FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Animals : an open access journal from MDPI2025; 15(6); 885; doi: 10.3390/ani15060885

A Systematic Literature Review of Mitochondrial DNA Analysis for Horse Genetic Diversity.

Abstract: This Systematic Literature Review (SLR) consolidates current research on mitochondrial DNA (mtDNA) analysis in horses, focusing on genetic variation, maternal lineage tracing, and haplogroup identification. The article selection process screened 1380 articles, with 76 fulfilling the inclusion criteria. Data extraction covered sampling techniques, studied mtDNA regions, sequencing methods, and haplogroup identification. Following the methodology of the PRISMA guidelines, this review encompasses studies published since 2012, obtained from Scopus, PubMed, Research4Life, Web of Science, and ScienceDirect. The major findings emphasise the use of mtDNA for tracing ancestry, validating maternal lineages, and identifying haplogroups along with their geographic distributions. This review identifies challenges, including the need to update the haplogroup classification system and potential information loss due to sequence trimming. Additionally, it examines promising avenues for future research, such as the implementation of next-generation sequencing and the merging of haplogroup data with performance traits, which could influence conservation initiatives and breeding programs. This review emphasises the necessity for standardised classification systems and further research on underrepresented breeds and regions to improve our understanding of equine genetic diversity.
Get Full Text
Publication Date: 2025-03-20 PubMed ID: 40150414PubMed Central: PMC11939364DOI: 10.3390/ani15060885Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article
  • Review

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.

This research consolidates current knowledge on using mitochondrial DNA (mtDNA) to explore the genetic diversity of horses. The major findings, based on systematic review of 76 selected articles, indicate that mtDNA can help uncover ancestry, validate maternal lines, and identify genetic groups, helping future research and breeding programs.

Research Methodology

  • The research is a Systematic Literature Review (SLR) that started with a pool of 1380 articles exploring mitochondrial DNA (mtDNA) analysis in horses.
  • Out of these, 76 articles met the required criteria for consideration and were included in the comprehensive review.
  • The SLR followed the PRISMA guidelines, a set of practices for conducting and reporting systematic reviews and meta-analyses.
  • All included research was published from the year 2012 onwards and sourced from databases such as Scopus, PubMed, Research4Life, Web of Science, and ScienceDirect.

Analysis Process

  • Data from the approved articles was extracted and categorized based on varied elements such as sampling techniques, explored mtDNA regions, methodologies of sequencing, and the identification of haplogroups.
  • Haplogroups are genetic groupings and are significant in understanding the origins and migratory patterns of species.

Major Findings

  • One of the key findings is that mtDNA can be effectively used in tracing ancestry and validating maternal lineage of horses. This has potential implications for breed identification, establishing breed purity, and understanding horse evolution.
  • Another major insight is that mtDNA can be used to identify haplogroups and understand their geographical distribution.
  • The use of mtDNA can provide a rich source of genetic information about the evolutionary history and adaptations of horses.

Challenges and Future Research

  • Despite its value, the study also highlights some challenges with using mtDNA. For example, the present classification system for haplogroups needs an update to accommodate new knowledge and variations.
  • The process of sequence trimming can lead to the potential loss of significant information, posing a methodological challenge.
  • Regarding future research, the paper signals promising areas such as the implementation of next-generation sequencing technologies which could improve accuracy and detail of genetic data.
  • It suggests a focus on the integration of haplogroup data with performance traits, which could have serious implications for horse conservation and breeding programs.
  • The paper also identifies the need for more studies on underrepresented horse breeds and regions to boost the comprehensiveness of existing genetic diversity databases.

Implications of the Study

  • The study emphasizes the need for standardizing classification systems to optimise the use of mtDNA in equine research.
  • It also encourages more intensive research on underrepresented horse breeds and regions to better grasp the genetic diversity and robustness of the species.
  • The systematic review provides a firm foundation for future research on horse genetic diversity, their evolutionary paths, and potential breeding and conservation initiatives.

Cite This Article

APA
Agbani A, Aminou O, Machmoum M, Germot A, Badaoui B, Petit D, Piro M. (2025). A Systematic Literature Review of Mitochondrial DNA Analysis for Horse Genetic Diversity. Animals (Basel), 15(6), 885. https://doi.org/10.3390/ani15060885

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 6
PII: 885

Researcher Affiliations

Agbani, Ayman
  • Laboratory of Veterinary Genetic Analysis, Department of Medicine, Surgery and Reproduction Agronomic, Veterinary Institute Hassan II Rabat, Rabat B.P. 6202, Morocco.
Aminou, Oumaima
  • Laboratory of Veterinary Genetic Analysis, Department of Medicine, Surgery and Reproduction Agronomic, Veterinary Institute Hassan II Rabat, Rabat B.P. 6202, Morocco.
Machmoum, Mohamed
  • Laboratory of Veterinary Genetic Analysis, Department of Medicine, Surgery and Reproduction Agronomic, Veterinary Institute Hassan II Rabat, Rabat B.P. 6202, Morocco.
Germot, Agnes
  • LABCiS, UR 22722, Faculty of Sciences and Technology, University of Limoges, F-87000 Limoges, France.
Badaoui, Bouabid
  • Department of Biology, Faculty of Science, Mohammed V University, Rabat B.P. 8007, Morocco.
Petit, Daniel
  • LABCiS, UR 22722, Faculty of Sciences and Technology, University of Limoges, F-87000 Limoges, France.
Piro, Mohammed
  • Laboratory of Veterinary Genetic Analysis, Department of Medicine, Surgery and Reproduction Agronomic, Veterinary Institute Hassan II Rabat, Rabat B.P. 6202, Morocco.

Conflict of Interest Statement

The authors declare no conflicts of interest.

References

This article includes 108 references
  1. Outram A.K., Stear N.A., Bendrey R., Olsen S., Kasparov A., Zaibert V., Thorpe N., Evershed R.P.. The Earliest Horse Harnessing and Milking. Science 2009;323:1332–1335.
    doi: 10.1126/science.1168594pubmed: 19265018google scholar: lookup
  2. Polak G., Gurgul A., Jasielczuk I., Szmatoła T., Krupiński J., Bugno-Poniewierska M.. Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs. Genes 2021;12:429.
    doi: 10.3390/genes12030429pmc: PMC8002693pubmed: 33802830google scholar: lookup
  3. Myćka G., Klecel W., Stefaniuk-Szmukier M., Jaworska J., Musiał A.D., Ropka-Molik K.. Mitochondrial Whole D-Loop Variability in Polish Draft Horses of Sztumski Subtype. Animals 2022;12:1870.
    doi: 10.3390/ani12151870pmc: PMC9332387pubmed: 35892520google scholar: lookup
  4. McGahern A., Bower M.a.M., Edwards C.J., Brophy P.O., Sulimova G., Zakharov I., Vizuete-Forster M., Levine M., Li S., MacHugh D.E.. Evidence for Biogeographic Patterning of Mitochondrial DNA Sequences in Eastern Horse Populations. Anim. Genet. 2006;37:494–497.
    doi: 10.1111/j.1365-2052.2006.01495.xpubmed: 16978180google scholar: lookup
  5. Khanshour A.M., Cothran E.G.. Maternal Phylogenetic Relationships and Genetic Variation among Arabian Horse Populations Using Whole Mitochondrial DNA D-Loop Sequencing. BMC Genet. 2013;14:83.
    doi: 10.1186/1471-2156-14-83pmc: PMC3847362pubmed: 24034565google scholar: lookup
  6. Moridi M., Masoudi A.A., Vaez Torshizi R., Hill E.W.. Mitochondrial DNA D-Loop Sequence Variation in Maternal Lineages of Iranian Native Horses. Anim. Genet. 2013;44:209–213.
    doi: 10.1111/j.1365-2052.2012.02389.xpubmed: 22732008google scholar: lookup
  7. Bowling A.T., Del Valle A., Bowling M.. A Pedigree-Based Study of Mitochondrial D-Loop DNA Sequence Variation among Arabian Horses. Anim. Genet. 2000;31:1–7.
    doi: 10.1046/j.1365-2052.2000.00558.xpubmed: 10690354google scholar: lookup
  8. Lippold S., Matzke N.J., Reissmann M., Hofreiter M.. Whole Mitochondrial Genome Sequencing of Domestic Horses Reveals Incorporation of Extensive Wild Horse Diversity during Domestication. BMC Evol. Biol. 2011;11:328.
    doi: 10.1186/1471-2148-11-328pmc: PMC3247663pubmed: 22082251google scholar: lookup
  9. Achilli A., Olivieri A., Soares P., Lancioni H., Kashani B.H., Perego U.A., Nergadze S.G., Carossa V., Santagostino M., Capomaccio S.. Mitochondrial Genomes from Modern Horses Reveal the Major Haplogroups That Underwent Domestication. Proc. Natl. Acad. Sci. USA 2012;109:2449–2454.
    doi: 10.1073/pnas.1111637109pmc: PMC3289334pubmed: 22308342google scholar: lookup
  10. 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;5:e15311.
    doi: 10.1371/journal.pone.0015311pmc: PMC3004868pubmed: 21187961google scholar: lookup
  11. Jansen T., Forster P., Levine M.A., Oelke H., Hurles M., Renfrew C., Weber J., Olek K.. Mitochondrial DNA and the Origins of the Domestic Horse. Proc. Natl. Acad. Sci. USA 2002;99:10905–10910.
    doi: 10.1073/pnas.152330099pmc: PMC125071pubmed: 12130666google scholar: lookup
  12. Page M.J., McKenzie J.E., Bossuyt P.M., Boutron I., Hoffmann T.C., Mulrow C.D., Shamseer L., Tetzlaff J.M., Akl E.A., Brennan S.E.. The PRISMA 2020 Statement: An Updated Guideline for Reporting Systematic Reviews. BMJ 2021;372:n71.
    doi: 10.1136/bmj.n71pmc: PMC8005924pubmed: 33782057google scholar: lookup
  13. Kumar S.. MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing. Mol. Biol. Evol. 2024;41:msae263.
    doi: 10.1093/molbev/msae263pmc: PMC11683415pubmed: 39708372google scholar: lookup
  14. Criscione A., Moltisanti V., Chies L., Marletta D., Bordonaro S.. A Genetic Analysis of the Italian Salernitano Horse. Animal 2015;9:1610–1616.
    doi: 10.1017/S1751731115001019pubmed: 26144256google scholar: lookup
  15. Giontella A., Cardinali I., Pieramati C., Cherchi R., Biggio G.P., Achilli A., Silvestrelli M., Lancioni H.. A Genetic Window on Sardinian Native Horse Breeds through Uniparental Molecular Systems. Animals 2020;10:1544.
    doi: 10.3390/ani10091544pmc: PMC7552234pubmed: 32882901google scholar: lookup
  16. Lu H., Bai H., Wang L., Zhang T.. Abundant Genetic Diversity and Maternal Origins of Modern Horses. Can. J. Anim. Sci. 2019;99:929.
    doi: 10.1139/cjas-2018-0201google scholar: lookup
  17. Cardinali I., Lancioni H., Giontella A., Capodiferro M.R., Capomaccio S., Buttazzoni L., Biggio G.P., Cherchi R., Albertini E., Olivieri A.. An Overview of Ten Italian Horse Breeds through Mitochondrial DNA. PLoS ONE 2016;11:e0153004.
    doi: 10.1371/journal.pone.0153004pmc: PMC4824442pubmed: 27054850google scholar: lookup
  18. Voronkova V., Nikolaeva E., Piskunov A., Babayan O., Takasu M., Tozaki T., Svishcheva G., Stolpovsky Y.. Assessment of Genetic Diversity and Structure of Russian and Mongolian Autochthonous Horse Breeds Using Nuclear and Mitochondrial DNA Markers. Russ. J. Genet. 2022;58:927–943.
    doi: 10.1134/S1022795422080105google scholar: lookup
  19. Musiał A.D., Ropka-Molik K., Stefaniuk-Szmukier M., Myćka G., Bieniek A., Yasynetska N.. Characteristic of Przewalski Horses Population from Askania-Nova Reserve Based on Genetic Markers. Mol. Biol. Rep. 2023;50:7121–7126.
    doi: 10.1007/s11033-023-08581-4pmc: PMC10374732pubmed: 37365410google scholar: lookup
  20. Cieslak J., Wodas L., Borowska A., Cothran E.G., Khanshour A.M., Mackowski M.. Characterization of the Polish Primitive Horse (Konik) Maternal Lines Using Mitochondrial D-Loop Sequence Variation. PeerJ 2017;5:e3714.
    doi: 10.7717/peerj.3714pmc: PMC5572418pubmed: 28852595google scholar: lookup
  21. Jimenez L.M., Mendez S., Dunner S., Cañón J., Cortés Ó.. Colombian Creole Horse Breeds: Same Origin but Different Diversity. Genet. Mol. Biol. 2012;35:790–796.
    doi: 10.1590/S1415-47572012005000064pmc: PMC3526087pubmed: 23271940google scholar: lookup
  22. Ahmed M., Sheikh A., Mutwakil M., Saini K., Alsulaimany F., El Hanafy A., Sabir J.. Comparative Analysis of Atp6 Mitochondrial Gene Diversity in Arabian and Non-Arabian Horse Breeds. J. Anim. Plant Sci. 2016;26:437–444.
  23. Winton C.L., Plante Y., Hind P., McMahon R., Hegarty M.J., McEwan N.R., Davies-Morel M.C.G., Morgan C.M., Powell W., Nash D.M.. Comparative Genetic Diversity in a Sample of Pony Breeds from the U.K. and North America: A Case Study in the Conservation of Global Genetic Resources. Ecol. Evol. 2015;5:3507–3522.
    doi: 10.1002/ece3.1562pmc: PMC4569044pubmed: 26380682google scholar: lookup
  24. Liu S., Fu C., Yang Y., Zhang Y., Ma H., Xiong Z., Ling Y., Zhao C.. Current Genetic Conservation of Chinese Indigenous Horses Revealed with Y-Chromosomal and Mitochondrial DNA Polymorphisms. G3 2021;11:jkab008.
    doi: 10.1093/g3journal/jkab008pmc: PMC8022964pubmed: 33604674google scholar: lookup
  25. Glazewska I., Gralak B., Naczk A.. Differences and Changes: An Evaluation of the Genetic Diversity of Arabian Mares from Polish State Studs Born between 1996 and 2013. Ann. Anim. Sci. 2022;22:1225–1233.
    doi: 10.2478/aoas-2022-0033google scholar: lookup
  26. Almarzook S., Reissmann M., Brockmann G.A.. Diversity of Mitochondrial DNA in Three Arabian Horse Strains. J. Appl. Genet. 2017;58:273–276.
    doi: 10.1007/s13353-016-0384-zpubmed: 27966062google scholar: lookup
  27. Ianella P., Albuquerque M.d.S.M., Paiva S.R., Egito A.A.d., Almeida L.D., Sereno F.T.P.S., Carvalho L.F.R., Mariante A. da S., McManus C.M.. D-Loop Haplotype Diversity in Brazilian Horse Breeds. Genet. Mol. Biol. 2017;40:604–609.
    doi: 10.1590/1678-4685-gmb-2016-0166pmc: PMC5596364pubmed: 28863209google scholar: lookup
  28. Khrabrova L.A., Blohina N.V., Belousova N.F., Cothran E.G.. Estimation of the Genealogical Structure of Vyatka Horse Breed (Equus Ferus Caballus) Using DNA Analysis. Russ. J. Genet. 2022;58:462–466.
    doi: 10.1134/S1022795422040068google scholar: lookup
  29. Engel L., Becker D., Nissen T., Russ I., Thaller G., Krattenmacher N.. Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse. Front. Genet. 2021;12:632500.
    doi: 10.3389/fgene.2021.632500pmc: PMC8320364pubmed: 34335677google scholar: lookup
  30. Álvarez I., Fernández I., Lorenzo L., Payeras L., Cuervo M., Goyache F.. Founder and Present Maternal Diversity in Two Endangered Spanish Horse Breeds Assessed via Pedigree and Mitochondrial DNA Information. J. Anim. Breed Genet. 2012;129:271–279.
    doi: 10.1111/j.1439-0388.2012.00995.xpubmed: 22775259google scholar: lookup
  31. Khaudov A.D., Duduev A.S., Kokov Z.A., Amshokov K.K., Zhekamukhov M.K., Zaitsev A.M., Reissmann M.. Genetic Analysis of Maternal and Paternal Lineages in Kabardian Horses by Uniparental Molecular Markers. Open Vet. J. 2018;8:40–46.
    doi: 10.4314/ovj.v8i1.7pmc: PMC5806666pubmed: 29445620google scholar: lookup
  32. Bigi D., Perrotta G., Zambonelli P.. Genetic Analysis of Seven Italian Horse Breeds Based on Mitochondrial DNA D-Loop Variation. Anim. Genet. 2014;45:593–595.
    doi: 10.1111/age.12156pubmed: 24702170google scholar: lookup
  33. Csizmár N., Mihók S., Jávor A., Kusza S.. Genetic Analysis of the Hungarian Draft Horse Population Using Partial Mitochondrial DNA D-Loop Sequencing. PeerJ 2018;6:e4198.
    doi: 10.7717/peerj.4198pmc: PMC5797449pubmed: 29404201google scholar: lookup
  34. Kobayashi I., Akita M., Takasu M., Tozaki T., Kakoi H., Nakamura K., Senju N., Matsuyama R., Horii Y.. Genetic Characteristics of Feral Misaki Horses Based on Polymorphisms of Microsatellites and Mitochondrial DNA. J. Vet. Med. Sci. 2019;81:707–711.
    doi: 10.1292/jvms.18-0565pmc: PMC6541847pubmed: 30867351google scholar: lookup
  35. Kusza S., Priskin K., Ivankovic A., Jedrzejewska B.. Genetic Characterization and Population Bottleneck in the Hucul Horse Based on Microsatellite and Mitochondrial Data. Biol. J. Linn. Soc. 2013;109:54–65.
    doi: 10.1111/bij.12023google scholar: lookup
  36. Nguyen T.B., Paul R.C., Okuda Y., Le T.N.A., Pham P.T.K., Kaissar K.J., Kazhmurat A., Bibigul S., Bakhtin M., Kazymbet P.. Genetic Characterization of Kushum Horses in Kazakhstan Based on Haplotypes of Mtdna and y Chromosome, and Genes Associated with Important Traits of the Horses. J. Equine Sci. 2020;31:35–43.
    doi: 10.1294/jes.31.35pmc: PMC7538259pubmed: 33061782google scholar: lookup
  37. Senju N., Tozaki T., Kakoi H., Almunia J., Maeda M., Matsuyama R., Takasu M.. Genetic Characterization of the Miyako Horse Based on Polymorphisms of Microsatellites and Mitochondrial DNA. J. Vet. Med. Sci. 2017;79:218–223.
    doi: 10.1292/jvms.16-0111pmc: PMC5289264pubmed: 27795462google scholar: lookup
  38. Effa K., Rosenbom S., Han J., Dessie T., Beja-Pereira A.. Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms. Genes 2021;12:155.
    doi: 10.3390/genes12020155pmc: PMC7912211pubmed: 33503948google scholar: lookup
  39. Machmoum M., Badaoui B., Petit D., Germot A., El Alaoui M.A., Boujenane I., Piro M.. Genetic Diversity and Maternal Phylogenetic Relationships among Populations and Strains of Arabian Show Horses. Animals 2023;13:2021.
    doi: 10.3390/ani13122021pmc: PMC10295422pubmed: 37370531google scholar: lookup
  40. Ovchinnikov I.V., Dahms T., Herauf B., McCann B., Juras R., Castaneda C., Cothran E.G.. Genetic Diversity and Origin of the Feral Horses in Theodore Roosevelt National Park. PLoS ONE 2018;13:e0200795.
    doi: 10.1371/journal.pone.0200795pmc: PMC6070244pubmed: 30067807google scholar: lookup
  41. Gemingguli M., Iskhan K.R., Li Y., Qi A., Wunirifu W., Ding L.Y., Wumaierjiang A.. Genetic Diversity and Population Structure of Kazakh Horses (Equus caballus) Inferred from mtDNA Sequences. Genet. Mol. Res. 2016;15:gmr.15048618.
    doi: 10.4238/gmr.15048618pubmed: 27808359google scholar: lookup
  42. Wolfsberger W., Ayala N., Castro-Marquez S., Irizarry-Negron V., Potapchuk A., Shchubelka K., Potish L., Majeske A., Oliver L., Lameiro A.. Genetic Diversity and Selection in Puerto Rican Horses. Sci. Rep. 2022;12:515.
    doi: 10.1038/s41598-021-04537-5pmc: PMC8752667pubmed: 35017609google scholar: lookup
  43. Evrigh N., Omri M., Boustan A., Seyedsharifi R., Vahedi V.. Genetic Diversity and Structure of Iranian Horses’ Population Based on Mitochondrial Markers. J. Equine Vet. Sci. 2018;64:107–111.
    doi: 10.1016/j.jevs.2018.02.011pubmed: 30973145google scholar: lookup
  44. Takasu M., Ishihara N., Tozaki T., Kakoi H., Maeda M., Mukoyama H.. Genetic Diversity of Maternal Lineage in the Endangered Kiso Horse Based on Polymorphism of the Mitochondrial DNA D-Loop Region. J. Vet. Med. Sci. 2014;76:1451–1456.
    doi: 10.1292/jvms.14-0231pmc: PMC4272977pubmed: 25056676google scholar: lookup
  45. Khrabrova L.A., Nikolaeva A.A., Blohina N.V., Sorokin S.I.. Genetic Diversity of Mitochondrial DNA Haplogroups in the Don Horse Breed. Sib. J. Life Sci. Agric. 2023;15:278–290.
    doi: 10.12731/2658-6649-2023-15-4-278-290google scholar: lookup
  46. 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;25:921–926.
    doi: 10.5713/ajas.2011.11483pmc: PMC4092969pubmed: 25049645google scholar: lookup
  47. 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
  48. Senju N., Tozaki T., Kakoi H., Shinjo A., Matsuyama R., Almunia J., Takasu M.. Genetic Diversity of the Yonaguni Horse Based on Polymorphisms in Microsatellites and Mitochondria DNA. J. Vet. Med. Sci. 2017;79:425–431.
    doi: 10.1292/jvms.16-0040pmc: PMC5326952pubmed: 28049866google scholar: lookup
  49. Deshpande K., Perez E., Leyva N., Suarez M., Mills D.K.. Genetic Structure of the Big Summit Herd and Neighboring Wild Horse Populations Inhabiting Herd Management Areas of Oregon. West. N. Am. Nat. 2019;79:85–98.
    doi: 10.3398/064.079.0109google scholar: lookup
  50. Kvist L., Niskanen M., Mannermaa K., Wutke S., Aspi J.. Genetic Variability and History of a Native Finnish Horse Breed. Genet. Sel. Evol. 2019;51:35.
    doi: 10.1186/s12711-019-0480-8pmc: PMC6604459pubmed: 31262246google scholar: lookup
  51. Giontella A., Sarti F., Cardinali I., Giovannini S., Cherchi R., Lancioni H., Silvestrelli M., Pieramati C.. Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse. Animals 2020;10:1018.
    doi: 10.3390/ani10061018pmc: PMC7341272pubmed: 32545354google scholar: lookup
  52. Cozzi M.C., Strillacci M.G., Valiati P., Rogliano E., Bagnato A., Longeri M.. Genetic Variability of Akhal-Teke Horses Bred in Italy. PeerJ 2018;2018:e4889.
    doi: 10.7717/peerj.4889pmc: PMC6129384pubmed: 30202639google scholar: lookup
  53. Kang Z., Shi J., Liu T., Zhang Y., Zhang Q., Liu Z., Wang J., Cheng S.. Genome-Wide Single-Nucleotide Polymorphism Data and Mitochondrial Hypervariable Region 1 Nucleotide Sequence Reveal the Origin of the Akhal-Teke Horse. Anim. Biosci. 2023;36:1499–1507.
    doi: 10.5713/ab.23.0044pmc: PMC10475378pubmed: 37170508google scholar: lookup
  54. Yang L., Kong X., Yang S., Dong X., Yang J., Gou X., Zhang H.. Haplotype Diversity in Mitochondrial DNA Reveals the Multiple Origins of Tibetan Horse. PLoS ONE 2018;13:e0201564.
    doi: 10.1371/journal.pone.0201564pmc: PMC6063445pubmed: 30052677google scholar: lookup
  55. Ropka-Molik K., Ayad A., Musiał A.D., Besseboua O., Aissanou S., Stefaniuk-Szmukier M., Piórkowska K.. Insight into the Genetic Diversity of Selle Français Horse Populations Based on Whole D-Loop Sequencing of Mitochondrial DNA. Folia Biol. 2024;72:65–73.
    doi: 10.3409/fb_72-2.07google scholar: lookup
  56. KOSEMAN A., OZSENSOY Y., ERDOGAN M., YARALI C., TOPRAK B., ZENGIN K., SEKER İ.. Investigation of Genetic Structures of Coloured Horses by Mtdna D-Loop Sequence Analysis in Turkey. Vet. Fak. Derg. 2019;25:769–778.
    doi: 10.9775/kvfd.2019.21844google scholar: lookup
  57. Ning T., Ling Y., Hu S., Ardalan A., Li J., Mitra B., Chaudhuri T., Guan W., Zhao Q., Ma Y.. Local Origin or External Input: Modern Horse Origin in East Asia. BMC Evol. Biol. 2019;19:217.
    doi: 10.1186/s12862-019-1532-ypmc: PMC6882189pubmed: 31775623google scholar: lookup
  58. Sild E., Värv S., Kaart T., Kantanen J., Popov R., Viinalass H.. Maternal and Paternal Genetic Variation in Estonian Local Horse Breeds in the Context of Geographically Adjacent and Distant Eurasian Breeds. Anim. Genet. 2019;50:757–760.
    doi: 10.1111/age.12835pmc: PMC6899971pubmed: 31475379google scholar: lookup
  59. Prystupa J.M., Hind P., Cothran E.G., Plante Y.. Maternal Lineages in Native Canadian Equine Populations and Their Relationship to the Nordic and Mountain and Moorland Pony Breeds. J. Hered. 2012;103:380–390.
    doi: 10.1093/jhered/ess003pubmed: 22504109google scholar: lookup
  60. Novoa-Bravo M., Bernal-Pinilla E., García L.F.. Microevolution Operating in Domestic Animals: Evidence from the Colombian Paso Horses. Mamm. Biol. 2021;101:181–192.
    doi: 10.1007/s42991-021-00103-8google scholar: lookup
  61. Liu G., Xu C.-Q., Cao Q., Zimmermann W., Songer M., Zhao S.-S., Li K., Hu D.-F.. Mitochondrial and Pedigree Analysis in Przewalski’s Horse Populations: Implications for Genetic Management and Reintroductions. Mitochondrial DNA 2014;25:313–318.
    doi: 10.3109/19401736.2013.800487pubmed: 23808923google scholar: lookup
  62. Yordanov G., Hristov P., Ivanova A., Mitkov I., Sirakova D., Mehandzyiski I., Radoslavov G.. Mitochondrial Diversity in Mountain Horse Population from the South-Eastern Europe. Mitochondrial DNA Part A DNA Mapp. Seq. Anal. 2017;28:787–792.
    doi: 10.1080/24701394.2016.1186667pubmed: 27247184google scholar: lookup
  63. Czernekova V., Kott T., Majzlik I.. Mitochondrial D-Loop Sequence Variation among Hucul Horse. Czech J. Anim. Sci. 2013;58:437–442.
    doi: 10.17221/6992-CJASgoogle scholar: lookup
  64. Dell A.C., Curry M.C., Yarnell K.M., Starbuck G.R., Wilson P.B.. Mitochondrial D-Loop Sequence Variation and Maternal Lineage in the Endangered Cleveland Bay Horse. PLoS ONE 2020;15:e0243247.
    doi: 10.1371/journal.pone.0243247pmc: PMC7714183pubmed: 33270708google scholar: lookup
  65. Musiał A.D., Radović L., Stefaniuk-Szmukier M., Bieniek A., Wallner B., Ropka-Molik K.. Mitochondrial DNA and Y Chromosome Reveal the Genetic Structure of the Native Polish Konik Horse Population. PeerJ 2024;12:e17549.
    doi: 10.7717/peerj.17549pmc: PMC11193968pubmed: 38912049google scholar: lookup
  66. Nikbakhsh M., Varkoohi S., Seyedabadi H.R.. Mitochondrial DNA D-Loop Hyper-Variable Region 1 Variability in Kurdish Horse Breed. Vet. Med. Sci. 2023;9:721–728.
    doi: 10.1002/vms3.996pmc: PMC10029883pubmed: 36367719google scholar: lookup
  67. Yang S.-L., Li A.-P., Xu L.-X., Yang H.. Short Communication: Mitochondrial DNA D-Loop Sequence Diversity and Origin of Chinese Pony Breeds (Equus caballus). Can. J. Anim. Sci. 2013;93:313–319.
    doi: 10.4141/cjas2012-160google scholar: lookup
  68. Othman O.E., Mahrous K.F., Shafey H.I.. Mitochondrial DNA Genetic Variations among Four Horse Populations in Egypt. J. Genet. Eng. Biotechnol. 2017;15:469–474.
    doi: 10.1016/j.jgeb.2017.06.004pmc: PMC6296616pubmed: 30647688google scholar: lookup
  69. Morelli L., Useli A., Sanna D., Barbato M., Contu D., Pala M., Cancedda M., Francalacci P.. Mitochondrial DNA Lineages of Italian Giara and Sarcidano Horses. Genet. Mol. Res. 2014;13:8241–8257.
    doi: 10.4238/2014.October.20.1pubmed: 25366719google scholar: lookup
  70. Yordanov G., Palova N., Mehandjyiski I., Hristov P.. Mitochondrial DNA Sequencing Illuminates Genetic Diversity and Origin of Hunagrian Nonius Horse Breed and His Relatives–Danubian Horse and Serbian Nonius. Anim. Biotechnol. 2023;34:3897–3907.
    doi: 10.1080/10495398.2023.2237533pubmed: 37489100google scholar: lookup
  71. Sheikh A.. Mitochondrial DNA Sequencing of Kehilan and Hamdani Horses from Saudi Arabia. Saudi J. Biol. Sci. 2023;30:103741.
    doi: 10.1016/j.sjbs.2023.103741pmc: PMC10413190pubmed: 37575470google scholar: lookup
  72. Giontella A., Cardinali I., Lancioni H., Giovannini S., Pieramati C., Silvestrelli M., Sarti F.M.. Mitochondrial DNA Survey Reveals the Lack of Accuracy in Maremmano Horse Studbook Records. Animals 2020;10:839.
    doi: 10.3390/ani10050839pmc: PMC7278429pubmed: 32408648google scholar: lookup
  73. Lancioni H., Cardinali I., Giontella A., Antognoni M.T., Miglio A.. Mitochondrial DNA Variation in the Italian Heavy Draught Horse. PeerJ 2020;2020:e8996.
    doi: 10.7717/peerj.8996pmc: PMC7233276pubmed: 32461825google scholar: lookup
  74. Hristov P., Yordanov G., Vladov V., Neov B., Palova N., Radoslavov G.. Mitochondrial Profiles of the East Bulgarian and the Pleven Horse Breeds. J. Equine Vet. Sci. 2020;88:102933.
    doi: 10.1016/j.jevs.2020.102933pubmed: 32303312google scholar: lookup
  75. Kvist L., Niskanen M.. Modern Northern Domestic Horses Carry Mitochondrial DNA Similar to Przewalski’s Horse. J. Mamm. Evol. 2021;28:371–376.
    doi: 10.1007/s10914-020-09517-6google scholar: lookup
  76. Devi K.M., Ghosh S.K.. Molecular Phylogeny of Indian Horse Breeds with Special Reference to Manipuri Pony Based on Mitochondrial D-Loop. Mol. Biol. Rep. 2013;40:5861–5867.
    doi: 10.1007/s11033-013-2692-2pubmed: 24068432google scholar: lookup
  77. Castaneda C., Juras R., Khanshour A., Randlaht I., Wallner B., Rigler D., Lindgren G., Raudsepp T., Cothran E.. Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines. Genes 2019;10:629.
    doi: 10.3390/genes10080629pmc: PMC6722507pubmed: 31434327google scholar: lookup
  78. Sharif M.B., Fitak R.R., Wallner B., Orozco-terWengel P., Frewin S., Fremaux M., Mohandesan E.. Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses. Animals 2022;12:3508.
    doi: 10.3390/ani12243508pmc: PMC9774138pubmed: 36552427google scholar: lookup
  79. Alvarez I., Fernandez I., Cuervo M., Martin D., Lorenzo L., Goyache F.. Short Communication. Mitochondrial DNA Diversity of the Founder Populations of the Asturcón Pony. Span. J. Agric. Res. 2013;11:702–707.
    doi: 10.5424/sjar/2013113-4127google scholar: lookup
  80. Ma H., Wu Y., Xiang H., Yang Y., Wang M., Zhao C., Wu C.. Some Maternal Lineages of Domestic Horses May Have Origins in East Asia Revealed with Further Evidence of Mitochondrial Genomes and HVR-1 Sequences. PeerJ 2018;6:e4896.
    doi: 10.7717/peerj.4896pmc: PMC5985762pubmed: 29868288google scholar: lookup
  81. Yang Y., Zhu Q., Liu S., Zhao C., Wu C.. The Origin of Chinese Domestic Horses Revealed with Novel mtDNA Variants. Anim. Sci. J. 2017;88:19–26.
    doi: 10.1111/asj.12583pubmed: 27071843google scholar: lookup
  82. Bower M.A., Whitten M., Nisbet R.E.R., Spencer M., Dominy K.M., Murphy A.M., Cassidy R., Barrett E., Hill E.W., Binns M.. Thoroughbred Racehorse Mitochondrial DNA Demonstrates Closer than Expected Links between Maternal Genetic History and Pedigree Records. J. Anim. Breed. Genet. 2013;130:227–235.
    doi: 10.1111/j.1439-0388.2012.01018.xpubmed: 23679948google scholar: lookup
  83. Alves J., Anjos M., Bastos M., de Oliveira L., Oliveira I., Pinto L., de Oliveira C., Costa R., de Camargo G.. Variability Analyses of the Maternal Lineage of Horses and Donkeys. Gene 2021;769:145231.
    doi: 10.1016/j.gene.2020.145231pubmed: 33065240google scholar: lookup
  84. Khrabrova L.A., Blohina N.V., Bazaron B.Z., Khamiruev T.N.. Variability of Mitochondrial DNA D-Loop Sequences in Zabaikalskaya Horse Breed. Vavilovskii Zhurnal Genet. I Sel. 2021;25:486–491.
    doi: 10.18699/VJ21.055pmc: PMC8453366pubmed: 34595371google scholar: lookup
  85. Hudson W.. Whole-Loop Mitochondrial DNA D-Loop Sequence Variability in Egyptian Arabian Equine Matrilines. PLoS ONE 2017;12:e0184309.
    doi: 10.1371/journal.pone.0184309pmc: PMC5578668pubmed: 28859174google scholar: lookup
  86. Miller S.. A Simple Salting-out Proceddure Tissue for Extracting DNA from Human Nucleated Cells. Nucleic Acids Res. 1988;16:221.
    doi: 10.1093/nar/16.3.1215pmc: PMC334765pubmed: 3344216google scholar: lookup
  87. Yoon S.H., Kim J., Shin D., Cho S., Kwak W., Lee H.-K., Park K.-D., Kim H.. Complete Mitochondrial Genome Sequences of Korean Native Horse from Jeju Island: Uncovering the Spatio-Temporal Dynamics. Mol. Biol. Rep. 2017;44:233–242.
    doi: 10.1007/s11033-017-4101-8pubmed: 28432484google scholar: lookup
  88. Rozas J., Ferrer-Mata A., Sánchez-DelBarrio J.C., Guirao-Rico S., Librado P., Ramos-Onsins S.E., Sánchez-Gracia A.. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol. Biol. Evol. 2017;34:3299–3302.
    doi: 10.1093/molbev/msx248pubmed: 29029172google scholar: lookup
  89. Tamura K., Stecher G., Kumar S.. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol. Biol. Evol. 2021;38:3022–3027.
    doi: 10.1093/molbev/msab120pmc: PMC8233496pubmed: 33892491google scholar: lookup
  90. Fluxus-Engineering.Com. [(accessed on 6 January 2025)]. Available online: https://www.fluxus-engineering.com/index.htm.
  91. Excoffier L., Lischer H.E.L.. Arlequin Suite Ver 3.5: A New Series of Programs to Perform Population Genetics Analyses under Linux and Windows. Mol. Ecol. Resour. 2010;10:564–567.
    doi: 10.1111/j.1755-0998.2010.02847.xpubmed: 21565059google scholar: lookup
  92. Thompson J.D., Higgins D.G., Gibson T.J.. 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;22:4673–4680.
    doi: 10.1093/nar/22.22.4673pmc: PMC308517pubmed: 7984417google scholar: lookup
  93. Hall T. BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. [(accessed on 6 January 2025)]. Available online: https://www.semanticscholar.org/paper/BIOEDIT%3A-A-USER-FRIENDLY-BIOLOGICAL-SEQUENCE-EDITOR-Hall/0ae262d9cf78536754bc064e07113ab5e978f208.
  94. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.. Basic Local Alignment Search Tool. J. Mol. Biol. 1990;215:403–410.
    doi: 10.1016/S0022-2836(05)80360-2pubmed: 2231712google scholar: lookup
  95. Kong S., Sánchez-Pacheco S.J., Murphy R.W.. On the Use of Median-Joining Networks in Evolutionary Biology. Cladistics 2016;32:691–699.
    doi: 10.1111/cla.12147pubmed: 34753275google scholar: lookup
  96. Vilà C., Leonard J.A., Götherström A., Marklund S., Sandberg K., Lidén K., Wayne R.K., Ellegren H.. Widespread Origins of Domestic Horse Lineages. Sci. (Am. Assoc. Adv. Sci.) 2001;291:474–477.
    doi: 10.1126/science.291.5503.474pubmed: 11161199google scholar: lookup
  97. Zemanova M.A.. Noninvasive Genetic Assessment Is an Effective Wildlife Research Tool When Compared with Other Approaches. Genes 2021;12:1672.
    doi: 10.3390/genes12111672pmc: PMC8625682pubmed: 34828277google scholar: lookup
  98. Gurău M.R., Crețu D.M., Negru E., Ionescu T., Udriste A.A., Cornea P., Bărăităreanu S.. Comparative Analysis of Total DNA Isolation Procedure from Blood and Hair Follicule Samples in Goats. Rev. Româna Med. Vet. 2021;31:82–86.
  99. Muko R., Ojima Y., Matsuda H., Toishi Y., Oikawa M., Shin T., Sato H., Tanaka A.. Comparison of DNA Extraction Methods for Genotyping Equine Histidine-Rich Glycoprotein Insertion/Deletion Polymorphisms Using Oral Mucosa Swabs and Feces. Vet. Anim. Sci. 2024;25:100361.
    doi: 10.1016/j.vas.2024.100361pmc: PMC11214520pubmed: 38947185google scholar: lookup
  100. 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;25:215–221.
    doi: 10.1111/j.1365-2052.1994.tb00196.xpubmed: 7985837google scholar: lookup
  101. Xiufeng X., Árnason Ú.. The Complete Mitochondrial DNA Sequence of the Horse, Equus caballus: Extensive Heteroplasmy of the Control Region. Gene 1994;148:357–362.
    doi: 10.1016/0378-1119(94)90713-7pubmed: 7958969google scholar: lookup
  102. Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P.. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Syst. Biol. 2012;61:539–542.
    doi: 10.1093/sysbio/sys029pmc: PMC3329765pubmed: 22357727google scholar: lookup
  103. Williams T.L., Moret B.M.E.. An Investigation of Phylogenetic Likelihood Methods; Proceedings of the Third IEEE Symposium on Bioinformatics and Bioengineering; Bethesda, MD, USA. 12 March 2003; Proceedings; pp. 79–86. .
  104. Beerli P.. Comparison of Bayesian and Maximum-Likelihood Inference of Population Genetic Parameters. Bioinformatics 2006;22:341–345.
    doi: 10.1093/bioinformatics/bti803pubmed: 16317072google scholar: lookup
  105. Suzuki Y., Glazko G.V., Nei M.. Overcredibility of Molecular Phylogenies Obtained by Bayesian Phylogenetics. Proc. Natl. Acad. Sci. USA 2002;99:16138–16143.
    doi: 10.1073/pnas.212646199pmc: PMC138578pubmed: 12451182google scholar: lookup
  106. Castañeda-Rico S., León-Paniagua L., Edwards C.W., Maldonado J.E.. Ancient DNA from Museum Specimens and Next Generation Sequencing Help Resolve the Controversial Evolutionary History of the Critically Endangered Puebla Deer Mouse. Front. Ecol. Evol. 2020;8:94.
    doi: 10.3389/fevo.2020.00094google scholar: lookup
  107. Engel L., Becker D., Nissen T., Russ I., Thaller G., Krattenmacher N.. Mitochondrial DNA Variation Contributes to the Aptitude for Dressage and Show Jumping Ability in the Holstein Horse Breed. Animals 2022;12:704.
    doi: 10.3390/ani12060704pmc: PMC8944467pubmed: 35327102google scholar: lookup
  108. Lin X., Zheng H.-X., Davie A., Zhou S., Wen L., Meng J., Zhang Y., Aladaer Q., Liu B., Liu W.-J.. Association of Low Race Performance with mtDNA Haplogroup L3b of Australian Thoroughbred Horses. Mitochondrial DNA Part A 2018;29:323–330.
    doi: 10.1080/24701394.2016.1278535pubmed: 28129729google scholar: lookup

Citations

This article has been cited 1 times.
  1. Pasicka E, Baca M, Popović D, Makowiecki D, Janeczek M. Sequencing and Analysis of mtDNA Genomes from the Teeth of Early Medieval Horses in Poland. Genes (Basel) 2026 Jan 18;17(1).
    doi: 10.3390/genes17010095pubmed: 41595516google scholar: lookup
Subscribe to our newsletter
Join 99,970 horse owners like you who receive our email updates on horse health and nutrition.