Sex determination and genetic screening of equine embryos with whole genome amplification and real-time PCR

Reliable pre-implantation sex determination and genetic screening enables informed embryo transfer decisions in equine breeding while avoiding later interventions. We developed a streamlined workflow that couples rapid whole genome amplification (WGA) with a multiplex real-time PCR targeting ETSTY5 as a Y-specific marker and UBC as an autosomal control. On purified equine DNA, sex was correctly assigned down to 10 pg gDNA and to a single fibroblast cell. Direct testing of embryo biopsies without WGA yielded inconsistent results, whereas introducing a short WGA step produced tight allelic-discrimination clusters and 100% diagnostic calls, including in cloned embryos of known sex. The same WGA product supported targeted genotyping for inherited disease screening of hyperkalemic periodic paralysis (HYPP) and hereditary equine regional dermal asthenia (HERDA) alleles. This WGA plus real-time PCR pipeline supports robust and practical embryo sexing and targeted pre-implantation genetic diagnostics within in vitro produced (IVP) equine embryo and embryo transfer workflows.