Development of SNP-genotyping arrays in two shellfish species

S. LAPEGUE,* E. HARRANG,* S. HEURTEBISE,* E. FLAHAUW,* C. DONNADIEU,† P. GAYRAL,‡§M. BALLENGHIEN,‡ L. GENESTOUT,¶ L. BARBOTTE,¶ R. MAHLA,¶ P. HAFFRAY** andC. KLOPP††*Ifremer, SG2M-LGPMM, Laboratoire de Genetique et Pathologie des Mollusques Marins, La Tremblade, France, †INRAUMR444, Laboratoire de Genetique Cellulaire, Plateforme GeT-PlaGe Genotoul, Castanet-Tolosan, France, ‡CNRS UMR 5554,Institut des Sciences de l’Evolution de Montpellier, Universite Montpellier 2, Montpellier, France, §CNRS UMR 7261, Institut deRecherche sur la Biologie de l’Insecte, Faculte des Sciences et Techniques, Universite Franc ois Rabelais, Tours, France,¶LABOGENA, Domaine de Vilvert, Jouy-en-Josas, France, **SYSAAF, Station LPGP/INRA, Campus de Beaulieu, 35042 Rennes,France, ††INRA, Sigenae, UR875 Biometrie et Intelligence Artificielle, Castanet-Tolosan, FranceAbstractUse of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the fallingcost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targetedsequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oysterspecies, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markerswere designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. Ineach 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 subsetof the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. Thissimulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panelsmight provide valuable tools to improve our understanding of the connectivity between wild (and selected) popula-tions and could contribute to future selective breeding programmes.Keywords: Crassostrea gigas, GoldenGate technology, Ostrea edulis, oysters, SNP genotypingReceived 10 October 2013; revision received 26 December 2013; accepted 8 January 2014