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BMC genomics2025; 26(1); 751; doi: 10.1186/s12864-025-11814-4

RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in Standardbred trotters.

Abstract: Racing without protective shoes is common in the Swedish harness racing industry, as it can enhance horses' performance on the track. Trainers typically decide whether a horse will race barefoot based on practical experience rather than objective measures. However, this practice can sometimes lead to excessive hoof wear, posing potential welfare concerns for racing horses. Gene expression differences may help reveal the underlying genetic mechanisms associated with different phenotypic traits. To explore an objective measure for assessing which horses are best suited for barefoot racing, we conducted a polyA-selected RNA-seq experiment on tissue from the growth zone at the coronary band of the hoof. This experiment compared tissues from Standardbred trotters capable of repeatedly racing barefoot without injury (n = 11) to those that could not (n = 7). By combining stringent phenotyping with racing records and trainer interviews, we aimed to elucidate the biological factors related to hoof strength in barefoot racing, focusing on differential abundant genes. Results: The RNA-seq analysis identified five significantly downregulated genes in horses capable of competing barefoot across consecutive races. These genes are associated with various biological processes relevant for hoof strength: ACCS, IRX2 and TRAPPAC6A contribute to enhancing the structural integrity of the hoof; MT2A regulates its metal homeostasis and SLC35F3 likely influences local vasoconstriction in the hoof. These gene findings suggest a coordinated genetic basis for structural reinforcement and physiological support of the hoof, which may be critical for sustaining performance under barefoot conditions. Conclusions: Our findings suggest that the ability of Standardbred trotters to race barefoot in consecutive events is reflected in distinct gene expression patterns, underscoring a genetic basis for hoof strength. This supports further genome-wide scans aimed at identifying genetic markers for hoof durability in these horses. The focused design of our study- comparing horses that could consistently race barefoot with those that could not- enabled us to isolate a select group of genes involved in diverse aspects of hoof biology essential for quality and resilience of horse hooves. This insight could ultimately be applied to augment both the performance and wellbeing of equine athletes across disciplines.
© 2025. The Author(s).
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Publication Date: 2025-08-18 PubMed ID: 40826322PubMed Central: PMC12363045DOI: 10.1186/s12864-025-11814-4Google 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.

Overview

  • This research identifies specific genes that contribute to the strength of horse hooves, enabling Standardbred trotters to perform barefoot racing without injury.
  • The study uses RNA sequencing to compare gene expression in hoof tissue between horses capable of barefoot racing repeatedly and those that are not, revealing genetic factors linked to hoof durability.

Background and Motivation

  • In Swedish harness racing, horses often race barefoot, which can improve performance but risks excessive hoof wear and potential welfare issues.
  • Currently, decisions about barefoot racing rely on trainers’ experience rather than objective scientific data.
  • Identifying genetic markers related to hoof strength could provide a more reliable method to determine which horses are best suited to race barefoot safely and effectively.

Research Objective

  • To pinpoint genes involved in hoof strength by comparing gene expression patterns in the hoof growth zone of Standardbred trotters that successfully race barefoot repeatedly to those that do not.
  • To develop an objective biological basis for assessing suitability for barefoot racing.

Methodology

  • Tissue samples were collected from the coronary band growth zone of horse hooves, as this site is critical for hoof structure and regeneration.
  • A polyA-selected RNA sequencing (RNA-seq) approach was used to profile gene expression in these tissues.
  • Two groups were compared:
    • 11 horses that repeatedly raced barefoot without injury.
    • 7 horses that could not race barefoot consistently.
  • Stringent phenotyping was performed, including:
    • Review of racing records.
    • Interviews with trainers to assess performance and injury history.
  • Statistical analysis identified genes with significantly different expression between groups, focusing on those downregulated in the barefoot group.

Key Findings

  • Five genes were significantly downregulated in horses able to race barefoot repeatedly:
    • ACCS: Related to enhancing structural integrity of the hoof.
    • IRX2: Implicated in developmental processes contributing to hoof strength.
    • TRAPPAC6A: Involved in maintaining structural components of the hoof.
    • MT2A: Plays a role in metal ion homeostasis, important for hoof physiological processes.
    • SLC35F3: Likely influences local vasoconstriction, affecting blood flow regulation in hoof tissue.
  • These genes suggest a coordinated biological mechanism combining structural reinforcement and physiological regulation to maintain hoof quality and resilience.

Interpretation and Implications

  • The distinct gene expression patterns in successful barefoot racers indicate a genetic basis for natural hoof strength and durability.
  • Expression changes in genes related to hoof structure building and physiological support provide insight into how some horses maintain hoof health under the stress of barefoot racing.
  • This knowledge supports the future development of genetic tests or markers to predict and select horses with superior hoof durability.
  • A better understanding of these mechanisms could help optimize horse welfare by wisely choosing barefoot racing candidates, minimizing injury and improving performance.

Conclusions

  • Consistency in barefoot racing ability among Standardbred trotters is underpinned by specific gene expression differences in hoof tissue.
  • The study successfully isolated a small set of genes intimately tied to diverse aspects of hoof biology essential for durability.
  • These findings pave the way for genome-wide marker discovery focused on improving equine hoof health and performance across disciplines.
  • Integrating genetic insights with training and management practices can enhance both the athletic capacity and well-being of racing horses.

Cite This Article

APA
Schwochow D, Alameddine A, Spörndly-Nees E, Montigny M, Naboulsi R, Jansson A, Niazi A, Lindgren G. (2025). RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in Standardbred trotters. BMC Genomics, 26(1), 751. https://doi.org/10.1186/s12864-025-11814-4

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 26
Issue: 1
Pages: 751
PII: 751

Researcher Affiliations

Schwochow, Doreen
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. doreen.schwochow@slu.se.
  • Division of Gene Technology, Science of Life Laboratory, Royal Institute of Technology, Stockholm, Sweden. doreen.schwochow@slu.se.
Alameddine, Asmaa
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Spörndly-Nees, Ellinor
  • Department of Pathology and Wildlife Diseases, Swedish Veterinary Agency, Uppsala, Sweden.
Montigny, Mathilde
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Naboulsi, Rakan
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
  • Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden.
Jansson, Anna
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Niazi, Adnan
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Lindgren, Gabriella
  • Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
  • Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Louvain, Belgium.

MeSH Terms

  • Animals
  • Horses / genetics
  • Horses / physiology
  • Hoof and Claw / physiology
  • Hoof and Claw / metabolism
  • RNA-Seq
  • Sequence Analysis, RNA
  • Gene Expression Profiling
  • Phenotype

Conflict of Interest Statement

Declarations. Ethics and approval and consent to participate: The horses sampled in this study were already euthanized at a licensed abattoir in Sweden for reasons unrelated to the study and before sample collection for the study was conducted. According to Swedish legislation, collecting tissue from animals already scheduled for euthanasia does not require an ethical permit or informed consent, as no experiments were conducted on the live animals. This approach aligns with the principles of the 3Rs (Replacement, Reduction and Refinement), ensuring responsible use of resources while avoiding additional harm to animals. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

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