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Background  Recently, a mutation was discovered in the  DMRT3  gene that controls pacing in horses. The mutant allele A is fixed in the American Standardbred trotter breed, while in the French trotter breed, the frequency of the wild-type allele C is still 24%. This study aimed at measuring the effect of  DMRT3  genotypes on the performance of French trotters and explaining why the polymorphism still occurs in this breed. Using a mixed animal model, genetic parameters and environmental effects on performance traits were estimated from data on 173 176 French trotter races. The effect of the  DMRT3  gene was then estimated by the effect of genotype at the highly linked SNP  BIEC2-620109  (C-C, A-T) for 630 horses. A selection scheme that included qualification and racing performances was modeled to (1) verify if the observed superiority of heterozygous CT horses at this SNP could be explained only by selection and (2) understand why allele C has not disappeared in French trotters.    Results  Heritability of racing performance traits was high for qualification test (0.56), moderate for annual earnings per finished race (0.26 to 0.31) and low for proportion of disqualified races (0.06 to 0.09). Genotype CC was always unfavorable compared to genotype TT for qualification: the probability to be qualified was 20% for CC  vs.  48% for TT and earnings were -0.96  σ   y   lower for CC than for TT. Genotype CT was also unfavorable for qualification (40%) and earnings at 3 years (-0.21  σ   y  ), but favorable for earnings at ages greater than 5 years: +0.41  σ   y   ( P  = 7.10 −4 ). Selection on qualification could not explain more than 19% of the difference between genotypes CC and CT in earnings at ages greater than 5 years. Only a scenario for which genotype CT has a favorable effect on the performance of horses older than 5 years could explain that the polymorphism at the  DMRT3  gene still exists in the French trotter breed.    Conclusions  The use of mature horses in the French racing circuit can explain that the CA genotype is still present in the French trotter horses.

Does heterozygosity at the DMRT3 gene make French trotters better racers?