Genome-wide Genic SNPs Development and Association Analysis with Abiotic Stress in the Pacific Oyster Crassostrea gigas

The sequenced genome of the Pacific oyster Crassostrea gigas can provide the reference for large-scale screening and validation of SNPs via mapping and alignments of great numbers of short reads generated from next generation sequencing (NGS) technologies. Wild oysters were collected from nature populations of C. gigas on coasts of Qingdao, Qinhuangdao and Dalian, China. Twenty individuals were randomly selected from each site. For each oyster the organisms including gill, mantle and adductor muscles were excised and total RNA was isolated for transcriptome sequencing on Illumina Solexa platform. Around 5.8×10⁵ SNPs were screened using samtools program. Among the predicted SNPs, more than 1500 were validated based on high resolution melting platform, accounting for 65.2% of the total selected SNPs. The SNP markers are distributed in 864 genes of 197 KEGG pathways, which involve metabolism, stress, immune, resistance, adjustment, reproduction and body composition of Crassostrea gigas. Notably, 88 HSP70s, 157 genes related to glycogen metabolism and 30 genes related to free amino acid were included. All the validated SNP markers are being used for the high-density linkage map construction, association study for temperature and salinity adaptation. In combination of the expression profile of the candidate genes under the abiotic challenge, two HSP70 SNPs were preliminarily proved to associate to the heat tolerance by now. The details of the linkage map and the association study will be presented at the meeting.