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Home / Equine Research Bank / Genet Sel Evol / Genetic characterisation of the Connemara pony and the Warmb...
Genetics, selection, evolution : GSE2023; 55(1); 60; doi: 10.1186/s12711-023-00827-w

Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach.

Abstract: The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds. Results: The k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne). Conclusions: Distinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.
© 2023. ’Institut National de Recherche en Agriculture, Alimentation et Environnement (INRAE).
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Publication Date: 2023-08-17 PubMed ID: 37592264PubMed Central: PMC10436415DOI: 10.1186/s12711-023-00827-wGoogle Scholar: Lookup
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Summary

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The study investigates the genetic differences between the Connemara pony (CP) and the Warmblood horse (WB) using comprehensive genetic screening and analysis methods. The aim is to provide insights into the genetic diversity, characteristics and potential health risks associated with both breeds.

Genomic Diversity and Breed Classification

  • Researchers used whole-genome sequencing data of 116 WB and 36 CP breeds, combining both UK and European versions to analyze their genomic diversity and population structure.
  • The k-means clustering approach was used to categorize both CP and WB populations into four distinct genetic groups. These groups reflected certain characteristics such as place of origin (US or UK) and specific breed types (e.g., Holsteiners).

Linkage Disequilibrium (LD) and Inbreeding

  • Next, they evaluated linkage disequilibrium (LD), a measure of the non-random association of alleles at different loci in a given population. They found significant differences in LD between the two breeds, with LD decay generally slower in CP than in WB, which means there is less genetic variation within the CP breed.
  • Inbreeding levels were evaluated using a measure called runs of homozygosity (ROH), where higher ROH values indicate more inbreeding. The research found that CP was less inbred overall than WB, but there were indications of recent inbreeding in specific CP genetic groups (C2, C3, C4).

Disease Risk and Other Findings

  • The study revealed possible health risks tied to certain genetic groups within the CP breed. The highest ranking pairwise fixation index (F) values indicated an association with cancer-related ontology terms when comparing the four CP genetic groups.
  • In regards to the ratio of the effective number of breeders (N) to effective population size (N), both CP and WB had similar ratios, indicating that the influence of popular sires, sires that are frequently used for breeding, is similar in both breeds.

Conclusions

  • The study successfully highlighted distinct genetic groups within each breed, and showed that WB genetic groups more accurately reflected population substructure than places of origin or studbook classifications.
  • The study also identified genetic markers associated with immune and inflammatory responses within CP genetic groups and revealed higher levels of recent inbreeding within the breed, even though overall inbreeding was less in CP than in WB.
  • The research provides valuable insight that could be used in the future for making informed breeding decisions and better managing the health risks of both breeds.

Cite This Article

APA
Lindsay-McGee V, Sanchez-Molano E, Banos G, Clark EL, Piercy RJ, Psifidi A. (2023). Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach. Genet Sel Evol, 55(1), 60. https://doi.org/10.1186/s12711-023-00827-w

Publication

Genetics, selection, evolution : GSE
ISSN: 1297-9686
NlmUniqueID: 9114088
Country: France
Language: English
Volume: 55
Issue: 1
Pages: 60

Researcher Affiliations

Lindsay-McGee, Victoria
  • Royal Veterinary College, London, UK.
  • Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
Sanchez-Molano, Enrique
  • The Roslin Institute, University of Edinburgh, Edinburgh, UK.
Banos, Georgios
  • Scotland's Rural College (SRUC), Edinburgh, UK.
Clark, Emily L
  • The Roslin Institute, University of Edinburgh, Edinburgh, UK.
Piercy, Richard J
  • Royal Veterinary College, London, UK.
Psifidi, Androniki
  • Royal Veterinary College, London, UK. apsifidi@rvc.ac.uk.

MeSH Terms

  • Animals
  • Horses / genetics
  • Inbreeding
  • Cluster Analysis
  • Genomics
  • Homozygote
  • Linkage Disequilibrium

Conflict of Interest Statement

The authors declare that they have no competing interests.

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