Discovery and validation of genic single nucleotide polymorphisms in the Pacific oyster Crassostrea gigas

• Published in: Molecular Ecology Resources
• Main Authors: Wang, Jiafeng, Qi, Haigang, Li, Li, Que, Huayong, Wang, Di, Zhang, Guofan
• Other Authors: Earmarked fund for Modern Agro-industry Technology Research System, High Technology Research and Development Program (863 Program), National Basic Research Program of China (973 Program), National Natural Science Foundation of China
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2014
• Subjects: Pacific; Crassostrea gigas; Pacific oyster
• Online Access: http://dx.doi.org/10.1111/1755-0998.12278; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12278; https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12278

Abstract The economic and ecological importance of the oyster necessitates further research on the molecular mechanisms, which both regulate the commercially important traits of the oyster and help it to survive in the variable marine environment. Single nucleotide polymorphisms ( SNP s) have been widely used to assess genetic variation and identify genes underlying target traits. In addition, high‐resolution melting ( HRM ) analysis is a potentially powerful method for validating candidate SNP s. In this study, we adopted a rapid and efficient pipeline for the screening and validation of SNP s in the genic region of Crassostrea gigas based on transcriptome sequencing and HRM analysis. Transcriptomes of three wild oyster populations were sequenced using Illumina sequencing technology. In total, 50–60 million short reads, corresponding to 4.5–5.4 Gbp, from each population were aligned to the oyster genome, and 5.8 × 10 5 SNP s were putatively identified, resulting in a predicted SNP every 47 nucleotides on average. The putative SNP s were unevenly distributed in the genome and high‐density (≥2%), nonsynonymous coding SNP s were enriched in genes related to apoptosis and responses to biotic stimuli. Subsequently, 1,671 loci were detected by HRM analysis, accounting for 64.7% of the total selected candidate primers, and finally, 1,301 polymorphic SNP markers were developed based on HRM analysis. All of the validated SNP s were distributed into 897 genes and located in 672 scaffolds, and 275 of these genes were stress inducible under unfavourable salinity, temperature, and exposure to air and heavy metals. The validated SNP s in this study provide valuable molecular markers for genetic mapping and characterization of important traits in oysters.