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Home / Equine Research Bank / Vet Med Sci / Mitochondrial DNA D-loop hyper-variable region 1 variab...
Veterinary medicine and science2022; 9(2); 721-728; doi: 10.1002/vms3.996

Mitochondrial DNA D-loop hyper-variable region 1 variability in Kurdish horse breed.

Abstract: Kurdish horse is one of the most valuable horse genetic resources in the Middle East. To assess the genetic diversity of Kurdish horses, Mitochondrial DNA D-loop hyper-variable region1 (HVR1) was sequenced in 29 non-related Kurdish horses which were sampled from diverse geographic regions of Iran. Total DNA was extracted from the collected blood samples by modified salting out method. The HVR1 was amplified by PCR and then sequenced using ABI PRISM BigDyeTM Terminator Cycle Sequencing Ready Reaction Kit. Consequently, the sequences were trimmed to 294 bp using BIOEDIT to become comparable with other reported HVR1 sequences in GeneBank. Sequence alignment was performed using CLUSTALW package. Haplotype and nucleotide diversity were estimated using DNASP5.10 and phylogenetic tree was constructed by neighbour joining method. Fourteen different haplotypes and 22 polymorphic sites were detected. Haplotype diversity, nucleotide diversity and Tajima D values were 0.901 ± 0.001, 0.01153 ± 0.0020 and -1.378, respectively. Kurdish horse showed a high haplotype and low nucleotide diversity. The compositional frequency of consensus sequences for base A was the highest (29.93%) compared to other three nucleotides (C = 28.91%, T = 26.53% and G = 14.63%). As expected, all of the detected Kurdish horse haplotypes belonged to haplogroup K (i.e., Kurdish horses). According to the phylogenetic analysis, Kurdish horses were genetically more closely related to Tibetan, Chinese, Bulgarian and Iranian native horse breeds, compared to other Asian horse breeds, but some traces of European horse breeds were detected in their maternal lines.
© 2022 The Authors. Veterinary Medicine and Science published by John Wiley & Sons Ltd.
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Publication Date: 2022-11-11 PubMed ID: 36367719PubMed Central: PMC10029883DOI: 10.1002/vms3.996Google Scholar: Lookup
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Summary

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The research article investigates the genetic diversity of the Kurdish horse, a valuable horse breed in the Middle East, using the mitochondrial DNA D-loop hyper-variable region1 (HVR1). The research findings show that the Kurdish horse has high haplotype and low nucleotide diversity, and is genetically closest to horses from Tibet, China, Bulgaria and Iran, with some genetic traces from European horse breeds.

DNA Extraction and Sequencing

  • The research began by obtaining DNA from collected blood samples of 29 non-related Kurdish horses found in different regions of Iran. This was done using a modified salting-out method.
  • The HVR1 region, a particularly variable section of the DNA, was then amplified through a Polymerase Chain Reaction (PCR), a technique used to make multiple copies of a specific DNA segment.
  • This amplified DNA was then sequenced with an ABI PRISM BigDyeTM Terminator Cycle Sequencing Ready Reaction Kit.

Data Analysis

  • The DNA sequences were trimmed to 294 base pairs to make them comparable with other reported HVR1 sequences in the GeneBank, a genetic sequence database.
  • Using sequence alignment and the CLUSTALW package, the researchers identified a total of 14 different haplotypes (unique sets of DNA variations) and 22 polymorphic sites (DNA locations where variation is common).
  • Haplotype and nucleotide diversity (difference in the genetic makeup) were calculated. The Kurdish horse showed high haplotype and low nucleotide diversity, with haplotype diversity values of 0.901 ± 0.001 and nucleotide diversity values of 0.01153 ± 0.0020.
  • These values signify that while there are many different haplotypes present, there is little variation at the individual nucleotide level.

Phylogenetic Analysis

  • A phylogenetic tree, a branching diagram showing the inferred evolutionary relationships among various biological species, was constructed using the neighbor-joining method.
  • All detected Kurdish horse haplotypes belonged to haplogroup K, indicative of their Kurdish origin.
  • The phylogenetic analysis revealed that the Kurdish horses were more genetically similar to horses from Tibet, China, Bulgaria, and Iranian native horse breeds as compared to other Asian horse breeds.
  • It is also noteworthy that some genetic traces from European horse breeds were detected in the Kurdish horses’ maternal lines.

Cite This Article

APA
Nikbakhsh M, Varkoohi S, Seyedabadi HR. (2022). Mitochondrial DNA D-loop hyper-variable region 1 variability in Kurdish horse breed. Vet Med Sci, 9(2), 721-728. https://doi.org/10.1002/vms3.996

Publication

Veterinary medicine and science
ISSN: 2053-1095
NlmUniqueID: 101678837
Country: England
Language: English
Volume: 9
Issue: 2
Pages: 721-728

Researcher Affiliations

Nikbakhsh, Milad
  • Department of Animal Science, College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran.
Varkoohi, Sheida
  • Department of Animal Science, College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran.
Seyedabadi, Hamid Reza
  • Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.

MeSH Terms

  • Horses / genetics
  • Animals
  • DNA, Mitochondrial / genetics
  • Phylogeny
  • Iran
  • Genetic Variation
  • Sequence Analysis, DNA / veterinary
  • Nucleotides

Conflict of Interest Statement

The authors declare no conflict of interest to be declared.

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