Molecular Biology Reports

, Volume 43, Issue 2, pp 91–98 | Cite as

De novo development and characterization of polymorphic microsatellite markers in a schilbid catfish, Silonia silondia (Hamilton, 1822) and their validation for population genetic studies

  • Sangeeta Mandal
  • J. K. Jena
  • Rajeev K. Singh
  • Vindhya Mohindra
  • W. S. Lakra
  • Geetanjali Deshmukhe
  • Abhinav Pathak
  • Kuldeep K. Lal
Original Article


The stock characterization of wild populations of Silonia silondia is important for its scientific management. At present, the information on genetic parameters of S. silondia is very limited. The species-specific microsatellite markers were developed in current study. The validated markers were used to genotype individuals from four distant rivers. To develop de novo microsatellite loci, an enriched genomic library was constructed for S. silondia using affinity–capture approach. The markers were validated for utility in population genetics. A total number of 76 individuals from four natural riverine populations were used to generate data for population analysis. The screening of isolated repeat sequences yielded eleven novel polymorphic microsatellite loci. The microsatellite loci exhibited high level of polymorphism, with 6–24 alleles per locus and the PIC value ranged from 0.604 to 0.927. The observed (Ho) and expected (He) heterozygosities ranged from 0.081 to 0.84 and 0.66 to 0.938, respectively. The AMOVA analysis indicated significant genetic differentiation among riverine populations (overall FST = 0.075; P < 0.0001) with maximum variation (92.5 %) within populations. Cross-priming assessment revealed successful amplification (35–38 %) of heterologous loci in four related species viz. Clupisoma garua, C. taakree, Ailia coila and Eutropiichthys vacha. The results demonstrated that these de novo polymorphic microsatellite loci are promising for population genetic variation and diversity studies in S. silondia. Cross-priming results indicated that these primers can help to get polymorphic microsatellite loci in the related catfish species of family Schilbidae.


Silonia silondia Microsatellite loci Polymorphic Population genetics Cross-species amplification 


  1. 1.
    Chondar SL (1999) Biology of finfishes and shellfishes. SCSC Publishers, HowrahGoogle Scholar
  2. 2.
    Talwar PK, Jhingran AG (1991) Inland fishes of India and adjacent countries, volume 2. Oxford & IBH Publishing Co. Pvt. Ltd., New DelhiGoogle Scholar
  3. 3.
    Sugunan VV (1995) Reservoir fisheries of India. FAO Fisheries Technical paper, RomeGoogle Scholar
  4. 4.
    Devi R, Boguskaya N (2009) Silonia silondia. In: IUCN 2012. IUCN red list of threatened species. Version 2012.2. Accessed on 14 June 2013
  5. 5.
    Molur S, Walker S (1998) Report on the workshop “Conservation assessment and management plan for freshwater fishes of India”. Zoo Outreach Organisation/CBSG, CoimbatoreGoogle Scholar
  6. 6.
    Lakra WS, Sarkar UK, Gopalakrishnan A, Kathivelpandian A (2010) Threatened freshwater fishes of India. NBFGR, LucknowGoogle Scholar
  7. 7.
    Ciftci Y, Okumus I (2002) Fish population genetics and molecular markers: I- Molecular markers and their applications in fisheries and aquaculture. Turkish J Fish Aqua Sci 2:145–155Google Scholar
  8. 8.
    Okumus I, Ciftci Y (2003) Fish population genetics and molecular markers: II- molecular markers and their applications in fisheries and aquaculture. Turkish J Fish Aqua Sci 3:51–79Google Scholar
  9. 9.
    Mandal S, Jena JK, Singh RK, Mohindra V, Lakra WS, Deshmukhe G, Kumar R, Lal KK (2014) Genetic characterization of Silond catfish, Silonia silondia (Hamilton, 1822) inferred from two mitochondrial markers. Mitochondrial DNA. doi:10.3109/19401736.2014.928874 Google Scholar
  10. 10.
    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 255:1–29CrossRefGoogle Scholar
  11. 11.
    Liu ZJ, Cordes JF (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238:1–37CrossRefGoogle Scholar
  12. 12.
    Wright JM, Bentzen P (1994) Microsatellites: genetic markers for the future. Fish Biol Fisheries 4:384–388CrossRefGoogle Scholar
  13. 13.
    Abdul-Muneer PM (2014) Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies. Genet Res Int. doi:10.1155/2014/691759 PubMedPubMedCentralGoogle Scholar
  14. 14.
    Nazia AK, Siti Azizah MN (2014) Isolation of microsatellites in the bighead catfish, Clarias macrocephalus and cross-amplification in selected Clarias species. Mol Biol Rep 41:1207–1213CrossRefPubMedGoogle Scholar
  15. 15.
    Gupta A, Lal KK, Punia P, Singh RK, Mohindra V, Sah RS, Kumar R, Luhariya RK, Dwivedi AK, Masih P, Mishra RM, Jena JK (2013) Characterization of polymorphic microsatellite markers and genetic diversity in wild bronze featherback, Notopterus notopterus (Pallas, 1769). Mol Biol Rep 40:6625–6631CrossRefPubMedGoogle Scholar
  16. 16.
    Libungan LA, Olafsdottir G, Skirnisdottir S, Palsson S, Pampoulie C, Bjornsdottir SH, Olafsson K, Oskarsson GJ, Danielsdottir AK (2012) Fourteen new microsatellite markers for Atlantic herring Clupea harengus. J Fish Biol 81:1422–1426CrossRefPubMedGoogle Scholar
  17. 17.
    Liu X, Luo W, Zeng C, Wang W, Gao Z (2011) Isolation of new 40 microsatellite markers in Mandarin fish (Siniperca chuatsi). Int J Mol Sci 12:4180–4189CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Masih P, Luhariya RK, Das R, Gupta A, Mohindra V, Singh RK, Srivastava R, Chauhan UK, Lal KK, Jena JK (2014) Cross-priming of microsatellite loci in subfamily cyprininae (family Cyprinidae): their utility in finding markers for population genetic analysis in three Indian major carps. Mol Biol Rep 41:5187–5197CrossRefPubMedGoogle Scholar
  19. 19.
    Bloor PA, Barker FS, Watts PC, Noyes HA, Kemp SJ (2001) Microsatellite libraries by enrichment. Protocol Accessed 12 Dec 2012
  20. 20.
    Ruzzante DE, Taggart C, Cook D, Goddard S (1996) Genetic differentiation between inshore and offshore Atlantic cod (Gadus morhua) off Newfoundland: microsatellite DNA variation and antifreeze level. Can J Fish Aquat Sci 53:634–645CrossRefGoogle Scholar
  21. 21.
    Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  23. 23.
    Belkhir K, Borsa P, Goudet J, Chikhi L, Bonhomme F (1997) GENETIX version 4.02, Genetics logiciel sous windows pour Ia ge’ ne’ Tique des populations. Accessed 14 July 2015
  24. 24.
    Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106CrossRefPubMedGoogle Scholar
  25. 25.
    Raymond M, Russet F (1998) GENEPOP Version 3.3d population genetics software for exact test and ecumenicism. Accessed 15 July 2015
  26. 26.
    Rousset F, Raymond M (1995) Testing heterozygote excess and deficiency. Genetics 140:1413–1419PubMedPubMedCentralGoogle Scholar
  27. 27.
    Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225CrossRefGoogle Scholar
  28. 28.
    Wright S (1978) Evolution and the genetics of populations. Variability within and among natural populations, vol 4. University of Chicago Press, ChicagoGoogle Scholar
  29. 29.
    Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1359–1370CrossRefGoogle Scholar
  30. 30.
    Slatkin M (1985) Rare alleles as indicators of gene flow. Evolution 39:53–65CrossRefGoogle Scholar
  31. 31.
    Wright S (1965) The interpretation of population structure by F statistics with special regard to systems of mating. Evolution 19:395–420CrossRefGoogle Scholar
  32. 32.
    Vrijenhoek RC (1998) Conservation genetics of freshwater fish. J Fish Biol 53(Supplement A): 394–412Google Scholar
  33. 33.
    Singh RK, Lal KK, Mohindra V, Punia P, Sah RS, Kumar R, Gupta A, Das R, Lakra WS, Ayyappan S (2012) Genetic diversity of Indian major carp, Labeo calbasu (Hamilton, 1822) populations inferred from microsatellite loci. Biochem Syst Ecol 44:307–316CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.National Bureau of Fish Genetic ResourcesLucknowIndia
  2. 2.Central Institute of Fisheries EducationMumbaiIndia
  3. 3.Network of Aquaculture Centres in Asia–PacificBangkokThailand

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