期刊
MOLECULAR ECOLOGY RESOURCES
卷 14, 期 4, 页码 820-830出版社
WILEY
DOI: 10.1111/1755-0998.12230
关键词
Crassostrea gigas; GoldenGate technology; Ostrea edulis; oysters; SNP genotyping
资金
- 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]
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 segregating 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 analysed 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) populations and could contribute to future selective breeding programmes.
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