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.
References
Boehm JT, Waldman J, Robinson JD, Hickerson MJ (2016) Population genomics reveals Seahorses (Hippocampus erectus) of the Western MidAtlantic coast to be residents rather than vagrants. PLoS ONE 10(1):e0116219. https://doi.org/10.1371/journal.pone.0116219
Guo L, Zhang N, Yang JW, Guo HY, Zhu KC, Liu BS, Liu TT, Zhang DC (2018) Comprehensive assessment of the genetic diversity and population structure of cultured populations of golden pompano, Trachinotus ovatus (Linnaeus, 1758), by microsatellites. Aquac Int 26(6):1445–1457. https://doi.org/10.1007/s10499-018-0289-4
Lin Q, Luo W, Wan SM, Gao ZX (2016) De novo transcriptome analysis of two seahorse species (Hippocampus erectus and H. mohnikei) and the development of molecular markers for population genetics. PLoS ONE 11(4):e0154096. https://doi.org/10.1371/journal.pone.0154096
Lourie SA, Vincent ACJ, Hall HJ (1999) The taxonomy of Vietnam’s exploited seahorses (family Syngnathidae). Biol J Linn Soc 66:231–325. https://doi.org/10.1111/j.1095-8312.1999.tb01886.x
Panithanarak T, Karuwancharoen R, Na-Nakorn U, Nguyen TTT (2010) Population genetics of the spotted seahorse (Hippocampus kuda) in Thai waters: implication for conservation. Zool Stud 49:564–576
Park SDE (2001) Trypanotolerance in West African cattle and the population genetic effects of selection. Ph.D. thesis, University of Dublin
Qin G, Zhang Y, Wang X, Lin Q (2016) Effects of anesthetic disposal on the physiological and behavioral responses of the lined seahorses, Hippocampus erectus. J World Aquac Soc 47:387–395. https://doi.org/10.1111/jwas.12282
Qu HY, Luo W, Lin Q (2016) Development of the novel SNP markers in lined seahorse (Hippocampus erectus) based on transcriptome sequencing. Conserv Genet Resour 8:1–4. https://doi.org/10.1007/s12686-015-0510-y
Schneider S, Roessli D, Excofer L (2000) Arlequin: a software for population genetics data analysis. V3.01. Genetics and Biometry Lab, Department of Anthropology, University of Geneva
Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5:16–18. https://doi.org/10.1038/NMETH1156
Singh KV, Gopalakrishnan A, Lakra WS, Sobti RC (2012) Microsatellite loci to determine population structure in the yellow seahorse (Hippocampus kuda) and the three-spotted seahorse (H. trimaculatus). Mar Biodivers 42:481–488. https://doi.org/10.1007/s12526-012-0122-7
Wang L, Huang SQ, Xia JH, Liu P, Wan ZY, Yue GH (2015) Genome wide discovery of gene-related SNPs in Barramundi Lates calcarifer. Conserv Genet Resour 7(3):605–608. https://doi.org/10.1007/s12686-015-0444-4
Yang JP, Li YF, Zhu SL, Chen WT, Li J, Xue HM, Li XH (2018) Development and characterization of 26 SNP markers in Ochetobius elongatus based on restriction site-associated DNA sequencing (RAD-seq). Conserv Genet Resour 12(1):53–55. https://doi.org/10.1007/s12686-018-1075-3
Yeh FC, Yang R, Boyle TJ, Ye Z, Xiyan JM (2000) POPGENE 32, Microsoft Windows-based freeware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton
Zhu KC, Yu WB, Huang JH, Zhou FL, Guo HY, Zhang N, Jiang SG, Zhang DC (2017) Parentage determination in black tiger shrimp (Penaeus monodon) based on microsatellite DNA markers. Aquac Int 25:827–836. https://doi.org/10.1007/s10499-016-0082-1
Zhu KC, Yu WB, Zhang DC, Guo HY, Zhang N, Jiang SG (2019) Identification, characterization, and evaluation of polymorphic microsatellite markers for parentage assignment in Pinctada fucata. J World Aquac Soc 50(1):155–162. https://doi.org/10.1111/jwas.12534
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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Zhu, KC., Ma, Q. & Zhang, DC. Isolation and characterization of 100 SNP markers in lined seahorse (Hippocampus erectus) using RAD sequencing. Conservation Genet Resour 12, 589–595 (2020). https://doi.org/10.1007/s12686-020-01163-7
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DOI: https://doi.org/10.1007/s12686-020-01163-7