement and population genetics studies. |
author2 |
Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Scea France Haliotis ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010) |
format |
Article in Journal/Newspaper |
author |
Harney, Ewan Lachambre, Sebastien Roussel, Sabine Huchette, Sylvain Enez, Florian Morvezen, Romain Haffray, Pierrick Boudry, Pierre |
author_facet |
Harney, Ewan Lachambre, Sebastien Roussel, Sabine Huchette, Sylvain Enez, Florian Morvezen, Romain Haffray, Pierrick Boudry, Pierre |
author_sort |
Harney, Ewan |
title |
Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata |
title_short |
Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata |
title_full |
Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata |
title_fullStr |
Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata |
title_full_unstemmed |
Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata |
title_sort |
transcriptome based snp discovery and validation for parentage assignment in hatchery progeny of the european abalone haliotis tuberculata |
publisher |
HAL CCSD |
publishDate |
2018 |
url |
https://hal.science/hal-02626095 https://hal.science/hal-02626095/document https://hal.science/hal-02626095/file/Harney_etal_Aquaculture_2018.pdf https://doi.org/10.1016/j.aquaculture.2018.03.006 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Atlantic salmon Crassostrea gigas Pacific oyster |
genre_facet |
Atlantic salmon Crassostrea gigas Pacific oyster |
op_source |
ISSN: 0044-8486 EISSN: 1873-5622 Aquaculture https://hal.science/hal-02626095 Aquaculture, 2018, 491, pp.105-113. ⟨10.1016/j.aquaculture.2018.03.006⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.aquaculture.2018.03.006 hal-02626095 https://hal.science/hal-02626095 https://hal.science/hal-02626095/document https://hal.science/hal-02626095/file/Harney_etal_Aquaculture_2018.pdf doi:10.1016/j.aquaculture.2018.03.006 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1016/j.aquaculture.2018.03.006 |
container_title |
Aquaculture |
container_volume |
491 |
container_start_page |
105 |
op_container_end_page |
113 |
_version_ |
1790598147847749632 |
spelling |
ftinsu:oai:HAL:hal-02626095v1 2024-02-11T10:02:13+01:00 Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata Harney, Ewan Lachambre, Sebastien Roussel, Sabine Huchette, Sylvain Enez, Florian Morvezen, Romain Haffray, Pierrick Boudry, Pierre Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Scea France Haliotis ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010) 2018 https://hal.science/hal-02626095 https://hal.science/hal-02626095/document https://hal.science/hal-02626095/file/Harney_etal_Aquaculture_2018.pdf https://doi.org/10.1016/j.aquaculture.2018.03.006 en eng HAL CCSD Elsevier info:eu-repo/semantics/altIdentifier/doi/10.1016/j.aquaculture.2018.03.006 hal-02626095 https://hal.science/hal-02626095 https://hal.science/hal-02626095/document https://hal.science/hal-02626095/file/Harney_etal_Aquaculture_2018.pdf doi:10.1016/j.aquaculture.2018.03.006 info:eu-repo/semantics/OpenAccess ISSN: 0044-8486 EISSN: 1873-5622 Aquaculture https://hal.science/hal-02626095 Aquaculture, 2018, 491, pp.105-113. ⟨10.1016/j.aquaculture.2018.03.006⟩ ACL Transcriptome pacific oyster Abalone atlantic salmon Selective breeding oyster crassostrea-gigas pecten-maximus reproductive success linkage disequilibrium effective population-size genetic diversity microsatellite markers Parentage assignment Pedigree single-nucleotide polymorphisms snp [SDE.BE]Environmental Sciences/Biodiversity and Ecology info:eu-repo/semantics/article Journal articles 2018 ftinsu https://doi.org/10.1016/j.aquaculture.2018.03.006 2024-01-24T17:34:09Z WOS:000431009400014 International audience Selective breeding strategies require pedigree information over generations, but many species produced in aquaculture are too small to be physically tagged at early stages. Consequently, maintaining a sufficient number of separate families is often needed but costly and logistically difficult. Alternatively, parentage assignment can be obtained using DNA markers. We developed a panel of single nucleotide polymorphism (SNP) markers for the European abalone Haliotis tuberculata using an existing transcriptomic resource. An initial set of 2,176,887 SNPs was filtered to select 500 for high throughput genotyping. Of these, 298 SNPs were amplified in at least 90% of our H. tuberculata samples, consisting of a mixed family cohort (945 offspring) generated by crossing 40 abalones, and 5 full-sib training families (70 offspring). Based on amplification success among parents, minimum allele frequency and checks carried out against the training families, a subset of 123 markers was used to carry out parentage assignment in our mixed family cohorts. Maximum likelihood and exclusion-based methods of parentage assignment yielded consistent results, allowing parentage to be assigned in 98.9% of the studied progeny. Optimization of markers suggests that the 60 most informative SNPs may be sufficient for 95% assignment success in these progeny. The panel was also used to estimate effective population size, and revealed a low N-e due to high variance of reproductive success between parents. Our panel could be used to estimate genetic parameters of traits in mixed family cohorts, an essential stage to initiate selective breeding in H. tuberculata. It could also be useful tool in the context of monitoring stock enhancement and population genetics studies. Article in Journal/Newspaper Atlantic salmon Crassostrea gigas Pacific oyster Institut national des sciences de l'Univers: HAL-INSU Pacific Aquaculture 491 105 113 |