Molecular Biology Reports

, Volume 38, Issue 5, pp 3505–3511 | Cite as

Genetic diversity and population structure of three Indian horse breeds

  • Mamta Chauhan
  • Ashok Kumar Gupta
  • Santosh Dhillon


The genetic relationships of three Indian horse breeds—Marwari, Spiti, and Kathiawari were studied by genotyping 96 individuals with 20 polymorphic microsatellite markers. A total of 157 alleles were detected across 20 polymorphic loci. The Marwari population showed the highest allelic diversity (A = 5.7 and Ar = 5.14), followed by Spiti (A = 4.9 and Ar = 4.74) and Kathiawari (A = 4.1 and Ar = 3.82). The gene diversity was highest in the Spiti population (He = 0.67), followed by Marwari (He = 0.66) and Kathiawari (He = 0.59). Within population inbreeding estimates (f) in Marwari, Spiti and Kathiawari breeds were 0.18, 0.08, and 0.07, respectively, suggesting high level of inbreeding in these breeds. Analysis of bottleneck revealed evidence of recent bottleneck in Spiti and Kathiawari populations. Pair-wise Fst analysis, AMOVA and assignment tests demonstrated high genetic differentiation and low gene flow between populations. The information about genetic diversity and population structure will be useful for the future development of effective breeding management in order to preserve these Indian horse breeds.


Horse Microsatellite Kathiawari Marwari Spiti Genotyping 


  1. 1.
    Gupta AK, Pal Yash (2010). Genetic resources of equines in India and their status. In Compendium: Equine Health and Production Management, held at NRCE, Hisar, p 103–106Google Scholar
  2. 2.
    Singh MK, Yadav MP, Mehta NT (2002) Characterization of Marwari and Kathiawari breed of horses. Ind J Anim Sci 72:366–370Google Scholar
  3. 3.
    Pundir RK (2003) Characterization of Spiti horses of India. AGRI 34:75–82Google Scholar
  4. 4.
    Behl R, Pundir RK, Behl J, Gupta N, Gupta SC, Singh G, Katoch S, Dogra PK, Ahlawat SPS (2005). Horse genetic resource of India—Spiti ponies (eds), Monograph 19, SPS Ahlawat, Director, NBAGR, Karnal, India., 1–16Google Scholar
  5. 5.
    Bhat PN, Bhat PP, Khan BU, Goswami OB, Singh B (1981) Animal genetic resources of India. National Dairy Research Institute Press, Karnal, India, pp 87–88Google Scholar
  6. 6.
    Singhvi NM (2001) Conservation and management of equines. Ind J Anim Genet Breed 23:292–295Google Scholar
  7. 7.
    Yadav MP, Ghei GC, Tandon SN (2001) Equine genetic resources in India and their conservation. Ind J Anim Genet Breed 23:296–301Google Scholar
  8. 8.
    Azor PJ, Valera M, Gomez MD, Goyache F, Molina A (2007) Genetic characterization of Spanish Trotter horse breed using microsatellite markers. Genet Mol Biol 30:37–42CrossRefGoogle Scholar
  9. 9.
    Bowling AT, Eggleston-Stott ML, Byrns G, Clark RS, Dileanis S, Wictum E (1997) Validation of microsatellite markers for routine horse parentage testing. Anim Genet 28:247–252PubMedCrossRefGoogle Scholar
  10. 10.
    Glowatzki-Mullis ML, Muntwyler J, Pfister W, Marti E, Rieder S, Poncet PA, Gaillard C (2006) Genetic diversity among horse populations with a special focus on the Franches-Montagnes breed. Anim Genet 37:33–39PubMedCrossRefGoogle Scholar
  11. 11.
    Marklund S, Ellegren H, Eriksson S, Sandberg K, Andersson L (1994) Parentage testing and linkage analysis in the horse using a set of highly polymorphic microsatellites. Anim Genet 25:19–23PubMedGoogle Scholar
  12. 12.
    Reis SP, Goncalves EC, Silva A, Schneider MPC (2008) Genetic variability and efficiency of DNA microsatellite markers for paternity testing in horse breeds from the Brazilian Marajo archipelago. Genet Mol Biol 31:68–72CrossRefGoogle Scholar
  13. 13.
    Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. A laboratory manual Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
  14. 14.
    Coogle L, Bailey E (1998) Equine dinucleotide repeat loci LEX064 through LEX070. Anim Genet 30:66–80Google Scholar
  15. 15.
    Eggleston-Stott ML, Valle AD, Bowling AT, Bautista M, Malyi W (1996) Four equine dinucleotide repeats at microsatellite loci UCDEQ5 UCDEQ14 UCDEQ46 and UCDEQ62. Anim Genet 27:129PubMedGoogle Scholar
  16. 16.
    Eggleston-Stott ML, Valle AD, Bautista M, Dileanis S, Wictum E, Bowling AT (1997) Nine equine dinucleotide repeats at microsatellite loci UCDEQ136 UCDEQ405 UCDEQ412 UCDEQ425 UCDEQ437 UCDEQ467 UCDEQ487 UCDEQ502 and UCDEQ505. Anim Genet 28:370–383PubMedCrossRefGoogle Scholar
  17. 17.
    Ellegren H, Johansson M, Sandberg K, Andersson L (1992) Cloning of highly polymorphic equine microsatellites in horse. Anim Genet 23:133–142PubMedCrossRefGoogle Scholar
  18. 18.
    Van Haeringen H, Bowling AT, Stott ML, Lenstra JA, Zwangstra KA (1994) A highly polymorphic horse microsatellite locus—VHL20. Anim Genet 25:207PubMedCrossRefGoogle Scholar
  19. 19.
    Van Haeringen WA, Van de Goor LHP, Van der Hout N, Lenstra JA (1998) Characterization of 24 equine microsatellite loci. Anim Genet 29:150–160CrossRefGoogle Scholar
  20. 20.
    Kakoi H, Tozaki T, Hirota K, Mashima S (1999) Genetic polymorphisms of equine microsatellite loci.TKY 16 TKY 19 and TKY 21. Anim Genet 30:68–69PubMedCrossRefGoogle Scholar
  21. 21.
    Lindgren G, Sandberg K, Persson H, Marklund S, Breen M, Sandgren B, Carlsten J, Ellegren H (1998) A primary male autosomal linkage map of the horse genome. Genome Res 8:951–966PubMedGoogle Scholar
  22. 22.
    Meyer AH, Valberg SJ, Hillers KR, Schweitzer JK, Mickelson JR (1997) Sixteen new polymorphic equine microsatellites. Anim Genet 28:58–71CrossRefGoogle Scholar
  23. 23.
    Swinburne JE, Marti E, Breen M, Binns MM (1997) Characterization of twelve new horse microsatellite loci: AHT12–AHT23. Anim Genet 28:453PubMedGoogle Scholar
  24. 24.
    Swinburne JE, Lockhart L, Aldridge V, Marti E, Breen M, Binns MM (2000) Characterisation of 25 new physically mapped horse microsatellite loci: AHT24++-48. Anim Genet 31:237–238PubMedGoogle Scholar
  25. 25.
    Bassam JB, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:82–83CrossRefGoogle Scholar
  26. 26.
    Lewis PO, Zaykin D (2000). Genetic data analysis:
  27. 27.
    Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinformatics 1:47–50Google Scholar
  28. 28.
    Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceed Nat Acad Sci USA 79:5269–5273CrossRefGoogle Scholar
  29. 29.
    Minch E (1996) Microsat, the microsatellite distance program:
  30. 30.
    Sneath PHA, Sokal RR (1973) Numerical Taxonomy. Freeman, San Francisco, CAGoogle Scholar
  31. 31.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  32. 32.
    Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genet Mol Biol 144:2001–2014Google Scholar
  33. 33.
    Behl R, Behl J, Gupta N, Gupta SC (2007) Genetic relationships of five Indian horse breeds using microsatellite markers. Anim 1:483–488CrossRefGoogle Scholar
  34. 34.
    Katoch S, Dogra PK, Thakur YP, Gupta K (2004) Phenotypic characterization of Spiti horse in its breeding tract—body measurements. Centaur 20:45–48Google Scholar
  35. 35.
    Gupta AK, Chauhan M, Tandon SN (2005) Genetic diversity and bottleneck studies in the Marwari horse breed. J Genet 84:295–301PubMedCrossRefGoogle Scholar
  36. 36.
    Koringa PG, Joshi CG, Solanki JV, Rank DN (2008) Genetic characterization and bottleneck studies in Kathiawari horse breed of India. Haryana Vet 47:77–83Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Mamta Chauhan
    • 1
  • Ashok Kumar Gupta
    • 1
  • Santosh Dhillon
    • 2
  1. 1.National Research Centre on EquinesHisarIndia
  2. 2.Department of Biotechnology & Molecular BiologyCCS HAUHisarIndia

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