Application of molecular markers in fisheries and aquaculture


  • Ghasem Askari Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
  • Ali Shabani Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
  • Hamed Kolangi Miandare Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran


Genetic Diversity; Molecular Markers; Microsatellite; Aquaculture


Genetic variation in a species enhances the capability of organism to adapt to changing environment and is necessary for survival of the species. Genetic variation arises between individuals leading to differentiation at the level of population, species and higher order taxonomic groups. The genetic diversity data has varied application in research on evolution, conservation and management of natural resources and genetic improvement programmes, etc. Development of Molecular genetic markers has powerful ability to detect genetic studies of individuals, populations or species. These molecular markers combined with new statistical developments have revolutionized the analytical power, necessary to explore the genetic diversity.

Molecular markers and their statistical analysis revolutionized the analytical power, necessary to explore the genetic diversity. Various molecular markers, protein or DNA (mt-DNA or nuclear DNA such as microsatellites, SNP or RAPD) are now being used in fisheries and aquaculture. These markers provide various scientific observations which have importance in aquaculture practice recently such as: 1) Species Identification 2) Genetic variation and population structure study in natural populations 3) Comparison between wild and hatchery populations 4) Assessment of demographic bottleneck in natural population 5) Propagation assisted rehabilitation programmes. In this review article, we have concentrated on the basics of molecular genetics, overview of commonly used markers and their application along with their limitations (major classes of markers) in fisheries and aquaculture studies.


Fisher, R.A., 1930. The Genetical Theory of Natural Selection. Oxford University Press, UK.

Askari, Gh., Shabani, A., 2013. Genetic diversity evaluation of Paraschistura bampurensis (Nikolskii, 1900) in

Shapour and Berim rivers (Iran) using microsatellite markers. J. Cell Biol. Gen., 3, 29-34.

Avise, J.C., 1994. Molecular Markers, Natural History and Evolution. Chapman and Hall, New York, London.

Linda, K.P., Paul, M., 1995. Developments in molecular genetic techniques in fisheries. In: G.R. Carvalho and T.J.

Pitcher, Eds., Molecular Genetics in Fisheries, Chapman and hall, London, 1-28.

Hillis, D.M., Mable, B.K., Moritz, C., 1996. Applications of molecular systematics: The state of the field and a look to

the future. In: Hillis, D.M., Moritz, C. and Mable, B.K. Eds., Molecular systematics, Sinauer Associates,

Massachusetts, 515-543.

Ferguson, A., Taggart, J.B., Prodohl, P.A., McMeel, O., Thompson, C., Stone, C., McGinnity, P. and Hynes, R.A., 1995.

The application of molecular markers to the study and conservation of fish populations with special reference

to Salmo. J. Fish Biol., 47(A), 103-126.

Liu, Z.J., Cordes, J.F., 2004. DNA marker technologies and their applications in aquaculture genetics. Aquacul., 238,


O’Brien, S.J., 1991. Molecular genome mapping: lessons and prospects. Curr. Opin. Gen. Develop., 1(1), 105-111.

Brown, B., Epifanio, J., 2003. Nuclear DNA. In: Hallermann, E.M. Ed., Population Genetics: Principles and

Applications for Fisheries Scientists. American Fisheries Society, Bethesda, 458-472.

Suneetha, B.K., 2000. Interspecific and inter specific genetic variation in selected mesopelagic fishes with emphasis

on microgeographic variation and species characterization. Dr. Scient. Dissertation, Department of Fisheries

and Marine Biology, University of Bergen, Bergen, Norway.

Menezes, M.R., Naik, S., Martins, M., 1993. Genetic characterization in four sciaenid species from the Arabian

Sea. J. Fish Biol., 43(1), 61-67.

Markert, C.L., Moller, F., 1959. Multiple forms of enzymes: Tissue, ontogenetic and species-specific patterns

Proceedings of the Naionall Academy of Science (USA), 45(5), 753-763.

Starck, M.G., 1998. Isozymes in Molecular tools for screening biodiversity. In: Angela, K., Peter, G.I. and. David, S.I.

Eds., Chapmann and Hall, London, 75-80.

Murphy, R.W., Sites, J.J.W., Buth, D.G., Haufler, C.H., 1996. Proteins I: Isozyme electrophoresis. In: Hillis, D.M.,

Moritz, C. and Mable, B.K. Eds., Molecular Systematics, Sinauer Associates, Sunderland, 51-132.

Brown, W.M., 1985. The mitochondrial genome of animals. In: MacIntyre, R.J. Ed., Molecular Evolutionary

Genetics, Plenum, New York, 95-130.

Wilson, A.C., Cann, R.L., Carr, S.M., George, M., Gyllensten, U.B., Helm-Bychowski, K.M., Higuchi, R.G., Palumbi,

S.R., Prager, E.M., 1985. Mitochondrial DNA and two perspectives on evolutionary genetics. Biol. J. Linnean

Soci., 26(4), 375-400.

Birky, C.W., Fuerst, P., Maruyama, T., 1989. Organelle gene diversity under migration, mutation, and drift:

equilibrium expectations, approach to equilibrium, effect of heteroplasmic cells, and comparison to nuclear

genes. Genetics, 121(3), 613-627.

Meyer, A., 1993. Evolution of mitochondrial DNA in fishes. In: Mochachka, P.W. and Mommsen, T.P. Eds.,

Biochemistry and molecular biology of fishes, Elsevier Press Amsterdam, New York, 1-38.

Brown, J.R., Bechenbach, A.T., Smith, M.J., 1993. Intraspecific DNA sequence variation of the mitochondrial control

region of white sturgeon (Acipenser transmontanus). Molecul. Biol. Evo., 10(2), 326-341.

Chow, S., Okamoto, H., Uozumi, Y., Takeuchi, Y., Takeyama, H., 1997. Genetic stock structure of the swordfish

(Xiphias gladius) inferred by PCR-RFLP analysis of the mitochondrial DNA control region. Marine Biol., 127(3),


Gold, J.R. Sun, F., Richardson, L.R., 1997. Population structure of red snapper from the Gulf of Mexico as inferred

from analysis of mitochondrial DNA. Trans. Amer. Fish. Soci., 126(3), 386-396.

Chow, S., Kishino, H., 1995. Phylogenetic relationships between tuna species of the genus Thunnus (Scombriidae:

Teleosrei): Inconsistent implications from morphology, nuclear and mitochondrial genomes. J. Molecul. Evol.,

, 741-748.

Avise, J.C., Helfman, G.S., Saunders, N.C., Hales, L.S., 1986. Mitochondrial DNA differentiation in North Atlantic

eels: Population genetic consequences of an unusual life history pattern. Proceeding of the National Academy

Science (USA), 83(12), 4350-4354.

Heist, E.J., Gold, J.R., 1999. Microsatellite DNA variation in sandbar sharks (Carcharhinus plumbeus) from the Gulf

of Mexico and mid-Atlantic bight. Copeia, 1, 182-186.

Baker, A.J., Marshall, H.D., 1997. Molecular evolution of the mitochondrial genome. In: Mindell, D.P. Ed., Avian

Molecular Evolution and Systematics, Academic Press, San Diego, 51-82.

Zink, R.M., Barrowclough, G.F., Atwood, J.L. and Blackwell-Rago, R.C. (2000) Genetics, taxonomy, and conservation

of the threatened California gnatcatcher. Conservation Biology, 14(5), 1394-1405.

Menotti-Raymond, M., O’Brien, S.J., 1993. Dating the genetic bottleneck of the African cheetah. Proceedings of the

National Academy of Science (USA.), 90(8), 3172-3176.

Avise, J.C., Walker, D., Johns, G.C., 1998. Speciation durations and Pleistocene effects on vertebrate

phylogeography. Proceedings of the Royal Society of London Series B, 265(1407), 1707-1712.

Shanker, K., Ramadevi, J., Choudhaury, B.C., Singh, L., Aggarawal, R.K., 2004. Phylogeny of olive ridley turtles

(Lepidochelys olivacea) on the east coast of India: implications for conservation theory. Moelcular Ecology,

(7), 1899-1909.

Mamuris, Z., Sfougaris, A.I., Stamatis, C., Suchentrunk, F., 2002. Assessment of genetic structure of Greek Brown

Hare (Lepus europeaus) populations based on variation in Random Amplified Polymorphic DNA (RAPD).

Biochem. Gen., 40(9-10), 323- 338.

Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A., Tingey, S.V., 1990. DNA polymorphisms amplified by

arbitrary primers are useful as genetic markers. Nucleic Acids Res., 18(22), 6531-6535.

Welsh, J., McClelland, M., 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res.,

(24), 7213-7218.

Haymer, D.S., 1994. Random amplified polymorphic DNAs and microsatellites: What are they, and can they tell us

anything we don’t already know? Annal. Entomol. Soci. Ameri., 87, 717-722.

Wirgin, I.I., Waldman, J.R., 1994. What DNA can do for you? Fisheries, 19, 16-27.

Morin, P.A., Luikart, G., Wayne, R.K., 1994. The SNP working group, SNPs in ecology, evolution and conservation.

Trend. Ecol. Evol., 19(4), 208-216.

Liu, Z.J., Cordes, J.F., 2004. DNA marker technologies and their applications in aquaculture genetics. Aquacul., 238,


Hecker, K.H., Taylor, P.D., Gjerde, D.T., 1999. Mutation detection by denaturing DNA chromatography using

fluorescently labeled polymerase chain reaction products. Analy. Biochem., 272(2), 156-164.

Tautz, D., 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic

Acids Res., 17(16), 6463-6471.

Litt, M., Luty, J.A., 1989. A hypervariable microsatellite revealed by in-vitro amplification of dinucleotide repeat

within the cardiac muscle actin gene. Ameri. J. Human Gen., 44(3), 397-401.

Wright, J.M., 1993. DNA fingerprinting in fishes. In: W. Hochachka, P. and Mommsen, T. Eds., Biochemistry and

Molecular Biology of Fishes, Elsevier, Amsterdam, 58-91.

Liu, Z.J., Li, P., Kocabas, A., Ju, Z., Karsi, A., Cao, D., Patterson, A., 2001. Microsatellite-containing genes from the

channel catfish brain: evidence of trinucleotide repeat expansion in the coding region of nucleotide excision

repair gene RAD23B. Biochem. Biophy. Res. Communi., 289(2), 317-324.

Taylor, A.C., Sherwin, W.B., Wayne, R.K., 1994. Genetic variation of microsatellite loci in a bottlenecked species:

The northern hairy-nosed wombat Lasiorhinus krefftii. Molecul. Ecol., 3(4), 277-290.

Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde,

B., Moreno, R.F., Kerlavage, A.R., McCombie, W.R., Venter, J.C., 1991. Complementary DNA sequencing:

Expressed sequence tags and human genome project. Science, 252(5013), 1651-1656.

Wang, K., Gan, L., Jeffry, E., Gayle, M., Gown, A.M., Skelly, M., Nelson, P.S., Ng, W.V., Schummer, M., Hood, L.,

Mulligan, J., 1999. Monotoring gene expression profile changes in ovarian carcinomas using cDNA microarray.

Gene, 229(1-2), 101-108.

Boguski, M.S., Schuler, G.D., 1995. Establishing a human transcript map. Nature Gen., 10(4), 369-371.

Cox, D.R., Burmeister, M., Price, E., Kim, S., Myers, R.M., 1990. Radiation hybrid mapping: a somatic cell genetic

method for constructing high-resolution map of mammalian chromosomes. Science, 250(4978), 245-250.

Korwin-Kossakowska, A., Reed, K.M., Pelak, C., Krause, E., Morrison, L., Alexander, L.J., 2002. Radiation hybrid

mapping of 118 new porcine microsatellites. Anim. Gen., 33(3), 224-227.

McCoard, S.A., Fahrenkrug, S.C., Alexander, L.J., Freking, B.A., Rohrer, G.A., Wise, T.H., Ford, J.J., 2002. An

integrated comparative map of the porcine X chromosome. Anim. Gen., 33(3), 178-185.

Liu, Z.J., Karsi, A., Dunham, R.A., 1999. Development of polymorphic EST markers suitable for geneticlinkage

mapping of catfish. Marine Biotechnol., 1(5), 437-447.

Dobson, A.P., Rodriguez, J.P., Roberts, W.M., Wilcove, D.S., 1997. Geographic distribution of endangered species

in the United States. Science, 275(5299), 550-555.

Daugherty, C.H., Cree, A., Hay, J.M., Thompson, M.B., 1990. Neglected taxonomy and continuing extinctions of

tuatara (Sphenodon). Nature, 347(6289), 177- 179.

Moritz, C., 2002. Strategies to protect diversity and the evolutionary processes that sustain it. Systematic Biology,

(2), 238-254.

McKinney, M.L., 1999. High rates of extinction and threat in poorly studied taxa. Conservation Biology, 13(6),


Novotny, V., Basset, Y., Miller, S.E., Weiblen, G.D., Bremer, B., Cizek, L., Drozd, P., 2002. Low host specificity of

herbivorous insects in a tropical forest. Nature, 416, 841-844.

Hebert, P.D.N., Ratnasingham, S., deWaard, J.R., 2003. Barcoding animal life: Cytochrome c oxidase subunit 1

divergences among closely related species. Royal Society London, 270 (Suppl 1), S96-S99.

Hebert, P.D.N., Stoeckle, M.Y., Zemlak, T.S., Francis, C.M., 2004. Identification of birds through DNA barcodes. PLoS

Biol., 2(10), 312-316.



How to Cite

Askari, G. ., Shabani, A. ., & Kolangi Miandare, H. . (2013). Application of molecular markers in fisheries and aquaculture. Scientific Journal of Animal Science, 2(4), 82-88. Retrieved from



Review Article