Animal cells and systems

The Korean Society for Integrative Biology (한국통합생물학회)
권호 표지
DOI QR코드

DOI QR Code

Development and characterization of microsatellite markers for an endangered species, $Epinephelus$ $bruneus$, to establish a conservation program

  • An, Hye-Suck (New Strategy Research Center, National Fisheries Research and Development Institute) ;
  • Kim, Jae-Woo (New Strategy Research Center, National Fisheries Research and Development Institute) ;
  • Lee, Jang-Wook (New Strategy Research Center, National Fisheries Research and Development Institute) ;
  • Kim, Shin-Kwon (New Strategy Research Center, National Fisheries Research and Development Institute) ;
  • Lee, Bae-Ik (New Strategy Research Center, National Fisheries Research and Development Institute) ;
  • Kim, Dae-Jung (New Strategy Research Center, National Fisheries Research and Development Institute) ;
  • Kim, Yi-Cheong (New Strategy Research Center, National Fisheries Research and Development Institute)
  • Received : 2011.04.29
  • Accepted : 2011.07.19
  • Published : 2012.02.28
Download PDF
⟨ Previous Next ⟩

Abstract

Kelp grouper ($Epinephelus$ $bruneus$ Bloch 1793) is a commercially important fish in Korea. In recent years, the catch of kelp grouper in the coastal waters of Korea has significantly declined. Despite its importance, little is known about its genetic diversity and conservation efforts are hampered. In this study, we isolated and characterized 12 microsatellite loci using an enrichment method based on magnetic/biotin capture of microsatellite sequences from a size-selected genomic library. All loci were readily amplified and contained TG/CA denucleotide repeats. To characterize each locus, 30 individuals from a natural E. bruneus population in the coastal waters of Jeju Island, Korea, were genotyped. All loci except three, KEm118, KEm154, and KEm219, were polymorphic, with an average of 8.1 alleles per locus (range 2-18). The mean observed and expected heterozygosities were 0.47 (range 0.19-1.00) and 0.61 (range 0.29-0.92), respectively. A significant deviation from Hardy-Weinberg equilibrium was observed at three loci (KEm134, KEm184, and KEm283). These findings will be useful for effective monitoring and management of genetic variation of kelp grouper as well as for the implementation of a fisheries conservation program.

Keywords

References

  1. Addison JA, Hart MW. 2005. Spawning, copulation and inbreeding coefficients in marine invertebrates. Biol Lett. 1:450-453. https://doi.org/10.1098/rsbl.2005.0353
  2. An HS, Cho KC, Park JY. 2005. Eleven new highly polymorphic microsatellite loci in the yellow croaker, Pseudosciaena crocea Inheritance. Mol Ecol Notes. 5:866-868. https://doi.org/10.1111/j.1471-8286.2005.01097.x
  3. An HS, Kim KS, Lee HY, Kim EM, Kwon MG. 2009. Isolation and characterization of polymorphic microsatellite markers for the black rockfish Sebastes inermis. Genes Genomics. 31:29-34. https://doi.org/10.1007/BF03191135
  4. An, Hye Suck, Lee, Jeong-ho, Noh, Jae Koo, Kim, Hyun Chul, Park, Chul Ji, Min, Byung Hwa, Myeong, Jeong- In. 2010. Ten new microsatellite markers in cutlassfish Trichiurus lepturus derived from an enriched genomic library. Anim Cells Syst. 14:169-174. https://doi.org/10.1080/19768354.2010.504347
  5. Asahida T, Kobayashi T, Saitoh K, Nakayama I. 1996. Tissue preservation and total DNA extraction from fish stored at ambient temperature using buffers containing high concentrations of urea. Fish Sci Tokyo. 62:727-730. https://doi.org/10.2331/fishsci.62.727
  6. Banks SC, Piggott LM, Williamson JE, Bove U, Holbrook NJ, Beheregaray LB 2007. Oceanic variability and coastal topography shape genetic structure in a long-dispersing sea urchin. Ecology. 88:3055-3064. https://doi.org/10.1890/07-0091.1
  7. Bohonak AJ. 1999. Dispersal, gene flow, and population structure. Q Rev Biol. 74:21-45. https://doi.org/10.1086/392950
  8. Brandstrom M, Ellegren H. 2008. Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias. Genome Res. 18:881-887. https://doi.org/10.1101/gr.075242.107
  9. Callen DF, Thompson AD, Shen Y, Phillips HA, Mulley JC, Sutherland GR. 1993. Incidence and origin of "null" alleles in the (AC)n microsatellite markers. Am J Hum Genet. 52:922-927.
  10. Carleton KL, Streelman JT, Lee BY, Garnhart N, Kidd M, Kocher TD. 2002. Rapid isolation of CA microsatellites from the tilapia genome. Anim Genet. 33:140-144. https://doi.org/10.1046/j.1365-2052.2002.00817.x
  11. Castro J, Bouza C, Sanchez L, Cal RM, Piferrer F, Martinez P. 2003. Gynogenesis assessment using microsatellite genetic markers in turbot (Scophthalmus maximus). Mar Biotechnol. 5:584-592. https://doi.org/10.1007/s10126-003-0004-x
  12. Cheng Y, Xinping Z, Xiaowen S. 2008. Development of microsatellite markers and their utilization in genetic diversity analysis of cultivated and wild populations of the mud carp (Cirrhina molitorella). J Genet Genom. 35:201-206. https://doi.org/10.1016/S1673-8527(08)60028-4
  13. Chistiakov DA, Hellemans B, Volckaert FAM. 2006. Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture. 255:1-29. https://doi.org/10.1016/j.aquaculture.2005.11.031
  14. Cruz P, Ibarra AM, Mejia-Ruiz H, Gaffney PM, Perez-Enriquez R. 2004. Genetic variability assessed by microsatellites in a breeding program of pacific white shrimp (Litopenaeus vannamei). Mar Biotechnol. 6:157-164.
  15. DeSalle R, Amato G. 2004. The expansion of conservation genetics. Nature Rev Genet. 5:702-712. https://doi.org/10.1038/nrg1425
  16. DeWoody JA, Avise JC. 2000. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J Fish Biol. 56:461-473. https://doi.org/10.1111/j.1095-8649.2000.tb00748.x
  17. Evans B, Bartlett J, Sweijd N, Cook P, Elliott NG. 2004. Loss of genetic variation at microsatellite loci in hatchery produced abalone in Australia (Haliotis rubra) and South Africa (Haliotis midae). Aquaculture. 233:109-127. https://doi.org/10.1016/j.aquaculture.2003.09.037
  18. Feral JP. 2002. How useful are the genetic markers in attempts to understand and manage marine biodiversity? J Exp Mar Biol Ecol. 268:121-145. https://doi.org/10.1016/S0022-0981(01)00382-3
  19. Frankham R, Ballou JD, Briscoe DA. 2002. Introduction to Population genetics. Cambridge: Cambridge University Press.
  20. Gardner MG, Cooper SJB, Bull CM, Grant WN. 1999. Isolation of microsatellite loci from a social lizard, Egernia stokesii, using a modified enrichment procedure. J Hered. 90:301-304. https://doi.org/10.1093/jhered/90.2.301
  21. Gondim SGCA, Resende LV, Brondani RPV, Collevatti RG, Silva-Ju'nior NJ, Pereira RR, Telles MPC. 2010. Development of microsatellite markers for Hoplias malabaricus (Erythrinidae). Genet Mol Res. 9:1513-1517. https://doi.org/10.4238/vol9-3gmr877
  22. Hamilton MB, Pincus EL, DiFiore A, Fleischer RC. 1999. Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechnology. 27:500-507.
  23. Hedgecock D, Barber PH, Edmands S. 2007. Genetic approaches to measuring connectivity. Oceanography. 20:70.
  24. Heemstra PC, Randall JE. 1993. FAO Species Catalogue. Vol. 16. Groupers of the world (family Serranidae, subfamily Epinephelinae). An annotated and illustrated catalogue of the grouper, rockcod, hind, coral grouper and lyretail species known to date. FAO Fish Synop. 125:382.
  25. Hoarau G, Rijnsdrop AD, Van der Veer HW, Stam WT, Olsen JL. 2002. Population structure of plaice (Pleuronectes platessa L.) in northern Europe: microsatellites revealed large scale spatial and temporal homogeneity. Mol Ecol. 11:1165-1176. https://doi.org/10.1046/j.1365-294X.2002.01515.x
  26. Holland BS. 2001. Invasion without a bottleneck: microsatellite variation in natural and invasive populations of the brown mussel Perna perna (L). Mar Biotechnol. 3:407-415. https://doi.org/10.1007/s1012601-0060-Z
  27. Li Q, Park C, Kijima A. 2002. Isolation and characterization of microsatellite loci in the Pacific abalone, Haliotis discus hannai. J Shell Res. 212:811-815.
  28. Liu ZJ, Cordes FJ. 2004. DNA marker technology and their applications in aquaculture genetics. Aquaculture. 238:1-37. https://doi.org/10.1016/j.aquaculture.2004.05.027
  29. Li Q, Park C, Kijima A. 2002. Isolation and characterization of microsatellite loci in the Pacific abalone, Haliotis discus hannai. J Shell Res. 212:811-815.
  30. Pampoulie C, Steingrund P, Stefansson MO, Danielsdottir AK. 2008. Genetic divergence among East Icelandic and Faroese populations of Atlantic cod provides evidence for historical imprints at neutral and non-neutral markers. ICES J Mar Sci. 65:65-71.
  31. Pemberton JM, Slate J, Bancroft DR, Barrett JA. 1995. Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies. Mol Ecol. 4:249-252. https://doi.org/10.1111/j.1365-294X.1995.tb00214.x
  32. Rice WR. 1989. Analyzing tables of statistical tests. Evol Int J Org Evol. 43:223-225. https://doi.org/10.1111/j.1558-5646.1989.tb04220.x
  33. Riginos C, Nachman MW 2001. Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus. Mol Ecol. 10:1439-1453. https://doi.org/10.1046/j.1365-294X.2001.01294.x
  34. Schneider S, Kueffer JM, Roessli D, Excoffier L. 2000. ARLEQUIN version 2.0: a software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
  35. Tauz D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucl Acids Res. 17:6463-6471. https://doi.org/10.1093/nar/17.16.6463
  36. Telles MPC, Resende LV, Brondani RPV, Collevatti RG, Costa MC, Silva Junior NJ. 2010. Isolation and characterization of microsatellite markers in the armored catfish Hypostomus gymnorhynchus (Loricariidae). Genet Mol Res. 9:1770-1774. https://doi.org/10.4238/vol9-3gmr868
  37. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes. 4:135.
  38. Ward RD, Woodwark M, Skibinski DOF. 1994. A comparision of genetic diversity levels in marine freshwater and anadromous fishes. J Fish Biol. 44:213-232. https://doi.org/10.1111/j.1095-8649.1994.tb01200.x
  39. Wang S, Zhang X, Liu Q, Dong J, Song Z. 2010. Isolation and characterization of ten tetranucleotide microsatellite loci in rock carp, Procypris rabaudi (Tchang). Conserv Genet. 11:1219-1222. https://doi.org/10.1007/s10592-009-9923-z
  40. Zhang Q, Allen SK Jr, Reece KS. 2005. Genetic variation in wild and hatchery stocks of Suminoe oyster (Crassostrea ariakensis) assessed by PCR-RFLP and microsatellite markers. Mar Biotechnol. 7:588-599. https://doi.org/10.1007/s10126-004-5105-7

Cited by

  1. When physical oceanography meets population genetics: The case study of the genetic/evolutionary discontinuity in the endangered goliath grouper (Epinephelus itajara; Perciformes: Epinephelidae) with vol.56, pp.None, 2012, https://doi.org/10.1016/j.bse.2014.06.004
  2. Microsatellite marker set for genetic diversity assessment of primitive Chitala chitala (Hamilton, 1822) derived through SMRT sequencing technology vol.46, pp.1, 2012, https://doi.org/10.1007/s11033-018-4414-2