Figure 1

PGT analysis of blastocyst-stage equine embryos. On the left side, the circos plots are depicted for two out of 14 blastocyst-stage equine embryos that were aneuploid. The outer and inner circles represent the genome constitution per chromosome (1-X) of the biopsy sample and the corresponding biopsied blastocyst sample, respectively. Different colors represent different types of aneuploidies. On the right, the parental haplarithm plots of the biopsy (upper plot) and the corresponding embryo sample (lower plot) of Mare01_Embryo01 are depicted containing the genome-wide LogR value (measure for the chromosome copy number), the maternal B-allele-frequency (Mat-BAF), the maternally inherited haplotype blocks (pink/red colors represent regions inherited from maternal homologue 1 or 2), the paternal B-allele-frequency (Pat-BAF) and the paternally inherited haplotype blocks (light/dark blue colors represent regions inherited from maternal homologue 1 or 2) from the bottom to the top, respectively. The inherited parental haplotypes of four disease-causing genes (B3GALNT2 for congenital hydrocephalus, MUTYH for cerebellar abiotrophy, PLOD1 for warmblood fragile foal syndrome, GBE1 for glycogen branching enzyme deficiency) and the gene causative for grey color coat (STX17) are indicated by the yellow line. Genome-wide haplarithm plots and detailed chromosome-wise haplarithm plots of the chromosomes carrying a gene of interest of all samples can be retrieved in Additional file 1, Figs. 1 and 2, respectively.