Skip to main content

Advertisement

SpringerLink
Log in

Comparative Assessment of Genetic Variability in the Populations of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma (Teleostei: Horabagridae), Based on Allozyme, RAPD, and Microsatellite Markers

  • Published:
Biochemical Genetics Aims and scope Submit manuscript

Abstract

The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F ST values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F ST/G ST, AMOVA, Nei’s genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Abdul Muneer PM (2006) Molecular genetic characterization of endemic yellow catfish, Horabagrus brachysoma (Gunther). Ph.D. Thesis, Cochin University of Science and Technology, Cochin, p 225

  • Abdul Muneer PM, Gopalakrishnan A, Basheer VS, Lakra WS (2008) Identification of RAPD markers in endemic yellow catfish, Horabagrus brachysoma (Gunther, 1864). Asian Fish Sci 21:293–304

    Google Scholar 

  • Abdul Muneer PM, Gopalakrishnan A, Sivanandan R, Basheer VS, Ponniah AG (2011a) Genetic variation and phylogenetic relationships between two species of yellow catfish, Horabagrus brachysoma and H. nigricollaris using RAPD and microsatellite markers. Mol Biol Rep 38(4):2225–2232

    Article  PubMed  CAS  Google Scholar 

  • Abdul Muneer PM, Sivanandan R, Gopalakrishnan A, Basheer VS, Musammilu KK, Ponniah AG (2011b) Identification and characterization of RAPD and microsatellite markers for genetic variation analysis in critically endangered yellow catfish, Horabagrus nigricollaris. Biochem Genet 49(1):83–95

    Article  PubMed  CAS  Google Scholar 

  • Appleyard SA, Mather PB (2002) Genetic characterization of cultured tilapia in Fiji using allozymes and random amplified polymorphic DNA. Asian Fish Sci 15:249–264

    Google Scholar 

  • Belkhir K, Borsa P, Goudet J, Chikhi L, Bonhomme F (1997) Genetix logicielsous Windows pour Ia ge’ne’tique des populations. http://www.univ-montp2.fr/~gentix/genetix/html

  • Bindu L (2006) Captive breeding protocols of two potential cultivable fishes, Etroplus suratensis (Bloch) and Horabagrus brachysoma (Gunther) endemic to the Western Ghat region, Kerala. Ph.D. Thesis, Mahatma Gandhi University, Kottayam, India, Cochin University of Science and Technology, Cochin, p 215

  • Cagigas ME, Vazquez E, Blanco G, Sanchez JA (1999) Combined assessment of genetic variability in populations of brown trout (Salmo trutta L.) based on allozymes, microsatellites and RAPD markers. Mar Biotechnol 1:286–296

    Article  PubMed  CAS  Google Scholar 

  • Callejas C, Ochando MD (2002) Phylogenetic relationships among Spanish Barbus species (Pisces, Cyprinidae) shown by RAPD. Heredity 89:36–43

    Article  PubMed  CAS  Google Scholar 

  • CAMP (1998) Conservation Assessment and Management Plan (CAMP) for freshwater fishes of India 1997. Zoo Outreach Organization/National Bureau of Fish Genetic Resources (NBFGR), Coimbatore/Lucknow, p 156

    Google Scholar 

  • Chaturvedi A, Mohindra V, Singh RK, Lal KK, Punia P, Bhaskar R, Mandal A, Narain L, Lakra WS (2011) Population genetic structure and phylogeography of cyprinid fish, Labeo dero (Hamilton, 1822) inferred from allozyme and microsatellite DNA marker analysis. Mol Biol Rep 38(5):3513–3529

    Article  PubMed  CAS  Google Scholar 

  • Chong LK, Tan SG, Yusoff K, Siraj SS (2000) Identification and characterization of Malaysian River catfish Mystus nemurus (C and V) by RAPD and AFLP analysis. Biochem Genet 38:63–76

    Article  PubMed  CAS  Google Scholar 

  • Cook BD, Bunn SE, Hughes JM (2002) Genetic structure and dispersal of Macrobrachium australiense (Decapoda: Palaemonidae) in Western Queensland, Australia. Freshw Biol 47(11):2098–2112

    Article  CAS  Google Scholar 

  • Donnelly MJ, Cuamba N, Charlwood JD, Collins FH, Townson H (1999) Population structure in the malaria vector, Anopheles arabiensis Patton, in East Africa. Heredity 83:408–417

    Article  PubMed  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    PubMed  CAS  Google Scholar 

  • Galbusera P, Volckaert F, Hellemans BA, Ollevier F (1996) Isolation and characterisation of microsatellite markers in the African catfish Clarias gariepinus (Burchell, 1822). Mol Ecol 5:703–705

    Article  PubMed  CAS  Google Scholar 

  • Gibbs HL, Prior KA, Weatherhead PJ, Johnson G (1997) Genetic structure of populations of the threatened eastern massasuaga rattlesnake, Sistrurus catenatus: evidence from microsatellite DNA markers. Mol Ecol 6:1123–1132

    Article  PubMed  CAS  Google Scholar 

  • Gopalakrishnan A, Abdul Muneer PM, Lal KK, Mohindra V, Kapoor D, Ponniah AG (2006a) Primers from the orders Siluriform and Osteoglossiform detect polymorphic microsatellite loci in sun-catfish, Horabagrus brachysoma. J Appl Ichthyol 22:456–458

    Article  CAS  Google Scholar 

  • Gopalakrishnan A, Abdul Muneer PM, Thomas PC, Lal KK, Mohindra V, Kapoor D, Ponniah AG (2006b) Identification of allozyme markers for population structure analysis in yellow catfish, Horabagrus brachysoma (Gunther, 1864). Indian J Fish 53(3):253–261

    Google Scholar 

  • Haniffa MA, Nagarajan M, Gopalakrishnan A, Musammilu KK (2007) Allozyme variation in a threatened freshwater fish, spotted murrel (Channa punctatus) in a South Indian River System. Biochem Genet 45:363–374

    Article  PubMed  CAS  Google Scholar 

  • Khoo G, Lim KF, Gan DKY, Chen F, Chan WK, Lim TM et al (2002) Genetic diversity within and among feral populations and domesticated strains of the guppy (Poecilia reticulata) in Singapore. Mar Biotechnol 4:367–378

    Article  PubMed  CAS  Google Scholar 

  • Klinbunga S, Boonyapakdee A, Pratoomchat B (2000) Genetic diversity and species-diagnostic markers of mud crabs (Genus Scylla) in Eastern Thailand determined by RAPD analysis. Mar Biotechnol 2:180–187

    PubMed  CAS  Google Scholar 

  • Kovacs B, Egedi S, Bartfai R, Orban L (2001) Male specific DNA markers from African catfish (Clarias gariepinus). Genetica 110:267–276

    Article  Google Scholar 

  • Lal KK, Kumar D, Srivastava SK, Mukherjee A, Mohindra V, Prakash S et al (2004) Genetic variation in Tenualosa ilisha (Hamilton-Buchnan) population in river Ganges. Indian J Fish 51(1):33–42

    Google Scholar 

  • Lessios HA (1992) Testing electrophoretic data for agreement with Hardy-Weinberg expectations. Marine Biol 112:517–523

    Article  Google Scholar 

  • Liao X, Yu X, Tong J (2006) Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers. Hydrobiologia 568:445–453

    Article  CAS  Google Scholar 

  • Liu ZJ, Li P, Argue B, Dunham R (1998) Inheritance of RAPD markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus) and their F1, F2 and backcross hybrids. Anim Genet 29:58–62

    Article  CAS  Google Scholar 

  • Ma H, Chen S (2011). Development of polymorphic microsatellite markers in barfin flounder (Verasper moseri) and spotted halibut (Verasper variegatus) by the cross-species amplification. Mol Biol Rep 38(7):4545–4551

    Article  PubMed  CAS  Google Scholar 

  • Mandal A, Lal KK, Mohindra V, Singh RK, Punia P, Chauhan UK et al. (2009) Evaluation of genetic variation in the clown knifefish, Chitala chitala, using allozymes, RAPD, and microsatellites. Biochem Genet 47(3–4):216–234

    Article  PubMed  CAS  Google Scholar 

  • Markert C, Moller F (1959) Multiple forms of enzymes: tissue, ontogenic and species specific patterns. Proc Natl Acad Sci USA 45:753–763

    Article  PubMed  CAS  Google Scholar 

  • McCormack GP, Keegan BF (2000) Comparative analysis of three populations of the Brittle star Amphiura filiformis (Echinodermata: Ophiuroides) with different life history strategies using RAPD markers. Mar Biotechnol 2:100–106

    PubMed  CAS  Google Scholar 

  • Menon AGK (1999) Check list, freshwater fishes of India. Rec Zool Surv India, Occas

  • Nagarajan M, Haniffa MA, Gopalakrishnan A, Basheer VS, Abdul Muneer PM (2006) Genetic variability of Channa punctatus popultions using randomly amplified polymorphic DNA. Aquacult Res 37:1151–1155

    Article  CAS  Google Scholar 

  • Na-Nakorn U, Taniguchi N, Nugroho E, Seki S, Kamonrat W (1999) Isolation and characterization of microsatellite loci of Clarias macrocephalus and their application to genetic diversity study. Fish Sci 65(4):520–526

    CAS  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    PubMed  CAS  Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

    Article  PubMed  CAS  Google Scholar 

  • Nevo E, Belles A, Shlomo RB (1984) The evolutionary significance of genetic diversity: ecological, demographic and life history correlates. In: Mani GS (ed) Evolutionary dynamics of genetic diversity. Springer, New York, pp 18–137

    Google Scholar 

  • Piel WH, Nutt KJ (2000) One species or several? Discordant patterns of geographic variation between allozymes and mtDNA sequences among spiders in the genus Metepiera (Araneae: Araneidae). Mol Phylogenet Evol 53:414

    Article  Google Scholar 

  • Ponniah AG, Gopalakrishnan A (2000) Endemic fish diversity of the Western Ghats. NBFGR NATP Publication 1. National Bureau of Fish Genetic Resources, Lucknow, p 347

    Google Scholar 

  • Pouyaud L, Teugels GG, Gustiano R, Legendre M (2000) Contribution to the phylogeny of pangasiid catfish (Siluriformes, Pangasiidae) based on allozymes and mitochondrial DNA. J Fish Biol 56:1509–1538

    Article  CAS  Google Scholar 

  • Raymond M, Rousset F (1998) Genepop (version 3.1): a population genetics software for exact test and ecumenicism. J Hered 86:248–249

    Google Scholar 

  • Rognon X, Teugels G, Guyomard R, Andramanga M, Volckaert F, Agnèse JF (1998) Morphometric and allozyme variation in the African catfishes, Clarias gariepinus and C. anguillaris. J Fish Biol 53:192–207

    CAS  Google Scholar 

  • Saini A, Dua A, Mohindra V, Lakra WS (2010) Molecular discrimination of six species of Bagrid catfishes from Indus river system using randomly amplified polymorphic DNA markers. Mol Biol Rep. doi: 10.1007/s11033-010-9960-1

  • Salini JP, Milton DA, Rahman MJ, Hussain MG (2004) Allozyme and morphological variation throughout the geographic range of the tropical shad, hilsa Tenualosa ilisha. Fish Res 66(1):53–69

    Article  Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2000) Arlequin: a software for population genetics data analysis, version 2.0. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Switzerland

    Google Scholar 

  • Scribner KT, Gust JR, Fields RL (1996) Isolation and characterization of novel salmon microsatellite loci: cross-species amplification and population genetic applications. Can J Fish Aquat Sci 53:833–841

    Article  CAS  Google Scholar 

  • Sen S, Skaria R, Abdul Muneer PM (2010) Genetic diversity analysis in Piper species (Piperaceae) using RAPD markers. Mol Biotech 46(1):72–79

    Article  CAS  Google Scholar 

  • Shaklee JB, Allendorf FW, Morizot DC, Whitt GS (1990) Gene nomenclature for protein-coding loci in fish. Trans Am Fish Soc 119:2–15

    Article  CAS  Google Scholar 

  • Shaw CR, Prasad R (1970) Starch gel electrophoresis of enzymes: a compilation of recipes. Biochem Genet 4:297–320

    Article  PubMed  CAS  Google Scholar 

  • Singh RK, Chauhan T, Mohindra V, Kapoor D, Punia P, Lal KK (2004) Identification of allozyme markers for population structure analysis in Cirrhinus mrigala (Hamilton-Buchanan, 1882). Indian J Fish 51(1):117–122

    Google Scholar 

  • Singh RK, Lal KK, Mohindra V, Punia P, Sah RS, Mishra AK, Kumar R, Mishra BN, Lakra WS (2010) Assessing genetic differentiation in geographic populations of Labeo calbasu using allozyme markers. Biochem Genet 48:760–778

    Article  PubMed  CAS  Google Scholar 

  • Sneath PH, Sokal RR (1973) Numerical taxonomy. W.H. Freeman and Co., San Francisco, p 573

    Google Scholar 

  • Sreeraj N, Rajeev R, Prasad G (2006) The diet of Horabagrus brachysoma, an endangered bagrid catfish from Lake Vembanad (S. India). J Fish Biol 69:637–642

    Article  Google Scholar 

  • Sullivan JP, Lundberg JG, Hardman M (2006) A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences. Mol Phylogenet Evol 41:636–662

    Article  PubMed  CAS  Google Scholar 

  • Sun G, Díaz O, Salomon B, Bothmer R (1999) Genetic diversity in Elymus caninus as revealed by isozyme, RAPD, and microsatellite markers. Genome 42(3):420–431

    PubMed  CAS  Google Scholar 

  • Taggart JB, Hynes RA, Prodohl PA, Ferguson A (1992) A simplified protocol for routine total DNA isolation from salmonid fishes. J Fish Biol 40:963–965

    Article  CAS  Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471

    Article  PubMed  CAS  Google Scholar 

  • Usmani S, Tan SG, Siraj SS, Yusoff K (2001) Isolation and characterisation of microsatellites in the Southeast Asian River catfish Mystus nemurus. Mol Ecol Notes 1:264–266

    Article  CAS  Google Scholar 

  • Usmani S, Tan SG, Siraj SS, Yusoff K (2003) Population structure of the southeast catfish, Mystus nemurus. Anim Genet 34:462–464

    Article  PubMed  CAS  Google Scholar 

  • Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Microchecker: software for identifying and correcting genotying errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  Google Scholar 

  • Van Oosterhout C, Weetman D, Hutchinson WF (2006) Estimation and adjustment of microsatellite null alleles in non equilibrium populations. Mol Ecol Notes 6:255–256

    Article  Google Scholar 

  • Volckaert FAM, Helleman BAS, Poyaud L (1999) Nine polymorphic microsatellite markers in the Southeast Asian catfishes Pangasius hypophthalmus and Clarias batrachus. Anim Genet 30:383

    Article  CAS  Google Scholar 

  • Watanabe K, Watanabe T, Nishida M (2001) Isolation and characterization of microsatellite loci from the endangered bagrid catfish, Pseudobagrus ichikawai. Mol Ecol Notes 1:61–63

    Article  CAS  Google Scholar 

  • Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396

    PubMed  CAS  Google Scholar 

  • Weir BS, Cockerham C (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  • Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218

    Article  PubMed  CAS  Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Reafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    Article  PubMed  CAS  Google Scholar 

  • Wright S (1951) The genetical structure of populations. Ann Eugenet 15:324–354

    Google Scholar 

  • Wright S (1978) Evolution and the genetics of populations, vol. 4: variability within and among natural populations. University of Chicago Press, Chicago

    Google Scholar 

  • Yan J, Liu S, Sun Y, Zhang C, Luo K, Liu Y (2005) RAPD and microsatellite analysis of diploid gynogens from allotetraploid hybrids of red crucian carp (Carassius auratus) × common carp (Cyprinus carpio). Aquaculture 243:49–60

    Article  CAS  Google Scholar 

  • Yeh FC, Yang RC, Boyle T (1999) Popgene 32, version 1.31. Population genetics software. Hyperlink http://www.ualberta.ca/~fyeh/fyeh/

  • Zardoya R, Vollmer DM, Craddock C, Streelman JT, Karl S, Meyer A (1996) Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes). Proc Roy Soc London B 263:1589–1598

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Indian Council of Agricultural Research, National Agricultural Technology Project (ICAR-NATP), which supported this study financially, is gratefully acknowledged. The authors are grateful to Dr. S. P. Singh (PI, NATP, NBFGR) for encouragement, support, and guidance.

Author information

Author notes

  1. P. M. Abdul Muneer

    Present address: Neurovascular Oxidative Injury Laboratory, Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5215, USA

Authors and Affiliations

  1. National Bureau of Fish Genetic Resources (NBFGR) Cochin Unit, CMFRI Campus, Cochin, Kerala, 682018, India

    P. M. Abdul Muneer, A. Gopalakrishnan, K. K. Musammilu & V. S. Basheer

  2. NBFGR, Canal Ring Road, P.O. Dilkusha, Lucknow, UP, 226002, India

    V. Mohindra, K. K. Lal & A. G. Ponniah

  3. Regional Agricultural Research Station, Kumarakom, Kerala, 686563, India

    K. G. Padmakumar

Authors
  1. P. M. Abdul Muneer
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. Gopalakrishnan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. K. K. Musammilu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. V. S. Basheer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. V. Mohindra
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. K. K. Lal
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. K. G. Padmakumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. A. G. Ponniah
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to P. M. Abdul Muneer.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Abdul Muneer, P.M., Gopalakrishnan, A., Musammilu, K.K. et al. Comparative Assessment of Genetic Variability in the Populations of Endemic and Endangered Yellow Catfish, Horabagrus brachysoma (Teleostei: Horabagridae), Based on Allozyme, RAPD, and Microsatellite Markers. Biochem Genet 50, 192–212 (2012). https://doi.org/10.1007/s10528-011-9462-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10528-011-9462-4

Keywords

Search

Navigation