Simultaneous genome-wide haplotyping and copy number detection enables universal equine preimplantation genetic testing

In different species, embryonic chromosomal aneuploidies are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explore the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A), monogenic (PGT-M) and polygenic (PGT-P) traits and diseases in the horse. To this end, over 70,000 single nucleotide polymorphism positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual cells from six arrested embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds ( GBE1, PLOD1, B3GALNT2, MUTYH ), and for one color coat-associated gene ( STX17 ) were determined and compared in biopsy-blastocyst combinations. The inherited parental haplotypes for loci of interest and the euploid (n = 12) or aneuploid (n = 2) state of the biopsied whole embryos were predicted by the biopsy samples in all successfully analyzed embryos. Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their cells, demonstrating the contribution of aneuploidy to equine embryonic arrest in vitro . The application of universal PGT would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.