Résumé
Use of SNPs has been favored 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 analyzed and compared with
other model and non-model 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 programs.