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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

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

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.

References

This article includes 52 references
  1. Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo MC, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt HJ, Torroni A. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication.. Proc Natl Acad Sci U S A 2012 Feb 14;109(7):2449-54.
    doi: 10.1073/pnas.1111637109pmc: PMC3289334pubmed: 22308342google scholar: lookup
  2. Amjadi MA, Yeganeh HM, Sadeghi M, Abbas Raza SH, Yang J, Najafabadi HA, Batool U, Shoorei H, Abdelnour SA, Ahmed JZ. Microsatellite Analysis of Genetic Diversity and Population Structure of the Iranian Kurdish Horse.. J Equine Vet Sci 2021 Mar;98:103358.
    doi: 10.1016/j.jevs.2020.103358pubmed: 33663714google scholar: lookup
  3. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. Sequence and organization of the human mitochondrial genome.. Nature 1981 Apr 9;290(5806):457-65.
    doi: 10.1038/290457a0pubmed: 7219534google scholar: lookup
  4. Ankel-Simons F, Cummins JM. Misconceptions about mitochondria and mammalian fertilization: implications for theories on human evolution.. Proc Natl Acad Sci U S A 1996 Nov 26;93(24):13859-63.
    doi: 10.1073/PNAS.93.24.13859pmc: PMC19448pubmed: 8943026google scholar: lookup
  5. Bigi D, Perrotta G, Zambonelli P. Genetic analysis of seven Italian horse breeds based on mitochondrial DNA D-loop variation.. Anim Genet 2014 Aug;45(4):593-5.
    doi: 10.1111/age.12156pubmed: 24702170google scholar: lookup
  6. Bjørnstad G, Røed KH. Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses.. Anim Genet 2002 Aug;33(4):264-70.
    doi: 10.1046/j.1365-2052.2002.00868.xpubmed: 12139505google scholar: lookup
  7. Cai DW, Han L, Xie CZ, Li SN, Zhou H, Zhu H. Mitochondrial DNA analysis of Bronge age horses recovered from Chifeng region, Inner Mongolia, China. Progress in National Science 17, 544–550.
    doi: 10.1080/10020070708541034google scholar: lookup
  8. Cai DW, Tang Z, Han L, Speller CF, Yang DY, Ma X, Cao J, Zhu H, Zhou H. Ancient DNA provides new insights into the origin of the Chinese domestic horse. Journal of Archaeological Science 36, 835–842.
    doi: 10.1016/j.jas.2008.11.006google scholar: lookup
  9. Cardinali I, Lancioni H, Giontella A, Capodiferro MR, Capomaccio S, Buttazzoni L, Biggio GP, Cherchi R, Albertini E, Olivieri A, Cappelli K, Achilli A, Silvestrelli M. An Overview of Ten Italian Horse Breeds through Mitochondrial DNA.. PLoS One 2016;11(4):e0153004.
    doi: 10.1371/journal.pone.0153004pmc: PMC4824442pubmed: 27054850google scholar: lookup
  10. Chang DD, Clayton DA. Priming of human mitochondrial DNA replication occurs at the light-strand promoter.. Proc Natl Acad Sci U S A 1985 Jan;82(2):351-5.
    doi: 10.1073/pnas.82.2.351pmc: PMC397036pubmed: 2982153google scholar: lookup
  11. Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A. Origin and history of mitochondrial DNA lineages in domestic horses.. PLoS One 2010 Dec 20;5(12):e15311.
    doi: 10.1371/journal.pone.0015311pmc: PMC3004868pubmed: 21187961google scholar: lookup
  12. Cothran EG, Juras R, Macijauskiene V. Mitochondrial DNA D‐loop sequence variation among 5 maternal lines of the Zemaitukai horse breed. Genetics and Molecular Biology 28, 677–681.
    doi: 10.1590/S1415-47572005000500006google scholar: lookup
  13. Cummins JM, Wakayama T, Yanagimachi R. Fate of microinjected sperm components in the mouse oocyte and embryo.. Zygote 1997 Nov;5(4):301-8.
    doi: 10.1017/S0967199400003889pubmed: 9563678google scholar: lookup
  14. Devi KM, Ghosh SK. Molecular phylogeny of Indian horse breeds with special reference to Manipuri pony based on mitochondrial D-loop.. Mol Biol Rep 2013 Oct;40(10):5861-7.
    doi: 10.1007/s11033-013-2692-2pubmed: 24068432google scholar: lookup
  15. Fu YX, Li WH. Statistical tests of neutrality of mutations.. Genetics 1993 Mar;133(3):693-709.
    doi: 10.5336/biostatic.2016-53446pmc: PMC1205353pubmed: 8454210google scholar: lookup
  16. Glazewska I. Speculations on the origin of the Arabian horse breed. Livestock Science 129, 49–55.
    doi: 10.1016/j.livsci.2009.12.009google scholar: lookup
  17. Gupta A, Bhardwaj A, Supriya Sharma P, Pal Y, Mamta Kumar S. Mitochondrial DNA—A tool for phylogenetic and biodiversity search in equines. Biodiversity and Endangered Species 1.
    doi: 10.4172/2332-2543.S1-006google scholar: lookup
  18. Hall TA. BIOEDIT: A user friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series 41, 95–98.
  19. Hudson W. Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines.. PLoS One 2017;12(8):e0184309.
    doi: 10.1371/journal.pone.0184309pmc: PMC5578668pubmed: 28859174google scholar: lookup
  20. Ianella P, Albuquerque MSM, Paiva SR, Egito AA, Almeida LD, Sereno FTPS, Carvalho LFR, Mariante AS, McManus CM. D-loop haplotype diversity in Brazilian horse breeds.. Genet Mol Biol 2017 Jul-Sep;40(3):604-609.
    doi: 10.1590/1678-4685-GMB-2016-0166pmc: PMC5596364pubmed: 28863209google scholar: lookup
  21. Ishida N, Hasegawa T, Takeda K, Sakagami M, Onishi A, Inumaru S, Komatsu M, Mukoyama H. Polymorphic sequence in the D-loop region of equine mitochondrial DNA.. Anim Genet 1994 Aug;25(4):215-21.
    doi: 10.1111/j.1365-2052.1994.tb00196.xpubmed: 7985837google scholar: lookup
  22. Ivankovic A, Ramljak J, Konjacic M, Kelava N, Dovc P, Mijic P. Mitochondrial D‐loop sequence variation among autochthonous horse breeds in Croatia. Czech Journal of Animal Science 54, 101–111.
    doi: 10.17221/1678-CJASgoogle scholar: lookup
  23. Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C, Weber J, Olek K. Mitochondrial DNA and the origins of the domestic horse.. Proc Natl Acad Sci U S A 2002 Aug 6;99(16):10905-10.
    doi: 10.1073/pnas.152330099pmc: PMC125071pubmed: 12130666google scholar: lookup
  24. Jiang Q, Wei Y, Huang Y, Jiang H, Guo Y, Lan G, Liao J. The complete mitochondrial genome and phylogenetic analysis of the Debao pony (Equus caballus).. Mol Biol Rep 2011 Jan;38(1):593-9.
    doi: 10.1007/s11033-010-0145-8pubmed: 20390359google scholar: lookup
  25. Jimenez LM, Mendez S, Dunner S, Cañón J, Cortés O. Colombian Creole horse breeds: Same origin but different diversity.. Genet Mol Biol 2012 Dec;35(4):790-6.
    doi: 10.1590/S1415-47572012005000064pmc: PMC3526087pubmed: 23271940google scholar: lookup
  26. Kavar T, Habe F, Brem G, Dovc P. Mitochondrial D-loop sequence variation among the 16 maternal lines of the Lipizzan horse breed.. Anim Genet 1999 Dec;30(6):423-30.
    doi: 10.1046/j.1365-2052.1999.00557.xpubmed: 10612231google scholar: lookup
  27. Kim KI, Yang YH, Lee SS, Park C, Ma R, Bouzat JL, Lewin HA. Phylogenetic relationships of Cheju horses to other horse breeds as determined by mtDNA D-loop sequence polymorphism.. Anim Genet 1999 Apr;30(2):102-8.
    doi: 10.1046/j.1365-2052.1999.00419.xpubmed: 10376300google scholar: lookup
  28. Lei CZ, Su R, Bower MA, Edwards CJ, Wang XB, Weining S, Liu L, Xie WM, Li F, Liu RY, Zhang YS, Zhang CM, Chen H. Multiple maternal origins of native modern and ancient horse populations in China.. Anim Genet 2009 Dec;40(6):933-44.
    doi: 10.1111/j.1365-2052.2009.01950.xpubmed: 19744143google scholar: lookup
  29. Lippold S, Matzke NJ, Reissmann M, Hofreiter M. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.. BMC Evol Biol 2011 Nov 14;11:328.
    doi: 10.1186/1471-2148-11-328pmc: PMC3247663pubmed: 22082251google scholar: lookup
  30. Lister AM, Kadwell M, Kaagan LM, Jordan WC, Richards MB, Stanley HF. Ancient and modern DNA in study of horse domestication. Ancient Biomolecules 2, 267–280.
  31. Liu G, Xu CQ, Cao Q, Zimmermann W, Songer M, Zhao SS, Li K, Hu DF. Mitochondrial and pedigree analysis in Przewalski's horse populations: implications for genetic management and reintroductions.. Mitochondrial DNA 2014 Aug;25(4):313-8.
    doi: 10.3109/19401736.2013.800487pubmed: 23808923google scholar: lookup
  32. Luis C, Bastos-Silveira C, Cothran EG, Oom MM. Variation in the mitochondrial control region sequence between the two maternal lines of the Sorraia horse breed. Genetics and Molecular Biology 25, 309–311.
  33. Luís C, Bastos-Silveira C, Cothran EG, Oom Mdo M. Iberian origins of New World horse breeds.. J Hered 2006 Mar-Apr;97(2):107-13.
    doi: 10.1093/jhered/esj020pubmed: 16489143google scholar: lookup
  34. MacHugh DE, Loftus RT, Cunningham P, Bradley DG. Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers.. Anim Genet 1998 Oct;29(5):333-40.
    doi: 10.1046/j.1365-2052.1998.295330.xpubmed: 9800321google scholar: lookup
  35. McGahern A, Bower MA, Edwards CJ, Brophy PO, Sulimova G, Zakharov I, Vizuete-Forster M, Levine M, Li S, MacHugh DE, Hill EW. Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populations.. Anim Genet 2006 Oct;37(5):494-7.
    doi: 10.1111/j.1365-2052.2006.01495.xpubmed: 16978180google scholar: lookup
  36. Miller KW, Dawson JL, Hagelberg E. A concordance of nucleotide substitutions in the first and second hypervariable segments of the human mtDNA control region.. Int J Legal Med 1996;109(3):107-13.
    doi: 10.1007/BF01369668pubmed: 8956982google scholar: lookup
  37. Moridi M. Analysis and study of Mt‐DNA in Iranian native horses. MSc thesis, Tarbiat Modares University, Tehran, Iran.
  38. Moridi M, Masoudi AA, Vaez Torshizi R, Hill EW. Mitochondrial DNA D-loop sequence variation in maternal lineages of Iranian native horses.. Anim Genet 2013 Apr;44(2):209-13.
    doi: 10.1111/j.1365-2052.2012.02389.xpubmed: 22732008google scholar: lookup
  39. Parkanyi V, Ondruska L, Vasicek D, Slamecka J. Multilevel D-loop PCR identification of hunting game.. Appl Transl Genom 2014 Mar 1;3(1):1-7.
    doi: 10.1016/j.atg.201pmc: PMC4881763pubmed: 27275406google scholar: lookup
  40. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods.. Bioinformatics 2003 Dec 12;19(18):2496-7.
    doi: 10.1093/bioinformatics/btg359pubmed: 14668244google scholar: lookup
  41. Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates.. Mol Phylogenet Evol 1999 Jul;12(2):105-14.
    doi: 10.1006/mpev.1998.0602pubmed: 10381314google scholar: lookup
  42. Sziszkosz N, Mihók S, Jávor A, Kusza S. Genetic diversity of the Hungarian Gidran horse in two mitochondrial DNA markers.. PeerJ 2016;4:e1894.
    doi: 10.7717/peerj.1894pmc: PMC4860319pubmed: 27168959google scholar: lookup
  43. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.. Genetics 1989 Nov;123(3):585-95.
    pmc: PMC1203831pubmed: 2513255doi: 10.1093/genetics/123.3.585google scholar: lookup
  44. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.. Mol Biol Evol 2013 Dec;30(12):2725-9.
    doi: 10.1093/molbev/mst197pmc: PMC3840312pubmed: 24132122google scholar: lookup
  45. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.. Nucleic Acids Res 1994 Nov 11;22(22):4673-80.
    doi: 10.1093/nar/22.22.4673pmc: PMC308517pubmed: 7984417google scholar: lookup
  46. Toro MA, Barragán C, Ovilo C. Estimation of genetic variability of the founder population in a conservation scheme using microsatellites.. Anim Genet 2003 Jun;34(3):226-8.
    doi: 10.1046/j.1365-2052.2003.00988.xpubmed: 12755825google scholar: lookup
  47. Upholt WB, Dawid IB. Mapping of mitochondrial DNA of individual sheep and goats: rapid evolution in the D loop region.. Cell 1977 Jul;11(3):571-83.
    doi: 10.1016/0092-8674(77)90075-7pubmed: 884736google scholar: lookup
  48. Vilà C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H. Widespread origins of domestic horse lineages.. Science 2001 Jan 19;291(5503):474-7.
    doi: 10.1126/science.291.5503.474pubmed: 11161199google scholar: lookup
  49. Xiao X, Yang S, Lin D, Wang Y, Hua Y. The complete mitochondrial genome and phylogenetic analysis of Chinese Jianchang horse (Equus caballus). Cloning and Transgenesis 5(149), 2.
    doi: 10.4172/2168-9849.1000149google scholar: lookup
  50. Xu X, Arnason U. The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region.. Gene 1994 Oct 21;148(2):357-62.
    doi: 10.1016/0378-1119(94)90713-7pubmed: 7958969google scholar: lookup
  51. Yang YH, Kim KI, Cothran EG, Flannery AR. Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism.. Biochem Genet 2002 Jun;40(5-6):175-86.
    doi: 10.1023/a:1015884125507pubmed: 12137332google scholar: lookup
  52. Zhang T, Lu H, Chen C, Jiang H, Wu S. Genetic Diversity of mtDNA D-loop and Maternal Origin of Three Chinese Native Horse Breeds.. Asian-Australas J Anim Sci 2012 Jul;25(7):921-6.
    doi: 10.5713/ajas.2011.11483pmc: PMC4092969pubmed: 25049645google scholar: lookup

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    doi: 10.1038/s41598-025-29107-xpubmed: 41423464google scholar: lookup
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    doi: 10.1371/journal.pone.0328633pubmed: 40700428google scholar: lookup
  3. Agbani A, Aminou O, Machmoum M, Germot A, Badaoui B, Petit D, Piro M. A Systematic Literature Review of Mitochondrial DNA Analysis for Horse Genetic Diversity. Animals (Basel) 2025 Mar 20;15(6).
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