Genomic analysis of gaits and racing performance of the French trotter.
Abstract: The aim was to disentangle gait characteristics from other qualities needed for racing performances with a genomic analysis of French trotters (FT). A sample of 1,390 horses were recruited, from which 46% were genotyped with Illumina chip of 54,602 SNPs, 49% with Affymetrix chip of 670,806 SNPs and 586 had a completed questionnaire on trotting technique. Racing performances cover the period 1996 to 2018. There were 252,368 FT-born; 96,617 qualified and 83,962 which participated in a race. After quality control, 377,611 SNPs were retained and imputed. Questionnaire described trotting technique over 13 questions which were summarized, after principal component analysis in 3 traits: pacer, heavy trot/gallop and other defects. GWAS and genomic evaluation were performed using single-step approach. We found 25 QTL for racing performances and 9 for trotting technique. Only DMRT3 mutation was significant for both traits. To tend to pace avoid the defect at gallop and lead to a better early career for earnings, less percentage of disqualified races at all ages and more harness than under saddle career. This is the portrait of AA genotype at DMRT3. We found 5 other QTL, not linked to gait traits, which might improve selection of genetically independent performance traits of earnings per races and percentage of finished races. For only earnings at different ages and in under saddle or harness races, genomic evaluation remains the best way to predict performances.
© 2020 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.
Publication Date: 2020-11-29 PubMed ID: 33249655PubMed Central: PMC7898598DOI: 10.1111/jbg.12526Google Scholar: Lookup
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Summary
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The research study focuses on understanding the genetic contributions to the distinctive gaits and racing performance of French Trotter horses. It does so by using genomic analysis.
Participants and Data Collection
- The study was conducted on 1,390 French Trotter horses, of which nearly half were genotyped using the Illumina chipset (which maps 54,602 single nucleotide polymorphisms, or SNPs) and another half using the Affymetrix chip (mapping 670,806 SNPs).
- A total of 586 horses had completed a questionnaire regarding their trotting technique.
- Racing performance data was collected from races conducted between 1996 and 2018. This data represented 252,368 FT-born horses, 96,617 qualified for racing, and 83,962 that participated in a race.
Data Analysis
- After quality control, a total of 377,611 SNPs were selected for analysis and the missing data were imputed.
- The questionnaire on trotting technique was summarized into three traits after principal component analysis: pacer, heavy trot/gallop, and other defects.
- A genome-wide association study (GWAS) and genomic evaluation were performed using a single-step approach.
Findings
- The results identified 25 quantifiable traits loci (QTL) linked to racing performances and 9 linked to trotting techniques.
- Interestingly, only the DMRT3 mutation was found to significantly affect both traits. Horses with the AA genotype at DMRT3 tended to pace avoiding gallop defect and had a better early career in terms of earnings, fewer percentage of disqualified races at all ages, and more harness than under saddle career.
- The team also identified five other QTLs that were not linked to gait traits but could still improve selection for performance traits independent of gait characteristics, specifically the earnings per race and the percentage of finished races.
- For earnings at different ages and in different types of races (under saddle or harness), genomic evaluation was found to be the best way to predict performances.
The results of this analysis provide insights into the genetic factors that might influence the specific gaits and racing performance of French Trotters. This understanding could help in selective breeding strategies and potentially improve racing performances of these horses.
Cite This Article
APA
Ricard A, Duluard A.
(2020).
Genomic analysis of gaits and racing performance of the French trotter.
J Anim Breed Genet, 138(2), 204-222.
https://doi.org/10.1111/jbg.12526 Publication
Researcher Affiliations
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
- Pole Développement Innovation Recherche, IFCE, Gouffern en Auge, France.
- Département Elevage & Santé Animale, LeTrot, Paris, France.
MeSH Terms
- Alleles
- Animals
- Gait
- Genomics
- Genotype
- Horses
- Phenotype
Grant Funding
- Fonds Eperon
- Institut Français du Cheval et de l'Equitation
Conflict of Interest Statement
The authors declare that they do not have any conflict of interest.
References
This article includes 46 references
Citations
This article has been cited 6 times.- Jafari H, Abebe BK, Cong L, Ahmed Z, Zhaofei W, Sun M, Muhatai G, Chuzhao L, Dang R. Review: Genomic insights into the adaptive traits and stress resistance in modern horses. Stress Biol 2026 Jan 12;6(1):5.
- Kingsley NB, Sandmeyer L, Dwyer A, Langefeld CD, McMullen RJ Jr, McCue M, Lassaline M, Bellone RR. A genome-wide investigation of insidious uveitis in Appaloosa horses. BMC Genomics 2025 Oct 9;26(1):904.
- Nazari-Ghadikolaei A, Fikse WF, Viklund ÅG, Mikko S, Eriksson S. Single-Step Genome-Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses. J Anim Breed Genet 2025 Sep;142(5):499-512.
- Vincelette A. The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits. Animals (Basel) 2023 Aug 8;13(16).
- Laseca N, Molina A, Ramón M, Valera M, Azcona F, Encina A, Demyda-Peyrás S. Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares. Front Vet Sci 2022;9:754028.
- Wolfsberger WW, Ayala NM, Castro-Marquez SO, Irizarry-Negron VM, Potapchuk A, Shchubelka K, Potish L, Majeske AJ, Oliver LF, Lameiro AD, Martínez-Cruzado JC, Lindgren G, Oleksyk TK. Genetic diversity and selection in Puerto Rican horses. Sci Rep 2022 Jan 11;12(1):515.
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