Isolationg And Characterization Of SNPs From EST Database Of Pacific Oyster (Crassostrea Giga)

Pacific oyster (Crassostrea giga) is one of the traditional and also most important mollusks that are being widely eultured in China. The marker-assisted selection (MAS) provides the fundamental theories and applied experiences for this task not only in better utilizing the available resources but also increasing production in aquaculture. This research is to isolate and characterize of SNP markers for Pacific oyster.Around 29,000 EST sequences of Crassostrea gigas from Genbank were clustered into 4548 groups, among which 1079 contained 4 or more than 4 ESTs. After the manual quality filtering, 313 clusters could be used for the SNP development. Eighty-two candidate SNPs were amplified with fragment length discrepant allele specific PCR (FLDAS-PCR), among which 17 are polymorphic in a wild population. The functions of the ESTs were predicted, as well as ORF were deduced based on BlastX analysis. The expected and observed heterozygosities of the SNPs ranged from 0.088 to 0.506 and 0.091 to 0.667, respectively. No significant linkage disequilibria were observed with most of the loci. Only three loci did not conform to Hardy–Weinberg equilibrium at the level of P < 0.05. The results show that EST database is an important resource to develop SNPs for the species whose genome research is on the primary stage.