Mitochondrial DNA Diversity of Wild and Hatchery Reared Strains of Indian Lates calcarifer (Bloch)

  • Prasanna Kumar
  • B. Akbar JohnEmail author
  • V. Kanagasabapathy


Lates calcarifer, locally known as seabass in Asia and barramundi in Australia, is a large, euryhaline member of the family Centropomidae that is widely distributed in the Indo-West Pacific region. Its hardy nature, high tolerance to wide range physiological condition and high commercial value has made it a good candidate species for aquaculture practices. In this study we compared the mtDNA diversity of hatchery reared and wild Lates calcarifer using universal DNA barcode gene (Cytochrome Oxidase C subunit 1 gene) to assess the genetic health of L. calcarifer hatchery practices in India. Sampling stations were randomly chosen to cover both East and West coasts of India. The phylogram constructed with COI sequences (n = 88) of L. calcarifer revealed that geographic distributions of clades are not restricted to any particular sampling stations. Gene flow appeared to have transported haplotypes between the clades from their likely origins across the sampled range. Both Nucleotide (π) and haplotyte (h) diversity of wild L. calcarifer was higher in East coast samples compared to West coast samples. The comparative genetic diversity analysis assessed through COI sequences between hatchery reared and wild catches of L. calcarifer showed that the nucleotide diversity of hatchery strains was 2.7 times lesser than that of wild strains, demanding immediate action plans to restore genetic diversity in L. calcarifer hatchery practices in India.


Lates calcarifer COI gene DNA barcoding Haplotype diversity Genetic diversity 



This work was partly supported by UGC fellowship. Our special thanks are due to the Dean of Centre of Advanced Studies in Marine Biology (CASMB), Annamalai University for his constant encouragement and University officials for providing the necessary facilities. Our special thanks to RGCA, Tamil Nadu and Takave farms, Maharastra for their helpfulness in sampling. We acknowledge the technical support extended by Priority Life Sciences, Coimbatore, India and Macrogen Inc., North Korea.


  1. Allendorf FW, Ryman N (1987) Genetic management of hatchery stocks. In: Ryman N, Utter F (eds) Population genetics and fisheries management. University of Washington Press, Seattle, pp 141–159Google Scholar
  2. Araki H, Schmid C (2010) Is hatchery stocking a help or harm? Evidence, limitations and future directions in ecological and genetic surveys. Aquaculture 308:S2–S11CrossRefGoogle Scholar
  3. Carr JW, Anderson JM, Whoriskey FG, Dilworth T (1997) The occurrence and spawning of cultured Atlantic salmon (Salmosalar) in a Canadian river. ICESJ Mar Sci 56:064–1073Google Scholar
  4. Chenoweth SF, Hughes JM, Keenan CP, Lavery S (1998) When Oceans meet: a teleost shows secondary intergradation at an India-Pacific interface. Proc R Soc Lond B 265:415–420CrossRefGoogle Scholar
  5. Cross T, Dillance E, Galvin P (2000) Which molecular markers should be chosen for different specific applications in fisheries and aquaculture? National University of Ireland.
  6. Crozier W (1993) Evidence of genetic interaction between escaped farmed salmon and wild Atlantic salmon (Salmosalar L.) in a Northern Irish river. Aquaculture 113:19–29CrossRefGoogle Scholar
  7. Doupe R, Recher H (1999) Gene pool management of hatchery Barramundi Lates calcarifer for production and stock augmentation programmes. Pac Conserv Biol 5:73–75CrossRefGoogle Scholar
  8. Doupe R, Horwitz P, Lymbery A (1999) Mitochondrial genealogy of western Australian barramundi: application of inbreeding coefficient coalescent analysis for separating temporal population process. Jr Fish Boil 54:1197–1209CrossRefGoogle Scholar
  9. FAO (2011) Asia-Pacific fishery commission—Report of the thirty-first session. RAP Publication 2010/14Google Scholar
  10. Ferguson MM, Ihssen PE, Hynes JD (1991) Are culture stocks of brown trout (Salmotruta) and rainbow trout (Oncorhynchusmykiss) genetically similar to their source populations? Can J Fish Aquat Sci 46:149–158Google Scholar
  11. Frost LA, Evans BS, Jerry DR (2006) Loss of genetic diversity due to hatchery culture practices in Barramundi (Lates calcarifer). Aquaculture 261:1056–1064CrossRefGoogle Scholar
  12. Grant WS, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89:415–426CrossRefGoogle Scholar
  13. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
  14. Hebert PDN, Cywinska A, Ball SL, Ward JR (2003) Biological identification through DNA barcode. Proc R Soc Lond B 270:313–321CrossRefGoogle Scholar
  15. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913PubMedCrossRefGoogle Scholar
  16. Hindar K, Ryman N, Utter F (1991) Genetic effects of cultured fish on natural fish populations. Can J Fish Aquat Sci 48:945–957CrossRefGoogle Scholar
  17. John BA, Kumar CP, Lyla PS, Khan AS, Jalal KCA (2010) DNA barcoding Lates calcarifer (Bloch 1970). Res J Biol Sci 5(6):414–419CrossRefGoogle Scholar
  18. Keenan CP (1994) Recent evolution of population-structure in Australian barramundi, Lates calcarifer (Bloch)—an example of isolation by distance in one-dimension. Aust J Mar Fresh Res 45:1123–1148CrossRefGoogle Scholar
  19. Khan S, Lyla PS, John BA, Kumar CP, Murugan S, Jalal KCA (2010) DNA barcoding of Stolephorus indicus, Stolephorus commersonnii and Terapon jarbua of Parangipettai coastal waters. Biotechnology 9(3):373–377CrossRefGoogle Scholar
  20. Kumar CP, John BA, Khan AS, Lyla PS, Murugan S, Rozihan M, Jalal KCA (2011) Efficiency of universal barcode gene (cox1) on morphologically cryptic Mugilidae fishes delineation. Tr Appl Sci Res 6(9):1028–1036CrossRefGoogle Scholar
  21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948PubMedCrossRefGoogle Scholar
  22. Lavery S, Moritz C, Fielder DR (1996) Indo-Pacific population structure and evolutionary history of the coconut crab Birguslatro. Molec Ecol 5:557–570CrossRefGoogle Scholar
  23. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452. doi: 10.1093/bioinformatics/btp187 PubMedCrossRefGoogle Scholar
  24. Liu ZJ, Li P, Argue BJ, Dunham RA (1999) Random amplified polymorphic DNA markers: usefulness for gene mapping and analysis of genetic variation of catfish. Aquaculture 174:59–68CrossRefGoogle Scholar
  25. Macbeth M, O’Brien L, Palmer P, Lewer R, Garrett R, Wingfield M, Knibb W (2002) Selective breeding in Barramundi: technical report for the Australian Barramundi Farmers Association, Department of Primary IndustriesGoogle Scholar
  26. Nei M, Jin L (1989) Variances of the average numbers of nucleotide substitutions within and between populations. Molec Biol Evol 6:290–300PubMedGoogle Scholar
  27. Nei M (1987) Evolutonary molecular genetics. University of Columbia Press, New YorkGoogle Scholar
  28. Pusey B, Kennardm M, Arthington A (2004) Freshwater fishes of North-Eastern Australia. CSIRO Publishing, CollingwoodGoogle Scholar
  29. Russell DJ, Garrett RN (1988) Movements of Juvenile Barramundi, Lates calcarifer (Bloch), in North-Eastern Queensland. Aust J Mar Freshwater Res 39:117–123CrossRefGoogle Scholar
  30. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Molec Biol Evol 4:406–425PubMedGoogle Scholar
  31. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mole Biol Evol 24:1596–1599CrossRefGoogle Scholar
  32. Tave D (1993) Genetics for fish hatchery managers. Van Nostr and Reinhold, New York, 415pGoogle Scholar
  33. Wang CM, Zhu ZY, Lo LC, Feng F, Lin G, Yang WT, Li J, Yue GH (2007) A microsatellite linkage map of Barramundi, Lates calcarifer. Genetics 175:907–915PubMedPubMedCentralCrossRefGoogle Scholar
  34. Ward RD, Holmes BH, Yearsley GK (2008) DNA barcoding reveals likely second species of Asian sea bass (Barramundi) (Lates calcarifer). J Fish Biol 72:458–463CrossRefGoogle Scholar
  35. Yue GH, Li Y, Chao TM, Chao R, Orban L (2002) Novel microsatellites from Asian seabass (Lates calcarifer) and their application to broodstock analysis. Mar Biotechnol 4:503–511PubMedCrossRefGoogle Scholar
  36. Zhu ZY, Lin G, LoL C, Xu YX, Renee C, Yue GH (2006) Genetic analyses of Asian seabass stocks using novel polymorphic microsatellites. Aquaculture 256:167–173CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Prasanna Kumar
    • 1
  • B. Akbar John
    • 2
    Email author
  • V. Kanagasabapathy
    • 3
    • 4
  1. 1.Centre of Advanced Study in Marine BiologyAnnamalai UniversityParangipettaiIndia
  2. 2.INOCEM Research Station (IRS), Kulliyyah of ScienceInternational Islamic University of MalaysiaKuantanMalaysia
  3. 3.Central Institute of Brackish Water Aquaculture (ICAR)ChennaiIndia
  4. 4.Unit of Live Feed Culture, Department of ZoologyUniversity of MadrasChennaiIndia

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