Genes2024; 15(6); 790; doi: 10.3390/genes15060790

Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China.

Abstract: This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.
Publication Date: 2024-06-15 PubMed ID: 38927726PubMed Central: PMC11203007DOI: 10.3390/genes15060790Google 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.
  • Journal Article
  • Historical Article

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 discusses an analysis of ancient DNA found in horse remains from the Shihuyao tombs that reveals new insights about the history of the Akhal-Teke horse breed in China. The study indicates that these horses were likely domesticated early on for military purposes and that their propagation was greatly influenced by the ancient Silk Road.

Analysis of Ancient DNA

  • The study was based on ancient DNA recovered from horse remains found in the tombs of Shihuyao, which date from the Han and Tang Dynasties in Xinjiang, China. This period ranges approximately from 2200 to 1100 years ago.
  • The researchers extracted and analyzed two high-quality mitochondrial genomes using next-generation sequencing technology. Mitochondrial genomes are key in this context because they provide information about the maternal lineage of a species.
  • Through genomic analysis, the genomes were split into two maternal haplogroups, B and D, in line with a previous study that included ancient and contemporary samples from Eurasia.

The History of the Akhal-Teke Horse

  • The analysis revealed a close genetic affinity between horses from the Tang Dynasty and the Akhal-Teke breed, as per the primitive horse haplotype G1. This points to a historical linkage between these two groups of horses.
  • Historical evidence, likely in the form of archaeological or archival data, suggests that the ancient Silk Road played a significant role in disseminating these horses. The Silk Road was an ancient network of trade routes connecting the East and the West and could have facilitated the spread of horse breeds.
  • Finally, through examining the matrilineal history (tracing descent through the female line) of the Akhal-Teke horse, the study suggests that the breed was domesticated early on, primarily for military purposes. This raises interesting questions about the possible uses of these horses in warfare or other military contexts during those ancient times.

Cite This Article

APA
Zhu S, Zhang N, Zhang J, Shao X, Guo Y, Cai D. (2024). Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China. Genes (Basel), 15(6), 790. https://doi.org/10.3390/genes15060790

Publication

ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 15
Issue: 6
PII: 790

Researcher Affiliations

Zhu, Siqi
  • Department of Archaeology, School of History, Wuhan University, Wuhan 430072, China.
Zhang, Naifan
  • Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China.
  • National Centre for Archaeology, Beijing 100013, China.
Zhang, Jie
  • Xinjiang Institute of Cultural Relics and Archaeology, u00dcru00fcmqi 830011, China.
Shao, Xinyue
  • Department of Archaeology, University of Southampton, Avenue Campus, Southampton SO17 1BF, UK.
Guo, Yaqi
  • Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China.
Cai, Dawei
  • Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China.

MeSH Terms

  • Animals
  • Horses / genetics
  • Genome, Mitochondrial / genetics
  • China
  • DNA, Ancient / analysis
  • Haplotypes
  • DNA, Mitochondrial / genetics
  • Phylogeny
  • History, Ancient
  • High-Throughput Nucleotide Sequencing
  • Domestication

Grant Funding

  • NO.17ZDA221 / Major Project of the National Social Science Foundation of China
  • NO.2020YFC1521606 / National Key Research and Development Program of China
  • NO. 2022M722460 / Project funded by China Postdoctoral Science Foundation
  • NO. 2022CXTD17 / Fundamental Research Funds for the Central Universities

Conflict of Interest Statement

The authors declare no conflicts of interest.

References

This article includes 40 references
  1. 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.0015311.
  2. Hendricks B.L. International Encyclopedia of Horse Breeds. University of Oklahoma Press; Norman, OK, USA: 1995.
  3. Mackay-Smith A. Speed and the Thoroughbred: The Complete History. Derrydale Press; New York, NY, USA: 2000.
  4. Sima Q. The Historical Records. Zhonghua Book Company; Beijing, China: 2019. (In Chinese)
  5. Ban G. History of the Han Dynasty. Zhonghua Book Company; Beijing, China: 2000. (In Chinese)
  6. Rong X.J. The Silk Road and Cultural Interaction between East and West (Chinese Edition) Peking University Press; Beijing, China: 2015.
  7. Shen Q. Artistic images of Han and Jin cultural relics of the Silk Road horse. Relics South. 2020;5:288u2013291.
  8. Wang Z. Mysterious u201csweat horseu201d. Sci. Cult. 2002;06:23u201324. (In Chinese)
  9. 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;99:10905u201310910. doi: 10.1073/pnas.152330099.
    doi: 10.1073/pnas.152330099pmc: PMC125071pubmed: 12130666google scholar: lookup
  10. Vila C., Leonard J.A., Goterstrom A., Marklund S., Sandberg K., Liden K., Wayne R.K., Ellegren H. Widespread Origins of Domestic Horse Lineages. Science. 2001;291:474u2013477. doi: 10.1126/science.291.5503.474.
    doi: 10.1126/science.291.5503.474pubmed: 11161199google scholar: lookup
  11. Achilli A., Olivieri A., Soares P., Lancioni H., Hooshiar Kashani B., Perego U.A., Nergadze S.G., Carossa V., Santagostino M., Capomaccio S., et al. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc. Natl. Acad. Sci. USA. 2012;109:2449u20132454. doi: 10.1073/pnas.1111637109.
    doi: 10.1073/pnas.1111637109pmc: PMC3289334pubmed: 22308342google scholar: lookup
  12. 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: 10.1186/1471-2148-11-328.
    doi: 10.1186/1471-2148-11-328pmc: PMC3247663pubmed: 22082251google scholar: lookup
  13. Librado P., Khan N., Fages A., Kusliy M.A., Suchan T., Tonasso-Calviu00e8re L., Schiavinato S., Alioglu D., Fromentier A., Perdereau A., et al. The origins and spread of domestic horses from the Western Eurasian steppes. Nature. 2021;598:634u2013640. doi: 10.1038/s41586-021-04018-9.
    doi: 10.1038/s41586-021-04018-9pmc: PMC8550961pubmed: 34671162google scholar: lookup
  14. 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;6:e4889. doi: 10.7717/peerj.4889.
    doi: 10.7717/peerj.4889pmc: PMC6129384pubmed: 30202639google scholar: lookup
  15. Annals, Editorial Board of Zhaosu County . Zhaosu County Annals. Xinjiang Peopleu2019s Publishing House; Urumchi, China: 2004. (In Chinese)
  16. Zhang J., Huang F. An excavation and discussion on Shihuyao Tomb Group in Xinjiang. Turfanological Res. 2020;2:142u2013146.
  17. Yang D.Y., Eng B., Waye J.S., Dudar J.C., Saunders S.R. Technical Note_ Improved DNA Extraction From Ancient Bones Using Silica-Based Spin Columns. Am. J. Phys. Anthropol. 1998;105:539u2013543. doi: 10.1002/(SICI)1096-8644(199804)105:4<539::AID-AJPA10>3.0.CO;2-1.
  18. Kalbfleisch T.S., Rice E.S., DePriest M.S., Walenz B.P., Hestand M.S., Vermeesch J.R., Ou2019Connell B.L., Fiddes I.T., Vershinina A.O., Saremi N.F., et al. Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun. Biol. 2018;1:197. doi: 10.1038/s42003-018-0199-z.
    doi: 10.1038/s42003-018-0199-zpmc: PMC6240028pubmed: 30456315google scholar: lookup
  19. Schubert M., Ermini L., Der Sarkissian C., Ju00f3nsson H., Ginolhac A., Schaefer R., Martin M.D., Fernu00e1ndez R., Kircher M., McCue M., et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Protoc. 2014;9:1056u20131082. doi: 10.1038/nprot.2014.063.
    doi: 10.1038/nprot.2014.063pubmed: 24722405google scholar: lookup
  20. Schubert M., Ginolhac A., Lindgreen S., Thompson J.F., Al-Rasheid K.A., Willerslev E., Krogh A., Orlando L. Improving ancient DNA read mapping against modern reference genomes. BMC Genom. 2012;13:178. doi: 10.1186/1471-2164-13-178.
    doi: 10.1186/1471-2164-13-178pmc: PMC3468387pubmed: 22574660google scholar: lookup
  21. Schubert M., Lindgreen S., Orlando L. AdapterRemoval v2: Rapid adapter trimming, identification, and read merging. BMC Res. Notes. 2016;9:88. doi: 10.1186/s13104-016-1900-2.
    doi: 10.1186/s13104-016-1900-2pmc: PMC4751634pubmed: 26868221google scholar: lookup
  22. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754u20131760. doi: 10.1093/bioinformatics/btp324.
  23. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297u20131303. doi: 10.1101/gr.107524.110.
    doi: 10.1101/gr.107524.110pmc: PMC2928508pubmed: 20644199google scholar: lookup
  24. Jonsson H., Ginolhac A., Schubert M., Johnson P.L., Orlando L. mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 2013;29:1682u20131684. doi: 10.1093/bioinformatics/btt193.
  25. Gaunitz C., Fages A., Hanghoj K., Albrechtsen A., Khan N., Schubert M., Seguin-Orlando A., Owens I.J., Felkel S., Bignon-Lau O., et al. Ancient genomes revisit the ancestry of domestic and Przewalskiu2019s horses. Science. 2018;360:111u2013114. doi: 10.1126/science.aao3297.
    doi: 10.1126/science.aao3297pubmed: 29472442google scholar: lookup
  26. Korneliussen T.S., Albrechtsen A., Nielsen R. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinform. 2014;15:356. doi: 10.1186/s12859-014-0356-4.
    doi: 10.1186/s12859-014-0356-4pmc: PMC4248462pubmed: 25420514google scholar: lookup
  27. Edgar R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792u20131797. doi: 10.1093/nar/gkh340.
    doi: 10.1093/nar/gkh340pmc: PMC390337pubmed: 15034147google scholar: lookup
  28. Kozlov A.M., Darriba D., Flouri T., Morel B., Stamatakis A. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019;35:4453u20134455. doi: 10.1093/bioinformatics/btz305.
  29. Kalyaanamoorthy S., Minh B.Q., Wong T.K.F., von Haeseler A., Jermiin L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods. 2017;14:587u2013589. doi: 10.1038/nmeth.4285.
    doi: 10.1038/nmeth.4285pmc: PMC5453245pubmed: 28481363google scholar: lookup
  30. Letunic I., Bork P. Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242u2013W245. doi: 10.1093/nar/gkw290.
    doi: 10.1093/nar/gkw290pmc: PMC4987883pubmed: 27095192google scholar: lookup
  31. Bouckaert R., Vaughan T.G., Barido-Sottani J., Duchene S., Fourment M., Gavryushkina A., Heled J., Jones G., Kuhnert D., De Maio N., et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 2019;15:e1006650. doi: 10.1371/journal.pcbi.1006650.
  32. Lanfear R., Calcott B., Ho S.Y., Guindon S. Partitionfinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 2012;29:1695u20131701. doi: 10.1093/molbev/mss020.
    doi: 10.1093/molbev/mss020pubmed: 22319168google scholar: lookup
  33. Keane T.M., Creevey C.J., Pentony M.M., Naughton T.J., McLnerney J.O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 2006;6:29. doi: 10.1186/1471-2148-6-29.
    doi: 10.1186/1471-2148-6-29pmc: PMC1435933pubmed: 16563161google scholar: lookup
  34. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007;7:214. doi: 10.1186/1471-2148-7-214.
    doi: 10.1186/1471-2148-7-214pmc: PMC2247476pubmed: 17996036google scholar: lookup
  35. Cooper A., Poinar H.N. Ancient DNA: Do it right or not at all. Science. 2000;289:1139. doi: 10.1126/science.289.5482.1139b.
  36. Henthorn W.E. Korea: The Mongol Invasions. Franklin Classics Trade Press; Sacramento, CA, USA: 2018.
  37. Institute of History, Inner Mongolia Academy of Social Sciences . Mongolian General History. Ethnic Publishing House; Beijing, China: 2002. (In Chinese)
  38. Xue W. Masteru2019s Dissertation. Minzu University of China; Beijing, China: 2011. Research on Animal Burial Found in Xinjiang Archaeology. (In Chinese)
  39. Valerie H. The Silk Road: A New History. Oxford University Press; Oxford, UK: 2015.
  40. Chen S.A.-O., Li J., Zhang F., Xiao B., Hu J.M., Cui Y.Q., Hofreiter M., Hou X.D., Sheng G.L., Lai X.L., et al. Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China. Mitochondrial DNA Part A DNA Mapp. Seq. Anal. 2019;30:786u2013793. doi: 10.1080/24701394.2019.1659250.
    doi: 10.1080/24701394.2019.1659250pubmed: 31542986google scholar: lookup

Citations

This article has been cited 0 times.