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BMC veterinary research2025; 21(1); 346; doi: 10.1186/s12917-025-04794-w

Selection signatures and inbreeding: exploring genetic diversity in five native horse breeds.

Abstract: Horses have undergone extensive natural and artificial selection, shaping the diversity of breeds observed today. Native Italian breeds present unique traits influenced by natural selection, such as adaptation to harsh climates, or hoof strength, but face challenges due to population declines and the reduction of their original breeding purpose. This study focuses on five local Italian breeds: Bardigiano, Haflinger, Maremmano, Murgese, and Italian Heavy Draught Horse, to understand how selection has shaped their populations. A total of 1620 individuals were genotyped with a medium-density SNP chip and remapped to EquCab3. After quality control, where data were filtered based on missing genotypes per SNP (> 0.10) and missing SNPs per sample (> 0.10), 1498 horses and 54,825 SNPs remained for analysis. Population structure and runs of homozygosity (ROH) were identified, and genomic inbreeding coefficients were calculated based on ROH coverage of autosomal SNPs. ROH islands shared by ≥ 70% of horses were identified as selection signatures, and candidate genes within these regions were annotated. The inbreeding coefficient (FROH) ranged from 0.15 to 0.23, with Bardigiano and Haflinger showing the highest values probably due to selective breeding, while Maremmano, Murgese, and Italian Heavy Draught Horse displayed lower FROH, reflecting a broader diversity. ROH islands were identified on 12 chromosomes, with 23 islands distributed among breeds. Cold-blooded breeds (Bardigiano, Haflinger, and Italian Heavy Draught Horse) showed the majority, particularly on Equine Chromosome 3 (ECA3). These islands overlapped with 83 quantitative trait loci (QTLs) and 76 genes associated with morphology and health. Health-related traits such as osteochondrosis and hoof health were linked to ROH patterns, particularly in Bardigiano and Haflinger, highlighting selection for disease resistance. Signature of selections were found in the proximity of MC1R and ASIP genes likely due to their role for coat color; especially in the Haflinger and Italian Heavy Draught Horse the genotype frequency of the BIEC2_816499 SNP which is in the vicinity of the causative mutation for chestnut coat color is due to linkage disequilibrium between the two. In conclusion, this study offered valuable insights that breeders could utilize to make sound decisions. This issue would ensure the maintenance of breed genetic diversity, and the preservation and improvement of the breed's distinct traits and health standards.
© 2025. The Author(s).
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Publication Date: 2025-05-16 PubMed ID: 40380299PubMed Central: PMC12082900DOI: 10.1186/s12917-025-04794-wGoogle Scholar: Lookup
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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 talks about the genetic diversity in five native Italian horse breeds and how natural and artificial selection have influenced their traits. The paper also examines the impact of population decline and original breeding purpose on the genetic makeup of these breeds and provides insights which breeders could use to maintain genetic diversity and improve breed health and traits.

Research Method

  • The researchers conducted a detailed examination of five native Italian horse breeds: Bardigiano, Haflinger, Maremmano, Murgese, and Italian Heavy Draught Horse.
  • They genotyped a total of 1620 individuals using a medium-density SNP chip and then remapped the data to EquCab3.
  • Quality control checks were performed and data that did not pass the cutoffs for missing genotypes per SNP (> 0.10) and missing SNPs per sample (> 0.10) were filtered out. This left 1498 horses and 54,825 SNPs for the main analysis.

Analysis Process

  • The team identified the population structure and runs of homozygosity (ROH).
  • They calculated genomic inbreeding coefficients based on ROH coverage of autosomal SNPs.
  • ROH islands, which are genome segments shared by at least 70% of the horses, were identified as selection signatures.
  • The researchers also annotated candidate genes within these regions.

Key Findings

  • The inbreeding coefficient (FROH) ranged from 0.15 to 0.23, with Bardigiano and Haflinger having the highest values potentially due to selective breeding.
  • Maremmano, Murgese, and Italian Heavy Draught Horse showed lower FROH, indicating greater diversity within their genotypes.
  • 23 ROH islands distributed among the breeds were discovered on 12 chromosomes, most of them being present in cold-blooded breeds (Bardigiano, Haflinger, and Italian Heavy Draught Horse).
  • 83 quantitative trait loci (QTLs) and 76 genes associated with morphology and health overlapped with these islands. Traits linked to disease resistance like osteochondrosis and hoof health were particularly associated with Bardigiano and Haflinger.
  • Selective breeding for coat color was also discovered, particularly in the Haflinger and Italian Heavy Draught Horse breeds where genotype frequency linked to chestnut coat color was found.

Research Contribution and Conclusion

  • The findings from the study provide valuable insights into the genetic diversity and specific traits of these Italian horse breeds.
  • These insights could help breeders make informed decisions regarding breeding programs, and assist in maintaining the genetic diversity, preservation, and improvement of the breed’s unique traits and health standards.

Cite This Article

APA
Asti V, Summer A, Ablondi M, Sartori C, Giontella A, Pilastro V, Mecocci S, Cappelli K, Mancin E, Oian A, Mantovani R, Capomaccio S, Sabbioni A. (2025). Selection signatures and inbreeding: exploring genetic diversity in five native horse breeds. BMC Vet Res, 21(1), 346. https://doi.org/10.1186/s12917-025-04794-w

Publication

BMC veterinary research
ISSN: 1746-6148
NlmUniqueID: 101249759
Country: England
Language: English
Volume: 21
Issue: 1
Pages: 346

Researcher Affiliations

Asti, Vittoria
  • Department of Veterinary Science, University of Parma, Parma, Italy.
Summer, Andrea
  • Department of Veterinary Science, University of Parma, Parma, Italy.
Ablondi, Michela
  • Department of Veterinary Science, University of Parma, Parma, Italy. michela.ablondi@unipr.it.
Sartori, Cristina
  • Department of Agronomy, Natural Resources, Animals, and Environment, University of Padua, Food, Padua, Italy.
Giontella, Andrea
  • Department of Veterinary Medicine, University of Perugia, Perugia, Italy.
  • Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy.
Pilastro, Valeria
  • Department of Veterinary Science, University of Parma, Parma, Italy.
Mecocci, Samanta
  • Department of Veterinary Medicine, University of Perugia, Perugia, Italy.
  • Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy.
Cappelli, Katia
  • Department of Veterinary Medicine, University of Perugia, Perugia, Italy.
  • Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy.
Mancin, Enrico
  • Department of Agronomy, Natural Resources, Animals, and Environment, University of Padua, Food, Padua, Italy.
Oian, Angelica
  • Department of Agronomy, Natural Resources, Animals, and Environment, University of Padua, Food, Padua, Italy.
Mantovani, Roberto
  • Department of Agronomy, Natural Resources, Animals, and Environment, University of Padua, Food, Padua, Italy.
Capomaccio, Stefano
  • Department of Veterinary Medicine, University of Perugia, Perugia, Italy.
  • Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy.
Sabbioni, Alberto
  • Department of Veterinary Science, University of Parma, Parma, Italy.

MeSH Terms

  • Animals
  • Horses / genetics
  • Inbreeding
  • Polymorphism, Single Nucleotide
  • Genetic Variation
  • Selection, Genetic
  • Italy
  • Genotype
  • Breeding
  • Male
  • Female

Conflict of Interest Statement

Declarations. Ethics approval and consent to participate: Animal Care and Use Committee approval was not obtained for this study because all the analyses were performed using pre-existing datasets provided by Italian Breeding associations within national Projects called Equinbio and Equinbio.2 where the animal study design was reviewed and approved by the MIPAAF—PSRN 2014–2020—10.2, ID: J59H18000030005; Approval D.M. 6695, 21/02/2018. The hair sampling procedure was non-invasive and caused no harm or discomfort to the animals. Informed consent was obtained from all horse owners prior to sample collection. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

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