High-Throughput SNP Discovery using Next Generation Transcriptomic Sequencing in Pacific White Shrimp Litopenaus vannamei

Abstract: The application of next generation sequencing technology has brought a new opportunity for high throughput single nucleotide polymorphism (SNP) discovery and genotyping for genetic research. In the present study, SNPs were predicted based on the transcriptome data using Solexa sequencing for larvae at different stages including embryo, nauplius, zoea, mysis, post-larva of L. vannamei. Through assembly of the transcriptome data, 66,815 unigenes were obtained, of which 32,398 have putative homologues in the non-redundant (nr) protein database from NCBI. SNPs were called by SAMtools software after mapping the original reads to the unigenes sequences by BWA software. Totally 181,289 high quality SNPs were discovered. Among these SNPs, 31,949 were predicted as non-synonymous while 66,843 were synonymous. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification. Over 60% accuracy of confirmation was obtained which indicated that approximately 108,773 SNPs were discovered. This study provides a comprehensive information of transcriptomic SNPs and the valuable SNP resource will be very helpful for population genetics and marker-assisted breeding.