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Genetics, selection, evolution : GSE2024; 56(1); 53; doi: 10.1186/s12711-024-00922-6

Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed.

Abstract: The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (F) by means of Runs of Homozygosity. Results: To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and F of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders. Conclusions: The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.
© 2024. The Author(s).
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Publication Date: 2024-07-10 PubMed ID: 38987703PubMed Central: PMC11238448DOI: 10.1186/s12711-024-00922-6Google Scholar: Lookup
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  • Journal 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.

This study explores the origins of the Franches-Montagnes, Switzerland’s last native horse breed, using a high volume of single nucleotide polymorphism data. Through studying various horse breeds, the research provides comprehensive insight into genetic diversity and potential protective management strategies for the breed.

Details of the Study

Researchers examined a high volume of genotype data—namely from Single Nucleotide Polymorphisms (SNPs)—gathered from 522 Franches-Montagnes (FM) horses. Other breeds examined included 514 horses of the European Warmblood (WB) breed, 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses. These breeds were selected due to their historical linkage as seen from pedigree data which showed their influence in the development of FM.

  • The goal of the research was to classify the population structure of the FM breed by estimating individual admixture levels and assessing genomic inbreeding through Runs of Homozygosity.
  • A three-step process was applied to evaluate the fine-scale population structures within the FM breed. This combined: admixture, genetic contribution, and F of individuals.

Results of the Research

The results demonstrated that population substructures were either linked with variances in genetic origin or the offspring of the most influential stallions.

  • The study found that admixed horses mainly accounted for the genetic variance in the current breeding population.
  • Old-type horses (OF), on the other hand, contributed to only a minor portion of the genetic variance.
  • The FM horses demonstrated high TB admixture levels.
  • The study identified discrepancies in the descent of FM horses from the Arabian stallion Doktryner.
  • Compared to the other breeds, with the exception of WB, FM horses were found to be less inbred. However, infrequent yet long ROH (Runs of Homozygosity) segments suggested a loss of diversity in both FM subpopulations.

Conclusions and Recommendations

Despite having experienced bottlenecks from intensive stallion selection, restrictive mating choices, and the selection of rare coat colours, the FM remains uniquely distinct from historically introgressed breeds, holding its status as the last native Swiss breed.

  • The researchers suggested that to maintain genetic diversity in FM horses, there needs to be a well-balanced selection of stallions, possibly by integrating OF stallions into the FM breeding population.
  • It was recommended to steer away from selecting rare coat colours, to prevent further reduction in genetic diversity.

Cite This Article

APA
Gmel AI, Mikko S, Ricard A, Velie BD, Gerber V, Hamilton NA, Neuditschko M. (2024). Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed. Genet Sel Evol, 56(1), 53. https://doi.org/10.1186/s12711-024-00922-6

Publication

Genetics, selection, evolution : GSE
ISSN: 1297-9686
NlmUniqueID: 9114088
Country: France
Language: English
Volume: 56
Issue: 1
Pages: 53
PII: 53

Researcher Affiliations

Gmel, Annik Imogen
  • Animal GenoPhenomics, Agroscope, Route de la Tioleyre 4, 1725, Posieux, Switzerland.
  • Equine Department, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8053, Zurich, Switzerland.
Mikko, Sofia
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden.
Ricard, Anne
  • Institut National de la Recherche Agronomique, Domaine de Vilvert, 78350, Jouy-en-Josas, France.
Velie, Brandon D
  • Equine Genetics and Genomics Group, School of Life and Environmental Sciences, University of Sydney, RMC Gunn B19-603, Sydney, NSW, 2006, Australia.
Gerber, Vinzenz
  • Institut Suisse de Médecine Equine ISME, Vetsuisse Faculty, University of Bern, Länggassstrasse 124, 3012, Bern, Switzerland.
Hamilton, Natasha Anne
  • Sydney School of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia.
Neuditschko, Markus
  • Animal GenoPhenomics, Agroscope, Route de la Tioleyre 4, 1725, Posieux, Switzerland. markus.neuditschko@agroscope.admin.ch.

MeSH Terms

  • Horses / genetics
  • Animals
  • Polymorphism, Single Nucleotide
  • Inbreeding
  • Pedigree
  • Male
  • Breeding / methods
  • Female
  • Switzerland
  • Genotype
  • Homozygote

Grant Funding

  • 625000469 / Bundesamt fu00fcr Landwirtschaft

Conflict of Interest Statement

The authors declare that they have no competing interests.

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Citations

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