Microsatellite based genetic variation among the buffalo breed populations in Pakistan

Open access


Introduction: Eight microsatellite loci were used to define genetic diversity among five native water buffalo breeds in Pakistan.

Material and Methods: Blood samples (10 mL) from 25 buffaloes of each of the Nili, Ravi, Nili-Ravi, Kundhi, and Azi-Kheli breeds were collected aseptically from the jugular vein into 50 ml Falcon tubes containing 200 μl of 0.5 M EDTA. The phenol-chloroform method was used to extract DNA and the regions were amplified for microsatellite analysis. The eight microsatellite markers ETH10, INRA005, ILSTS029, ILSTS033, ILSTS049, ILSTS052, ETH225, and CSSM66 were analysed.

Results: The effective number of alleles across all loci was as usual lower than the observed values with a mean value of 2.52 alleles per locus. The overall allele frequency varied from 0.0041 for alleles B, I, and J over respective loci ILSTS052, INRA005, and ILSTS029 to 0.80 for allele H over locus ILSTS029. The average observed and expected heterozygosity values across all polymorphic loci in all studied buffalo breeds were 0.43 and 0.53, respectively. The overall value for polymorphic information content of considered microsatellite markers was 0.53, suggesting their appropriateness for genetic diversity analysis in buffalo. The mean Fis value was 0.13 and all loci except ILSTS049 were found significantly deviated from HWE, most likely due to non-random breeding. The five buffalo populations were genetically less diverse as indicated by a small mean Fst value (0.07). The average gene flow (Nm) indicative for population migration was calculated as 3.31. Nei’s original measures of genetic distance (Ds) revealed ancient divergence of the Nili and Azi-Kheli breeds (Ds = 0.1747) and recent divergence of the Nili and Ravi breeds (Ds = 0.0374).

Conclusion: These estimates of genetic diversity were seen to coincide with phenotypic differentiation among the studied buffalo breeds. The present study reports the first microsatellite marker-based genetic diversity analysis in Pakistani buffalo breeds, and might facilitate similar studies in other livestock breeds of Pakistan.

If the inline PDF is not rendering correctly, you can download the PDF file here.

  • 1. Abbas G.: Phylogenetic relationship among buffalo breeds of Pakistan using RAPD analysis. MSc Thesis. Depart. Anim. Breed. Genet. Univ. Agri. Faisalabad Pakistan 2007.

  • 2. Arora R. Lakhchaura P.R.B. Tantia M.S. Vijh R.K.: Genetic diversity analysis of two buffalo populations of northern India using microsatellite markers. J Anim Breed Genet 2004 121 111–118.

  • 3. Babar M.E. Imran M. Nawaz M. Benkel B.F. Farid H. Jabeen R. Abdullah M. Javed M. Javed M.: Genetic identification of three Pakistani buffalo breeds through a homozygosity pattern in the PRKAG3 gene. Pak J Zool 2008 40 409–415.

  • 4. Barker J.S.F. Moore S.S. Hetzel D.J.S. Evans D. Tan S.G. Byrne K.: Genetic diversity of Asian water buffalo (Bubalus bubalis): microsatellite variation and a comparison with protein-coding loci. Anim Genet 1997 28 103–115.

  • 5. Botstein D. White R.L. Skolnick M. Davis R.W.: Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 1980 32 314–331.

  • 6. Bruford M.W. Bradley D.G. Luikart G.: DNA markers reveal the complexity of livestock domestication. Nature Rev Genet 2003 4 900–910.

  • 7. Cañón J. García D. García-Atance M.A. Obexer-Ruff G. Lenstra J.A. Ajmone-Marsan P. Dunner S.: Geographical partitioning of goat diversity in Europe and the Middle East. Anim Genet 2006 37 327–334.

  • 8. Consortium E.C.G.D.: Marker-assisted conservation of European cattle breeds: an evaluation. Anim Genet 2006 37 475–481.

  • 9. Crawford A.M. Cuthbertson R.P.: Mutations in sheep microsatellites. Genome Res 1996 6 876–879.

  • 10. Elbeltagy A.R. Galal S. Abdelsalam A.Z. El-Keraby F.E. Blasi M. Mohamed M.M.: Biodiversity in Mediterranean buffalo using two microsatellite multiplexes. Livest Sci 2008 114 341–346.

  • 11. FAO: Animal production and health guidelines. Molecular genetic characterization of Animal Genetic Resources. Commission on Genetic Resources for Food and Agriculture Food and Agriculture Organization of the United Nations. Rome Italy 2011.

  • 12. GOP: GEconomic Survey 2006–2007. Economic Affairs Division Government of Pakistan Isalamabad 2007.

  • 13. GOP: Economic Survey 2007–2008. Economic Affairs Division Government of Pakistan Isalamabad 2008.

  • 14. Hillel J. Groenen M.A.M. Tixier-Boichard M. Korol A.B. David L. Kirzhner V.M. Burke T. Barre-Dirie A. Crooijmans R.P.M.A. Elo K. Feldman M.W. Freidlin P.J. Mäki-Tanila A Oortwijn M. Thomson P. Vignal A. Wimmers K. Weigend S.: Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet Sel Evol 2003 35 533–357.

  • 15. Kathiravan P. Mishra B.P. Kataria R.S. Sadana D.K.: Evaluation of genetic architecture and mutation drift equilibrium of Marathwada buffalo population in Central India. Livest Sci 2008 5 13–17.

  • 16. Khan M.S. Ahmad N. Khan M.A.: Genetic resources and diversity in dairy buffaloes of Pakistan. Pak Vet J 2007 27 201–207.

  • 17. Kimura M. Crow J.F.: The number of alleles that can be maintained in a finite population. Genetics 1964 49 725–738.

  • 18. Kumar S. Gupta J. Kumar N. Dikshit K. Navani N. Jain P. Nagarajan M.: Genetic variation and relationships among eight Indian riverine buffalo breeds. Mol Ecol 2006 15 593–600.

  • 19. Levene H.: On a matching problem in genetics. Ann Math Stat 1949 20 91–94.

  • 20. Lindgren G. Backström N. Swinburne J. Hellborg L. Einarsson A. Sandberg K. Cothran G. Vilà C. Binns M. Ellegren H.: Limited number of patrilines in horse domestication. Nature Genet 2004 36 335–336.

  • 21. Manly B.F.J.: The statistics of natural selection on animal populations. Chapman and Hall London 1985.

  • 22. Michelizzi V.N. Dodson M.V. Pan Z. Amaral M.E.J. Michal J.J. McLean D.J. Womack J.E. Jiang Z.: Water buffalo genome science comes of age. Int Biol Sci 2010 6 333–349.

  • 23. Mishra B.P. Kataria R.S. Bulandi S.S. Prakash B. Kathiravan P. Mukesh M. Sadana D.K.: Riverine status and genetic structure of Chilika buffalo of eastern India as inferred from cytogenetic and molecular marker-based analysis. J Anim Breed Genet 2009 126 69–79.

  • 24. Moioli B. Georgoudis A. Napolitano F. Catillo G. Giubilei E. Lgda C. Hassanane M.: Genetic diversity between Italian Greek and Egyptian buffalo populations. Live Prod Sci 2001 70 203–211.

  • 25. Mukesh M. Sodhi M. Bhatia S. Mishra B.P.: Genetic diversity of Indian native cattle breeds as analyzed with 20 microsatellite loci. J Anim Breed Genet 2004 121 416–424.

  • 26. Nei M.: Genetic distance between populations. Amer Nat 1972 106 283–292.

  • 27. Nei M.: Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U.S.A 1973 70 3321–3323.

  • 28. Nei M.: Mathematical models of speciation and genetic distance. In: Population Genetics and Ecology. Edited by Karlin S. Nevo E. Academic Press New York 1976 pp. 723–766.

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

  • 30. Peter C. Bruford M. Perez T. Dalamitra S. Hewitt G. Erhardt G.: Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds. Anim Genet 2007 38 37–44.

  • 31. Sajid I.A.: Molecular genetic variation among Nili Ravi and Nili-Ravi buffalo breeds. MSc Thesis. Dept. Anim. Breed. Genet. Univ. Agri. Faisalabad Pakistan 2005.

  • 32. Sambrook J. Russell D.W.: Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press Cold Spring Harbor New York 2001.

  • 33. SanCristobal M. Chevalet C. Haley C.S. Joosten R. Rattink A.P. Harlizius B. Groen M.A.M Amigues Y. Boscher M.Y. Russell G. Law A. Davoli R. Russo V. Désautés A. Fimland E. Bagga M. Delgado J.V. Vega-Pla J.L. Martinez A.M. Ramos M. Glodek P. Meyer J.N. Gandini G.C. Matassino D. Plastow G.S. Siggens K.W. Laval G. Archibald A.L. Milan D. Hammond K. Cardellino R.: Genetic diversity within and between European pig breeds using microsatellite markers. Anim Genet 2006 37 189–198.

  • 34. Toro M.A. Fernández J. Caballero J.: Molecular characterization of breeds and its use in conservation. Livest Sci 2009 120 174–195.

  • 35. Weir B.S.: Inferences about linkage disequilibrium. Biometrics 1979 35 235–254.

  • 36. Yeh F. Boyle C. Rongcai T. Ye Z.Y. Xian J.M.: A Microsoft window based free ware for population genetic analysis. University of Alberta Edmonton (available at: http://www.ualberta.ca/~fyeh/). 1999.

  • 37. Zhang Y. Sun D. Yu Y. Zhang Y.: Genetic diversity and differentiation of Chinese domestic buffalo based on 30 microsatellite markers. Anim Genet 2007 38 569–575.

Journal information
Impact Factor

IMPACT FACTOR J Vet Res 2018: 0.829
5-year IMPACT FACTOR: 0.938

CiteScore 2018: 0.68

SCImago Journal Rank (SJR) 2018: 0.291
Source Normalized Impact per Paper (SNIP) 2018: 0.501

Cited By
All Time Past Year Past 30 Days
Abstract Views 0 0 0
Full Text Views 489 264 3
PDF Downloads 244 146 2