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Development of SNP markers in lined seahorse (Hippocampus erectus) based on transcriptome sequencing

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Abstract

The population of lined seahorse (Hippocampus erectus) rapidly reduced because of the heavy exploitation in the wild. The single nucleotide polymorphism (SNP), known as one of the popular third-generation molecular markers can be developed easier and faster from high-throughput transcriptome sequencing. In this study, we developed 46 novel SNP markers based on transcriptome of H. erectus. Genetic diversity analysis showed that observed heterozygosity (Ho) and expected heterozygosity (He) were varied from 0.1724 to 0.5250 and from 0.1588 to 0.5000, respectively, and the minor allele frequency value was from 0.0625 to 0.5000. Seven loci were significantly different from Hardy–Weinberg equilibrium (P < 0.05) and significant linkage disequilibrium occurred between HeSNP24 and HeSNP38 (P < 0.01). The present study can provide an effective tool for population study and genetic breeding.

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Acknowledgments

This study was funded by the National Natural Science Foundation of China (41576145) and the Guangdong Oceanic and Fisheries Science and Technology Foundation (A201501A12).

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Authors and Affiliations

  1. Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People’s Republic of China

    Hongyue Qu, Wei Luo & Qiang Lin

  2. University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China

    Hongyue Qu

Authors
  1. Hongyue Qu
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  2. Wei Luo
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  3. Qiang Lin
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Correspondence to Qiang Lin.

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Qu, H., Luo, W. & Lin, Q. Development of SNP markers in lined seahorse (Hippocampus erectus) based on transcriptome sequencing. Conservation Genet Resour 8, 1–4 (2016). https://doi.org/10.1007/s12686-015-0510-y

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  • DOI: https://doi.org/10.1007/s12686-015-0510-y

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