Chromosomal chaos: understanding aneuploidy associated with assisted reproductive technologies

Pregnancy loss remains a significant challenge for the equine breeding industry, with substantial economic and management consequences. Chromosomal abnormalities have emerged as a central driver of pregnancy loss, particularly during early gestation, highlighting the need to better understand the etiology of this inherent genetic instability. Concurrently, the rapid expansion of assisted reproductive technologies (ART) offers promise for improving equine reproductive efficiency alongside the traditional practice of natural cover. However, the increasing use of in vitro embryo production (IVP) raises important questions regarding the genetic stability and long-term health of resulting offspring. Here we extensively review the mechanistic basis, putative origins, and subtypes of genetic abnormalities, underscoring specific biases in points of lethality during pregnancy loss. Although evidence remains limited, we also examine emerging data suggesting distinct patterns of developmental tolerance and genetic instability between IVP and in vivo derived (IVD) embryos. Notably, available studies report complex and widespread genomic disruptions associated with IVP embryos, underscoring the need for systematic characterization of genetic profiles and offspring outcomes across breeding modalities. Decoding the genetic consequences of ART represents an important frontier in equine reproduction research, with broad implications for optimizing ART protocols and maintaining healthy and sustainable equine lineages.