A de-novo large ECAX partial deletion in a fertile Pura Raza Española mare detected using genomic data

PIROSANTO YAMILA; ANA ENCINA; GABRIEL ANAYA; MERCEDES VALERA; DEMYDA-PEYRÁS, SEBASTIÁN

Cape Town

Congreso; 39th international Society for Animal Genetics; 2023

Chromosomal abnormalities are a well-known source of infertility in the domestic horse. Nowadays, its detection rate is being increased, thanks to the development of SNP-based copy number aberration (CNA) analysis which can detect the loss or gain of DNA in the genome of an individual with increased accuracy. However, large chromosomal structural anomalies were barely reported in the species.Hereby, we report the case of a Pura Raza Española 5 years-old fertile mare bearing a large deletion in the ECAX p-arm. DNA samples from the mare and both parents were obtained from blood samples. All of them were genotyped using the 75K GGP equine SNP-bead chip (Neogen, Scotland), and analyzed using a CNA bioinformatic pipeline developed by our group based on BAF and LRR results. In addition, the mare was examined by the veterinary services of the Pura Raza Español breeder´s association.Results showed a large de-novo heterozygous deletion in the ECAX, between positions 2,153,000 and 10,651,000 approximately, depicted by a hemizygous pattern in CNV analysis (BAF values close to 0 or 1 and a reduction of LRR to -0.5). Interestingly, no DNA loss was detected in the distal region of the p-arm, in which the pseudoautosomal region is located, nor was any sign of cell chimerism. In addition, the reproductive tract was normal, to the point that the mare foaled a healthy colt very recently. Finally, a follow-up in-silico bioinformatic analysis revealed the presence of 38 genes included in the physical region affected. Among them, 13 were previously related to fertility and 2 of them (OFD1 and TRAPPC2) to abortion in mammals. To our knowledge, this is the first report of a fertile mare bearing a large deletion in the ECAX. Further studies on the colt are being performed to determine if the offspring inherited the mare´s deletion.