Molecular biology reports2010; 38(5); 3505-3511; doi: 10.1007/s11033-010-0461-z

Genetic diversity and population structure of three Indian horse breeds.

Abstract: 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.
Publication Date: 2010-11-21 PubMed ID: 21104137DOI: 10.1007/s11033-010-0461-zGoogle Scholar: Lookup
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This research article examines the genetic diversity and population structure of Marwari, Spiti, and Kathiawari Indian horse breeds through genotyping, revealing findings of high allelic diversity, gene diversity, and inbreeding.

Genotyping and Allelic Diversity

  • A main method employed in the research involved the genotyping of 96 individual horses from the three breeds using 20 polymorphic microsatellite markers, which are DNA sequences that vary in the number of repetitions among individuals and are often used in genetic studies to evaluate genetic diversity and population structure.
  • The researchers discovered 157 unique alleles (variants of the same gene) encompassing 20 polymorphic loci (genetic locations); this data was instrumental in assessing the allelic diversity among the horse breeds.
  • The Marwari breed demonstrated the highest allelic diversity with an average of 5.7 (A) and 5.14 (Ar), followed by the Spiti (A = 4.9 and Ar = 4.74) and then the Kathiawari (A = 4.1 and Ar = 3.82). This suggests that the Marwari breed has the greatest genetic variability.

Gene Diversity and Inbreeding

  • Looking at gene diversity, the Spiti breed topped the list (He = 0.67), followed by Marwari (He = 0.66) and Kathiawari (He = 0.59). Higher He values indicate greater gene diversity, meaning Spiti horses have the most diverse genetic makeup among the three breeds examined.
  • Inbreeding levels within these breeds were found to be high—an undesirable characteristic as it could lead to an increase in harmful genetic conditions. In particular, the inbreeding estimates (referred to as ‘f’) were 0.18 for Marwari, 0.08 for Spiti, and 0.07 for Kathiawari, with Marwari being the most inbred breed.

Genetic Differentiation, Gene Flow and Conservation

  • Additional analyses such as pair-wise Fst analysis, Analysis of Molecular Variance (AMOVA) and assignment tests showcased high genetic differentiation and low gene flow between the horse populations, indicating significant genetic distinction between them.
  • Evidence of recent genetic bottlenecks were found in the Spiti and Kathiawari populations, suggesting these breeds have experienced significant reductions in population size recently that may decrease genetic diversity and adaptability.
  • The findings from this study provide valuable information regarding these Indian horse breeds and can guide future breeding management strategies to enhance their preservation.

Cite This Article

Chauhan M, Gupta AK, Dhillon S. (2010). Genetic diversity and population structure of three Indian horse breeds. Mol Biol Rep, 38(5), 3505-3511.


ISSN: 1573-4978
NlmUniqueID: 0403234
Country: Netherlands
Language: English
Volume: 38
Issue: 5
Pages: 3505-3511

Researcher Affiliations

Chauhan, Mamta
  • National Research Centre on Equines, Sirsa Road, Hisar, 125 001 Haryana, India.
Gupta, Ashok Kumar
    Dhillon, Santosh

      MeSH Terms

      • Alleles
      • Animals
      • Breeding
      • Cluster Analysis
      • Genetic Markers
      • Genetic Variation
      • Genetics, Population
      • Genotype
      • Horses / classification
      • Horses / genetics
      • India
      • Microsatellite Repeats
      • Phylogeny


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