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Home / Equine Research Bank / PLoS One / Mitochondrial D-loop sequence variation and maternal lineage...
PloS one2020; 15(12); e0243247; doi: 10.1371/journal.pone.0243247

Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse.

Abstract: Genetic diversity and maternal ancestry line relationships amongst a sample of 96 Cleveland Bay horses were investigated using a 479bp length of mitochondrial D-loop sequence. The analysis yielded at total of 11 haplotypes with 27 variable positions, all of which have been described in previous equine mitochondrial DNA d-loop studies. Four main haplotype clusters were present in the Cleveland Bay breed describing 89% of the total sample. This suggests that only four principal maternal ancestry lines exist in the present-day global Cleveland Bay population. Comparison of these sequences with other domestic horse haplotypes (Fig 2) shows a close association of the Cleveland Bay horse with Northern European (Clade C), Iberian (Clade A) and North African (Clade B) horse breeds. This indicates that the Cleveland Bay horse may not have evolved exclusively from the now extinct Chapman horse, as previous work as suggested. The Cleveland Bay horse remains one of only five domestic horse breeds classified as Critical on the Rare Breeds Survival Trust (UK) Watchlist and our results provide important information on the origins of this breed and represent a valuable tool for conservation purposes.
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Publication Date: 2020-12-03 PubMed ID: 33270708PubMed Central: PMC7714183DOI: 10.1371/journal.pone.0243247Google Scholar: Lookup
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Summary

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The research analyzes genetic diversity and maternal ancestry of the endangered Cleveland Bay horse breed to provide insights into its conservation and origins. It proposes that the breed may not have evolved singly from the now extinct Chapman horse, and identifies four principal maternal ancestry lines.

Genetic Analysis and Haplotype Identification

  • The researchers undertook a study on 96 Cleveland Bay horses in order to scrutinize their genetic diversity and maternal ancestry connections.
  • The study focused on examining a 479 base pair length of mitochondrial D-loop sequence (a portion of DNA responsible for the control of replication and transcription in mitochondria).
  • The analysis gave out a total of 11 haplotypes, which are groups of genes within an organism that are inherited together from a single parent. There were 27 variable positions identified within these haplotypes, consistent with earlier research findings in equine mitochondrial DNA D-loop studies.

Haplotype Clusters in Cleveland Bay Horses

  • Four main haplotype clusters were found in the Cleveland Bay breed, which made up 89% of the total sample.
  • This finding hints at the existence of only four dominant maternal lineage lines in today’s Cleveland Bay population worldwide.

Comparison with Other Domestic Horse Breeds

  • Upon comparing the Cleveland Bay haplotypes to other domestic horse haplotypes, the research findings suggested a close relationship of the Cleveland Bay horse with Northern European (Clade C), Iberian (Clade A) and North African (Clade B) horse breeds.
  • This link hinted that the Cleveland Bay horse may not have evolved solely from the now extinct Chapman horse, which challenges prior theories.

Conservation of Cleveland Bay Horses

  • Today, the Cleveland Bay horse is one of only five domestic horse breeds that are classified as Critical on the Rare Breeds Survival Trust (UK) Watchlist, emphasizing the pressing need for conservation.
  • The research results present important data on the breed’s origins, forming a vital asset for guiding conservation programs to secure this breed’s survival.

Cite This Article

APA
Dell AC, Curry MC, Yarnell KM, Starbuck GR, Wilson PB. (2020). Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse. PLoS One, 15(12), e0243247. https://doi.org/10.1371/journal.pone.0243247

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 15
Issue: 12
Pages: e0243247

Researcher Affiliations

Dell, Andy C
  • Department of Biological Sciences, University of Lincoln, Lincoln, United Kingdom.
  • Rare Breeds Survival Trust, Stoneleigh, Warwickshire, United Kingdom.
Curry, Mark C
  • Department of Biological Sciences, University of Lincoln, Lincoln, United Kingdom.
Yarnell, Kelly M
  • School of Animal, Rural and Environmental Sciences, Brackenhurst Campus, Nottingham Trent University, Southwell, Nottinghamshire, United Kingdom.
Starbuck, Gareth R
  • School of Animal, Rural and Environmental Sciences, Brackenhurst Campus, Nottingham Trent University, Southwell, Nottinghamshire, United Kingdom.
Wilson, Philippe B
  • Rare Breeds Survival Trust, Stoneleigh, Warwickshire, United Kingdom.
  • School of Animal, Rural and Environmental Sciences, Brackenhurst Campus, Nottingham Trent University, Southwell, Nottinghamshire, United Kingdom.

MeSH Terms

  • Animals
  • Cluster Analysis
  • DNA, Mitochondrial / genetics
  • Endangered Species
  • Genetic Variation / genetics
  • Haplotypes / genetics
  • Horses / genetics
  • Maternal Inheritance / genetics
  • Mitochondria / genetics
  • Phylogeny
  • Sequence Analysis, DNA / methods
  • Sequence Analysis, DNA / veterinary

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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Citations

This article has been cited 5 times.
  1. Carlentini M, Tumino S, Chessari G, Antoci A, Criscione A, Marletta D, Mastrangelo S, Bordonaro S. Variability Survey at Different Genetic Markers as Effective Tools for the Management of the Endangered Breeds: The Case of the Sicilian Native Donkeys. Animals (Basel) 2025 Dec 28;16(1).
    doi: 10.3390/ani16010090pubmed: 41514778google scholar: lookup
  2. Hu J, Wei H, Jiang Y, Xue Q, Wang F. DNA Barcoding in Meat Authentication: Principles, Applications, and Future Perspectives. Foods 2025 Oct 16;14(20).
    doi: 10.3390/foods14203522pubmed: 41154061google 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).
    doi: 10.3390/ani15060885pubmed: 40150414google scholar: lookup
  4. Musiał AD, 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.
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  5. Dell A, Curry M, Hunter E, Dalton R, Yarnell K, Starbuck G, Wilson PB. 16 Years of breed management brings substantial improvement in population genetics of the endangered Cleveland Bay Horse. Ecol Evol 2021 Nov;11(21):14555-14572.
    doi: 10.1002/ece3.8118pubmed: 34765125google scholar: lookup
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