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Single nucleotide polymorphisms (SNPs) are the marker of choice in genetic and genomic studies due to their abundance in the genome, slow mutation rate, ease automated genotyping and ease of calibration among laboratories.Development of a large number of SNPs used to be time-and cost-intensive especially for scallops whose genomic information is usually very limited.The advent of next-generation sequencing technologies enables producing gigabases of DNA sequence in a short time and at minimal cost, making it possible to discover large amounts of SNPs in an efficient and economical way.Our group has recently sequenced the transcriptome of Zhikong scallop using Roche 454 sequencing technology.By mining our EST dataset, more than 31,000 putative SNPs were found, 5,630 of which were selected for marker development using 54 individuals from five geographical populations (DL, CD, RC, QD, RZ) in China.The simple, fast and cost-effective high resolution melting (HRM) method was utilized for SNP genotyping.Of the 5,630 putative SNPs tested, 3,806 (67.6%) produced amplifications with expected size, and 1,694 (30.1%) proved to be polymorphic among individuals.Our approach for SNP marker development represents a rapid and cost-effective way to obtain a large number of SNP markers for scallops, and these markers should be useful for future genetic and genomic studies on Zhikong scallop.