Development of SNP-genotyping arrays in two shellfish species
International audience Use of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the...
Published in: | Molecular Ecology Resources |
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Main Authors: | , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2014
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Subjects: | |
Online Access: | https://hal.archives-ouvertes.fr/hal-01082464 https://hal.archives-ouvertes.fr/hal-01082464/document https://hal.archives-ouvertes.fr/hal-01082464/file/Lapegue%20al%20MER%202014.pdf https://doi.org/10.1111/1755-0998.12230 |
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Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
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English |
topic |
Golden Gate technology SNP genotyping Oyster Crassostrea gigas Ostrea edulis [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
spellingShingle |
Golden Gate technology SNP genotyping Oyster Crassostrea gigas Ostrea edulis [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] Lapegue, S. Harrang, E Heurtebise, S Flahauw, E Donnadieu, C Gayral, P Ballenghien, M Genestout, L Barbotte, L Mahla, R Haffray, Pierrick Development of SNP-genotyping arrays in two shellfish species |
topic_facet |
Golden Gate technology SNP genotyping Oyster Crassostrea gigas Ostrea edulis [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
description |
International audience Use of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. In each case, oyster samples were obtained from wild and selected populations and from three-generation families seg-regating for traits of interest in aquaculture. The rate of successfully genotyped polymorphic SNPs was about 60% for each species. Effects of SNP origin and quality on genotyping success (Illumina functionality Score) were analy-sed and compared with other model and nonmodel species. Furthermore, a simulation was made based on a subset of the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. This simulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panels might provide valuable tools to improve our understanding of the connectivity between wild (and selected) popula-tions and could contribute to future selective breeding programmes. |
author2 |
Laboratoire de Génétique et Pathologie (LGP) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Génétique et évolution des populations végétales (GEPV) Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS) Laboratoire d'hydrodynamique (LadHyX) École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS) Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI) Université de Tours-Centre National de la Recherche Scientifique (CNRS) Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS) Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA) Institut National de la Recherche Agronomique (INRA) Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF) GigADN - FranceAgrimer SIVAL NL: 2010-1021 GAMETOGENES - Agence Nationale de la Recherche 'Genomique animale' Programme ANR-08-GENM-041 SEAFARE (Sustainable and Environmentally Friendly Aquaculture for the Atlantic Region of Europe) 2009-1/123 Atlantic Area Transnational Program; Hi-Flo; Agence Nationale de la Recherche ANR-08-blanc-0334-01 European Research Council ERC PopPhyl 232971 ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008) ANR-08-BLAN-0334,Hi-Flo,The genetic basis and history of adaptive differentiation in high gene flow marine species(2008) |
format |
Article in Journal/Newspaper |
author |
Lapegue, S. Harrang, E Heurtebise, S Flahauw, E Donnadieu, C Gayral, P Ballenghien, M Genestout, L Barbotte, L Mahla, R Haffray, Pierrick |
author_facet |
Lapegue, S. Harrang, E Heurtebise, S Flahauw, E Donnadieu, C Gayral, P Ballenghien, M Genestout, L Barbotte, L Mahla, R Haffray, Pierrick |
author_sort |
Lapegue, S. |
title |
Development of SNP-genotyping arrays in two shellfish species |
title_short |
Development of SNP-genotyping arrays in two shellfish species |
title_full |
Development of SNP-genotyping arrays in two shellfish species |
title_fullStr |
Development of SNP-genotyping arrays in two shellfish species |
title_full_unstemmed |
Development of SNP-genotyping arrays in two shellfish species |
title_sort |
development of snp-genotyping arrays in two shellfish species |
publisher |
HAL CCSD |
publishDate |
2014 |
url |
https://hal.archives-ouvertes.fr/hal-01082464 https://hal.archives-ouvertes.fr/hal-01082464/document https://hal.archives-ouvertes.fr/hal-01082464/file/Lapegue%20al%20MER%202014.pdf https://doi.org/10.1111/1755-0998.12230 |
long_lat |
ENVELOPE(-134.237,-134.237,59.616,59.616) |
geographic |
Golden Gate Pacific |
geographic_facet |
Golden Gate Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology https://hal.archives-ouvertes.fr/hal-01082464 Molecular Ecology, Wiley, 2014, 14 (4), pp.820-830. ⟨10.1111/1755-0998.12230⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.12230 info:eu-repo/semantics/altIdentifier/pmid/24447767 hal-01082464 https://hal.archives-ouvertes.fr/hal-01082464 https://hal.archives-ouvertes.fr/hal-01082464/document https://hal.archives-ouvertes.fr/hal-01082464/file/Lapegue%20al%20MER%202014.pdf doi:10.1111/1755-0998.12230 PRODINRA: 261446 WOS: 000337611400016 PUBMED: 24447767 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1111/1755-0998.12230 |
container_title |
Molecular Ecology Resources |
container_volume |
14 |
container_issue |
4 |
container_start_page |
820 |
op_container_end_page |
830 |
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spelling |
ftccsdartic:oai:HAL:hal-01082464v1 2023-05-15T15:58:10+02:00 Development of SNP-genotyping arrays in two shellfish species Lapegue, S. Harrang, E Heurtebise, S Flahauw, E Donnadieu, C Gayral, P Ballenghien, M Genestout, L Barbotte, L Mahla, R Haffray, Pierrick Laboratoire de Génétique et Pathologie (LGP) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Génétique et évolution des populations végétales (GEPV) Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS) Laboratoire d'hydrodynamique (LadHyX) École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS) Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI) Université de Tours-Centre National de la Recherche Scientifique (CNRS) Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS) Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA) Institut National de la Recherche Agronomique (INRA) Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF) GigADN - FranceAgrimer SIVAL NL: 2010-1021 GAMETOGENES - Agence Nationale de la Recherche 'Genomique animale' Programme ANR-08-GENM-041 SEAFARE (Sustainable and Environmentally Friendly Aquaculture for the Atlantic Region of Europe) 2009-1/123 Atlantic Area Transnational Program; Hi-Flo; Agence Nationale de la Recherche ANR-08-blanc-0334-01 European Research Council ERC PopPhyl 232971 ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008) ANR-08-BLAN-0334,Hi-Flo,The genetic basis and history of adaptive differentiation in high gene flow marine species(2008) 2014 https://hal.archives-ouvertes.fr/hal-01082464 https://hal.archives-ouvertes.fr/hal-01082464/document https://hal.archives-ouvertes.fr/hal-01082464/file/Lapegue%20al%20MER%202014.pdf https://doi.org/10.1111/1755-0998.12230 en eng HAL CCSD Wiley info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.12230 info:eu-repo/semantics/altIdentifier/pmid/24447767 hal-01082464 https://hal.archives-ouvertes.fr/hal-01082464 https://hal.archives-ouvertes.fr/hal-01082464/document https://hal.archives-ouvertes.fr/hal-01082464/file/Lapegue%20al%20MER%202014.pdf doi:10.1111/1755-0998.12230 PRODINRA: 261446 WOS: 000337611400016 PUBMED: 24447767 info:eu-repo/semantics/OpenAccess ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology https://hal.archives-ouvertes.fr/hal-01082464 Molecular Ecology, Wiley, 2014, 14 (4), pp.820-830. ⟨10.1111/1755-0998.12230⟩ Golden Gate technology SNP genotyping Oyster Crassostrea gigas Ostrea edulis [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] info:eu-repo/semantics/article Journal articles 2014 ftccsdartic https://doi.org/10.1111/1755-0998.12230 2021-11-21T03:21:34Z International audience Use of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. In each case, oyster samples were obtained from wild and selected populations and from three-generation families seg-regating for traits of interest in aquaculture. The rate of successfully genotyped polymorphic SNPs was about 60% for each species. Effects of SNP origin and quality on genotyping success (Illumina functionality Score) were analy-sed and compared with other model and nonmodel species. Furthermore, a simulation was made based on a subset of the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. This simulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panels might provide valuable tools to improve our understanding of the connectivity between wild (and selected) popula-tions and could contribute to future selective breeding programmes. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Golden Gate ENVELOPE(-134.237,-134.237,59.616,59.616) Pacific Molecular Ecology Resources 14 4 820 830 |