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Characterization of novel EST-derived SNP markers using 454 pyrosequencing in Sinonovacula constricta

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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.

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Acknowledgments

This study was supported by the grants of the National Natural Science Foundation of China (31101897), “863” Hi-tech research and development program of China (2012AA10A400-3), the Leading Academic Discipline Project of Shanghai Municipal Education Commission (J50701) (Marine Biology). We appriated Fanyue Sun in Auburn University for English revision.

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Authors and Affiliations

  1. Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Hucheng Huan Road, Shanghai, 201306, China

    Lie Wang, Donghong Niu & Jiale Li

Authors
  1. Lie Wang
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  2. Donghong Niu
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  3. Jiale Li
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Corresponding author

Correspondence to Jiale Li.

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Lie Wang and Donghong Niu contributed equally to the manuscript.

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Wang, L., Niu, D. & Li, J. Characterization of novel EST-derived SNP markers using 454 pyrosequencing in Sinonovacula constricta . Conservation Genet Resour 5, 191–193 (2013). https://doi.org/10.1007/s12686-012-9765-8

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  • DOI: https://doi.org/10.1007/s12686-012-9765-8

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