Genomic Copy Number Variation in Horses with Disorders of Sexual Development

Genomic copy number variants (CNVs) are an important source of genetic diversity and play a role in complex diseases and congenital disorders, including disorders of sexual development (DSDs). Here we used an equine whole genome 400K tiling array by comparative genomic hybridization (CGH) to investigate the involvement of CNVs in SRY-positive XY sex reversal syndrome and cryptorchidism in horses. The sex reversal females (n=4; Appaloosa, QH, two Standardbreds) had a normal male 64XY karyotype with an intact SRY gene. At conservative CNV calling criteria (log₂ > 0.5; 5 probes) 187 CNVs were detected (126 gains, 61 losses) which varied in numbers, locations and size between the individuals. Among shared CNVs, the most functionally relevant was a ~300 kb deletion in two Standardbreds on ECA29 involving aldo-keto reductase gene cluster known to catalyze the conversion of sex hormones. The deletion was validated by PCR and FISH and is the first evidence about a likely molecular component of SRY-positive sex reversal in horses. Concurrently, CNV studies were initiated for cryptorchidism which is a complex disorder with poorly understood genetic component, and affects about 8% of live male births. Since research in humans proposes the involvement of CNVs, array CGH was conducted in four bilateral abdominal cryptorchids yielding in over 100 CNVs and 10 CNV regions. The data are currently analyzed for functional relevance and confirmed by qPCR and/or FISH. These pilot studies effectively validate the utility of the tiling array and suggest the involvement of CNVs in the genetics of equine DSDs.