Characterization of novel EST-derived SNP markers using 454 pyrosequencing in Sinonovacula constricta
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TECHNICAL NOTE
Characterization of novel EST-derived SNP markers using 454 pyrosequencing in Sinonovacula constricta Lie Wang • Donghong Niu • Jiale Li
Received: 13 August 2012 / Accepted: 23 August 2012 / Published online: 5 September 2012 Ó Springer Science+Business Media B.V. 2012
Abstract The razor clam (Sinonovacula constricta) is an important aquaculture clam. But no single nucleotide polymorphisms (SNP) markers were characterized from expressed sequence tags (ESTs) in the species previously. Here, we designed 18 primers for 25 SNP loci generated from the transtriptome of S. constricta by 454 pyrosequencing. All the SNP loci were characterized on 24 individuals. The observed (Ho) and expected (He) heterozygosity ranged from 0.042 to 0.833 (mean 0.325) and from 0.082 to 0.515 (mean 0.360), respectively. Nine loci showed significant departure from Hardy–Weinberg equilibrium (p \ 0.05). No linkage disequilibrium was detected between loci pairs. These new EST-SNP markers are useful for conservation genetics and genetic breeding of S. constricta. Keywords Sinonovacula constricta Single nucleotide polymorphism (SNP) Genetic diversity
Sinonovacula constricta, a commercially important species of bivalve, is widely distributed in intertidal zones and estuarine water in China, Japan, and Korea. It is one of the four major aquacultural clams along with Crassostrea gigas, Ruditapes philippinarum and Tegillarca granosa in China. However, its genetic resources were limited.
Lie Wang and Donghong Niu contributed equally to the manuscript. L. Wang D. Niu J. Li (&) Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Hucheng Huan Road, Shanghai 201306, China e-mail: [email protected]; [email protected]
Recently, microsatellites were developed (Niu et al. 2008) and used to analysis of population genetics for the species (Niu et al. 2012). Compared with microsatellites, single nucleotide polymorphisms (SNPs) have gained more popularity and now become an important molecular marker (Garvin et al. 2010), due to their high abundance in the genome, hereditable stability and allele portability, and the possibility for high-throughput analysis. Next-generation sequencing allows more accurate de novo sequence assemblies for non-model organisms and discovery of large numbers of SNPs in species with little genomic information (Renaut et al. 2010). The EST-SNP markers have already been developed in shellfish and fish (Wang et al. 2012; Zhu et al. 2012). Although EST-database mining is an efficient way to obtain SNP markers, few EST-SNPs have been characterized in this clam. With the purpose of constructing more genetic dataset and analyzing the genetic diversity for this species, we designed this experiment. In this study, we developed novel EST-SNPs from transcriptome of S. constricta, which would be useful in genetics and breeding studies. Recently, the transcriptome of the razor clam was sequenced using 454 technology and 824 SNP loci were obtained.
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