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Research (Published online: 12-08-2015)

5.  Microsatellite based genetic diversity study in indigenous chicken ecotypes of Karnataka - B. H. Rudresh, H. N. N. Murthy, M. R. Jayashankar, C. S. Nagaraj, A. M. Kotresh and S. M. Byregowda

Veterinary World, 8(8): 970-976



   doi: 10.14202/vetworld.2015.970-976


B. H. Rudresh: Department of Animal Genetics and Breeding, Veterinary College, Karnataka Veterinary, Animal and Fisheries Sciences University, Shimoga, Karnataka, India;

H. N. N. Murthy: Department of Livestock Production and Management, Veterinary College, Karnataka Veterinary, Animal and Fisheries Sciences University, Bangalore, Karnataka, India;

M. R. Jayashankar: Department of Animal Genetics and Breeding, Veterinary College, Karnataka Veterinary, Animal and Fisheries sciences University, Bangalore, Karnataka, India;

C. S. Nagaraj: All India Coordinated Research Project on Poultry Meat, Karnataka Veterinary, Animal and Fisheries Sciences University, Veterinary College, Bangalore, Karnataka, India;

A. M. Kotresh: Department of Veterinary Physiology and Biochemistry, Veterinary College, Karnataka Veterinary, Animal and Fisheries sciences University, Shimoga, Karnataka, India;

S. M. Byregowda: Institute of Animal Health & Veterinary Biologicals, Bangalore, Karnataka Veterinary, Animal and Fisheries Sciences University, Karnataka, India;


Received: 12-02-2015, Revised: 30-06-2015, Accepted: 08-07-2015, Published online: 12-08-2015


Corresponding author: B. H. Rudresh, e-mail:

Citation: Rudresh BH, Murthy HNN, Jayashankar MR, Nagaraj CS, Kotresh AM, Byregowda SM (2015) Microsatellite based genetic diversity study in indigenous chicken ecotypes of Karnataka, Veterinary World 8(8): 970-976.

Aim: The current study was the first of its kind taken upon indigenous ecotypes of the Karnataka in order to unravel the diversity details at 20 chicken microsatellite regions.

Materials and Methods: 210 indigenous chicken belonging to six districts of Bangalore and Mysore division formed the target sample for the present study. The genomic deoxyribonucleic acid was isolated by phenol chloroform isoamyl alcohol method. A panel of 20 microsatellite regions, including 14 recommended by FAO and six identified from published scientific literature became the targeted chicken genomic region. 27-33 samples were successfully genotyped in each of the six ecotypes through simplex or multiplex polymerase chain reactions, polyacrylamide gel electrophoresis and silver staining for the selected microsatellite panel.

Results: The chickens of Ramanagara and Chamrajnagara were most distant with a Nei’s genetic distance value of 0.22. The chickens of Bangalore rural and Mysore were least distant with a value of 0.056. The Ramanagara and Chamrajnagara pair had Nei’s genetic identity value of 0.802, which is least among all pairs of ecotypes. There were five main nodes from which the six ecotypes evolved on the basis 20 microsatellite markers used in this study. This study indicates that the four ecotypes Ramnagara, Bangalore Rural, Chickaballapura and Mysore are genetically identical due to their common ancestral evolution while, Mandya and Chamrajnagara ecotypes formed a relatively different cluster due to a separate common ancestral chicken population and less number of generations since drifting from bifurcation node.

Conclusion: Twenty microsatellite markers based genetic diversity study on six indigenous ecotypes indicated lower genetic distances as well as lower FST values compared to the distinguished breeds reported. There were two main clusters, which differentiated into six ecotypes. They may differentiate into more distinct varieties if bred in isolation for a longer number of generations.
Keywords: animal genetic resources, ecotypes, microsatellites, polyacrylamide gel.

1. Groeneveld, L.F., Lenstra, J.A., Eding, H., Toro, M.A., Scherf, B., Pilling, D., Negrini, R., Finlay, E.K., Jianlin, H., Groeneveld, E., Weigend, S. and The Globaldiv Consortium. (2010) Genetic diversity in livestock breeds – A review. Anim. Genet., 41 Suppl 1: 6-31.
2. Khosravinia, H., Narasimha Murthy, H.N., Therthaparasad, D. and Pirany, N. (2007) Optimizing factors influencing DNA extraction from fresh whole avian blood. Afr. J. Biotech., 6(4): 481-486.
3. Chang, C.S., Chen, C.F., Berthouly Salazar, C., Chazara, O., Lee, Y.P., Chang, C.M., Chang, K.H., Bedhom, B. and Tixier-Boichard, M. (2011) A global analysis of molecular marker and phenotypic traits in local chicken breeds in Taiwan. Anim. Genet., 43: 172-182.
4. Sangwon, S., Sharma, A., Lee, S., Cho, C.Y., Kim, J.H., Choi, S.B., Kim, H., Seong, H.H., Yeon, S.H., Kim, D.H. and Ko, Y.G. (2014) Genetic diversity and relationships of Korean chicken breeds based on 30 microsatellite markers. Asian Aust. J. Anim. Sci., 27(10): 1399-1405.
PMid:25178290 PMCid:PMC4150171
5. Choi, N.R., Hoque, R., Seo, D.W., Sultana, H., Park, H.B., Lim, H.T., Heo, K.N., Kang, B.S., Jo, C. and Lee, J.H. (2012) ISAG recommennded microsatellite marker analysis among five korean native chicken lines. J. Anim. Sci. Technol., 54(6): 401-409.
6. Eltanany, M., Philipp, U., Weigend, S. and Distl, O. (2011) Genetic diversity of ten Egyptian chicken strains using 29 microsatellite markers. Anim. Genet., 42: 666-669.
7. Halima, B., Jean-Marie, J., Jean-Pierre, B. and Guy, M. (2006) Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnol. Agron. Soc. Environ., 10(2): 77-81.
8. Barton, N.H. and Hewitt, G.M. (1985) Analysis of hybrid zones. Ann. Rev. Ecol. Syst., 16: 113-148.
9. Nei, M. (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89: 583-590.
PMid:17248844 PMCid:PMC1213855
10. Nei, M. (1987) Molecular Evolutionary Genetics. Columbia Press, New York.
11. Pirany, N., Romanov, M.N., Ganpule, S.P., Devegowda, G. and Prasad, D.T. (2007) Microsatellite analysis of genetic diversity in Indian chicken populations. J. Poult. Sci., 44: 19-28.
12. Balloux, F. and Lugon-Moulin, N. (2002) The estimation of population differentiation with microsatellite markers. Mol. Ecol., 11: 155-165.
13. Chatterjee, R.N., Niranjan, M., Sharma, R.P., Dange, M. and Bhattacharya, T.K. (2010) Estimation of genetic heterogeneity of chicken germplasm being used for development of rural varieties utilizing DNA markers. J. Genet., 89: e33-e37.
14. FAO. (2011) Molecular genetic characterization of animal genetic resources. Animal Production and Health Guidelines. No. 9. 14. FAO, Rome.
15. Hartl, D.L. and Clark, A.G. (1997) Principles of Population Genetics. 3rd ed. Sinauer Associates Inc., Sunderland, MA. p275-284.