Fertility traits are pointed out as one of the most important breeding values in livestock production. However, they were scarcely evaluated in horses, probably due to the lack of phenotypic data as well as the effect produced by the variations in the reproductive management associated with different breeds and activities. Among them, foaling number (FN), determined as the number of foals produced per year of reproductive life, is considered an interesting reproductive trait since it is influenced at the same time by the fertility and the longevity of the individuals. But studies assessing its genetic component in a large dataset of individuals are still absent. Additionally, molecular inbreeding (the actual degree of homozygosity molecular-values, FROH) it was also associated with fertility in livestock. In this study, we evaluated the effect of Froh in the foaling number estimated breeding value (EBVFN) in 243 Pura Raza Español mares (PRE). EBV’s were estimated based on 72,982 phenotypical records belonging to the PRE studbook using a bivariate REML model implemented in the VCE-6 package. The model included breeding stud size, owner stud size, owner stud country and birth year of the mother and the age of mare as a covariate. Molecular-based inbreeding values were estimated individually as the percentage of the genome harboring runs of homozygosity (FROH) using

600,345 SNP markers (27,569 from ECAX) through the Axiom™ Equine genotyping array (Affymetrix). FROH values were also determined using ROH longer than 16Mb (FROH16; depicting a recent increase of inbreeding) as well as only SNP markers located in ECAX (FROHX). EBVFN ranged from-1.72 to 2.78 depicting an ample genetic variation for these traits. Similarly, FROH and FROHX varied from 0.005 to 0.3986 and 0 to 0.969 respectively (with an average of 0.1461) also showing an ample variability in terms of homozygosity. Our results also determined the existence of a large negative correlation (r=-0.398; p< 0.001) between FROH and EBVFN, which was also observed, to a lesser extent, when we analyzed the inbreeding generated during the last three generations (FROH16; r=-0.262; p< 0.001). But interestingly, correlation values were even higher in mares when the FROHX and FROHX16 were correlated with EVBFN (r=-0.423 and r=-0.321; P< 0.001 respectively), in agreement with recent studies performed in livestock individuals which suggested that fertility traits are highly related to the genomic variants located in the X chromosome. In conclusion, we demonstrate, using HD genomic data, that an increase in genomic homozygosity, and particularly in ECAX, produce a large decrease in the fertility of the mare estimated as the number of foals produced per year.