Early pregnancy loss (EPL) affects ~5–10% of clinically recognized and ~20% of pre-clinical equine pregnancies, increasing breeding costs and reducing healthy foal production. Chromosomal abnormalities, particularly aneuploidy, are the predominant cause, but the underlying genetic and molecular causes – especially chromosome-specific driving factors in very early losses – are unknown. The centromere, a chromosomal locus critical for accurate cell division, is a potential molecular driver of EPL risk. Identifying centromere variants linked to EPL offers a path to prenatal diagnostics for mares and stallions, enabling improved pregnancy outcomes. Our overarching hypothesis is that underlying variation in centromere genetics influences error correction, thus contributing significantly to EPL risk. Our major goals are: 1) generate high-resolution whole genomic resources to understand genetic basis of EPL and other equine diseases 2) characterize and identify genetic centromere variants linked to aneuploidy risk in EPL, and 3) assess the impact of parental centromere variation on the incidence and type of chromosomal abnormality in very early-stage embryos. This project is an ongoing, successful collaboration led by Dr Das, along with Dr. de Mestre.