Isolation and characterization of 100 SNP markers in lined seahorse (Hippocampus erectus) using RAD sequencing

Abstract

Lined seahorse (Hippocampus erectus), an important economic and medicinal fish in China, exists widely in Atlantic Ocean. However, habitat destruction for its spawning and overfishing has led to profound decline the wild populations in recent years. Therefore, to improve the molecular-assisted selection (MAS) and resources conservation of H. erectus, the 100 novel single nucleotide polymorphism (SNP) loci are developed by restriction-site associated DNA (RAD) sequencing in this species. In the present study, the observed heterozygosity (Ho) and expected heterozygosity (HE) varied from 0.0263 to 0.8154 and 0.0261 to 0.506, respectively. The minor allele frequency (MAF) ranged from 0.0132 to 0.5000. The PIC value was between with 0.0257 and 0.375. Fifteen loci displayed prominent deviations from the Hardy–Weinberg equilibrium (HWE) after Bonferroni correction (P < 0.05), but no remarkable linkage disequilibrium was observed. These novel isolated SNPs will be useful for selective breeding and conservation genetics studies of Seahorse.

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Acknowledgements

This work was supported by Guangdong Provincial Fishing port construction and fishery industry development Project (A201701A03), Financial Fund of Ministry of Agriculture and Rural affairs of China (NHYYSWZZZYKZX2020), Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0605), China-ASEAN maritime cooperation fund (00-201620821), National Infrastructure of Fishery Germplasm Resources Project (2019DKA30470) and Science and Technology Infrastructure Construction Project of Guangdong Province (2019B030316030).

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Correspondence to Dian-Chang Zhang.

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Zhu, K., Ma, Q. & Zhang, D. Isolation and characterization of 100 SNP markers in lined seahorse (Hippocampus erectus) using RAD sequencing. Conservation Genet Resour (2020). https://doi.org/10.1007/s12686-020-01163-7

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Keywords

  • Hippocampus erectus
  • SNP
  • RAD
  • Selective breeding
  • Conservation genetics