Evaluation of Genetic Variation and Phylogenetic Relationship among North Indian Cattle Breeds

Sharma, Rekha;Pandey, A.K.;Singh, Y.;Prakash, B.;Mishra, B.P.;Kathiravan, P.;Singh, P.K.;Singh, G.

  • Received : 2007.01.20
  • Accepted : 2008.03.20
  • Published : 2009.01.01


In the present study, genetic analyses of diversity and differentiation were performed on four breeds of Indian zebu cattle (Bos indicus). In total, 181 animals belonging to Ponwar, Kherigarh, Gangatiri and Kenkatha breeds were genotyped for 20 cattle specific microsatellite markers. Mean number of alleles observed per locus (MNA) varied between 5.75 (Kenkatha) to 6.05 (Kherigarh). The observed and expected heterozygosity for the breeds varied from 0.48 (Gangatiri) to 0.58 (Kherigarh) and 0.65 (Kenkatha) to 0.70 (Kherigarh), respectively. $F_{IS}$ estimates of all the breeds indicated significant deficit of heterozygotes being 28.8%, 25.9%, 17.7% and 17.7% for Gangatiri, Ponwar, Kherigarh and Kenkatha, respectively. The $F_{ST}$ estimates demonstrated that 10.6% was the average genetic differentiation among the breeds. Nei's genetic distance DA and Cavalli- Sforza and Edwards Chord distance ($D_C$) and the phylogenetic tree constructed from these reflected the close genetic relationship of Gangatiri and Kenkatha, whereas Ponwar appears to be more distant.


Cattle;Genetic Variation;India;Microsatellite


  1. Felsenstein, J. 1993. PHYLIP: Phylogeny inference package. Version 3.5p, Department of Genetics, University of Washington, Seattle,WA
  2. Mukesh, M., M. Sodhi, S. Bhatia and B. P. Mishra. 2004. Genetic diversity of Indian native cattle breeds as analyzed with 20 microsatellites. J. Anim. Breed. Genet. 121:416-424
  3. Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genet. 89:583-590
  4. Weir, B. S. and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evol. 38:1358-1370
  5. Pritchard, J. K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genet. 155:945-959
  6. Barker, J. S. F. 1999. Conservation of livestock breed diversity. AGRI. 25:33-43
  7. Blott, S. C., J. L. Williams and C. S. Haley. 1998. Genetic variation within the Hereford breed of cattle. Anim. Genet. 29:202-211
  8. Naveen Kumar, S., C. S. Nagaraja, M. G. Govindaiah, S. M. Saravanan and K. Karthickeyan. 2006. Molecular characterization of hallikar breed of cattle using microsatellite markers. Asian-Aust. J. Anim. Sci. 19:622-626
  9. MacHugh, D. E., R. T. Loftus, P. Cunningham and D. G. Bradley. 1998. Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers. Anim. Genet. 29:333-340
  10. Nei, M. 1976. Mathematical models of speciation and genetic distance. In: Population genetics and ecology (Ed. S. Karlin and E. Nevo). pp. 723-766. Academic press, New York
  11. Yeh, Francis C., R-C Yang, B. J. Boyle Timothy, Z-H Ye and Judy X. Mao. 1999. POPGENE version 1.32, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada. (
  12. Acharya, R. M. and P. N. Bhat. 1984. Livestock and poultry genetic resources of India. IVRI, Research Bulletin No. 1, Indian Veterinary Research Institute, Izatnagar, U.P. India
  13. Bradley, D. G., D. G. Mac Hugh, R. T. Loftus, R. S. Sow, C. H. Hoste and E. P. Cunningham. 1994. Zebu-taurine variation in Y chromosome DNA: a sensitive assay for introgression in West African trypnotolerant cattle populations. Anim. Genet. 25:7-12
  14. Goldstein, D. V., A. Ruiz-Linares, L. L. Cavalla-Sforza and M. W. Heldman. 1995. Genetic absolute dating based on the origin of modern humans. Proc. Natl. Acad. Sci. USA. 92:6723-6727
  15. Cavalli-Sforza, L. L. and A. W. F. Edwards. 1967. Phylogenetic analysis models and estimation procedure. Am. J. Human Genet. 19:233-257
  16. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, NewYork
  17. Schmid, M., N. Saitbekova, C. Gaillard and G. Dolf. 1999. Genetic diversity in Swiss cattle breeds. J. Anim. Breed. Genet. 116:1-8
  18. Barker, J. S. F., S. S. Moore, D. J. S. Hetzel, D. Evans, S. G. Tan and K. Byrne. 1997. Genetic diversity of Asian water buffalo (Bubalis bubalis): microsatellite variation and a comparison with protein coding loci. Anim. Genet. 28:103-115
  19. Shriver, M. D., L. Jin, E. Boerwinkle, R. Deka, R. E. Ferrell and R. Chakraborty. 1995. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Genet. 12:914-920
  20. Kantanen, J., I. Olsaker, L. E. Holm, S. Lian, J. Vilkki, K. Brusgaard, E. Eythorsdottir, B. Danell and S. Adalsteinsson. 2000. Genetic diversity and population structure of 20 North European cattle breeds. J. Hered. 91:446-457
  21. Takazaki, N. and M. Nei. 1996 Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genet. 144:389-399
  22. Dieringer, D. and C. Schlotterer. 2003. MICROSATELLITE ANANLYZER (MSA): A platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3:167-169
  23. Livestock Census. 2003. Ministry of Statistics and Programme Implementation, Govt. of India
  24. Nei, M. 1983. Genetic polymorphism and the role of nutrition in evolution. In: Evolution of genes and proteins (Ed. M. Nei and R. Koehn). pp. 165-190. Sunderland, MA: Sinauer Associates
  25. Page, R. D. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12:357-358
  26. Sodhi, M., M. Mukesh, B. P. Mishra, K. R. Mitkari, B. Prakash and S. P. S. Ahlawat. 2005. Evaluation of Genetic differentiation in Bos indicus cattle breeds from Marathwada region of India using microsatellite polymorphism. Anim. Biotech. 16:127-137
  27. Maniatis, T., J. Sambrook and E. F. Fritish. 1982. Molecular cloning: A laboratory manual. 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
  28. Pandey, A. K., R. Sharma, Y. Singh, B. Prakash and S. P. S. Ahlawat. 2006. Evaluation of genetic variability in kenkatha cattle by microsatellite markers. Asian-Aust. J. Anim. Sci. 19:1685-1690
  29. Edwards, C., G. Dolf, C. Looft, R. Loftus and D. Bradley. 2000. Relationship between the endangered Pustertaler-Sprinzen and three related European cattle breeds as analyzed with 20 microsatellite loci. Anim. Genet. 31:329-332
  30. Crawford, A. M. and R. P. Cuthbertson. 1996. Mutations in sheep microsatellites. Genome Res. 6:876-879
  31. Bassam, B. J., G. Coetano-Anolles and P. M. Gresshoff. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196:80-83
  32. Goudet, J. 1995. FSTAT (version1.2): A computer programme to calculate F-statistics. J. Hered. 86:485-486

Cited by

  1. Effect of SNP origin on analyses of genetic diversity in cattle vol.50, pp.8, 2010,
  2. Detection of occurrence of a recent genetic bottleneck event in Indian hill cattle breed Bargur using microsatellite markers vol.44, pp.8, 2012,
  3. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers vol.16, pp.1, 2015,
  4. Genetic diversity and relationship of cattle populations of East India: distinguishing lesser known cattle populations and established breeds based on STR markers vol.2, pp.1, 2013,


Supported by : Indian Council of Agricultural Research