Development of SNP-genotyping arrays in two shellfish species

• Published in: Molecular Ecology Resources
• Main Authors: Lapegue, S., Harrang, E, Heurtebise, S, Flahauw, E, Donnadieu, C, Gayral, P, Ballenghien, M, Genestout, L, Barbotte, L, Mahla, R, Haffray, Pierrick
• Other Authors: Unité Santé, Génétique et Microbiologie des Mollusques (SGMM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire d'hydrodynamique (LadHyX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche sur la biologie de l'insecte (IRBI), Université de Tours (UT)-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
• Language: English
• Published: HAL CCSD 2014
• Subjects: Oyster; SNP genotyping; Golden Gate technology; Ostrea edulis; Crassostrea gigas; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; Pacific oyster
• Online Access: https://hal.science/hal-01082464; https://hal.science/hal-01082464/document; https://hal.science/hal-01082464/file/Lapegue%20al%20MER%202014.pdf; https://doi.org/10.1111/1755-0998.12230

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.