Cytogenetic, genomic, and reproductive characterization of four Pura Raza Española Mares carrying a 64, X, del(X), t(X; Y) complex karyotype.

Chromosomal abnormalities involving the sex chromosomes constitute critical genetic factors influencing fertility in horses. Nevertheless, a substantial proportion of individuals carrying sex chromosomal abnormalities exhibit normal reproductive phenotypes, which complicates their identification until adulthood. Here, we present four mares carrying a complex deletion/translocation rearrangement with the karyotype formula 64, X, del(X)(p∼25), t(X; Y)(p∼25; q∼15). The cases analyzed belong to three unrelated families of Pura Raza Española (PRE), all presenting the same chromosomal abnormality. Two of the individuals analyzed were a fertile mare and her foal, demonstrating vertical transmission of the rearrangement to the next generation. The animals were initially flagged for sex chromosome abnormalities due to incompatibilities between phenotypic and genotypic sex detected during STR analysis for parentage. They were subsequently analyzed for copy number abnormalities and sex chromosome assessment using an equine commercial SNP-array-based methodology, detecting a large heterozygous 10 Mb deletion located at the distal part of the ChrX p-arm, as well as the existence of a genomic region associated with ChrY. Fluorescence in situ hybridization (FISH) further confirmed that ChrY-derived material was translocated to the same distal part of the ChrX p-arm. Finally, bioinformatic tools were used to evaluate the abundance of CpG islands and to perform a functional analysis of the genes located in the affected regions. These results may suggest that reproductive competence in the fertile mare could be explained by the production of euploid zygotes carrying at least one copy of the intact X chromosome. This study highlights the importance of accurate detection and characterization of chromosomal abnormalities in horses, particularly in individuals with apparently normal reproductive phenotypes.