Genomic analysis of gaits and racing performance of the French trotter.

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.