Involvement of CNVs in Equine Cryptorchidism

Cryptorchidism (CO) is the most common non-lethal congenital disorder in male horses and negatively impacts the economy of the horse industry globally. The composite genetic component of CO is as yet poorly understood though findings in human suggest the involvement of DNA copy number variants (CNVs). Here we conducted genome-wide CNV analysis by array comparative genomic hybridization in normal and CO horses. We revealed a 200 kb homozygous deletion in chromosome 29 in some CO horses. Homozygosity of the CNV was confirmed by PCR and fluoresence in situ hybridization (FISH). The deletion disrupted a cluster of AKR1C genes known to be involved in sex hormone metabolism and sexual development. Further analysis by FISH in selected CO and control horses showed that the deletion is homozygous in some CO horses and heterozygous in others, while no deletion was detected in controls. The findings suggested potentially causative relationship between the CNV and equine CO. Therefore, attempts were made to precisely demarcate deletion breakpoints and design a PCR test for population analysis to identify homozygous and heterozygous carriers, and ascertain genotype-phenotype association. We observed that the deletion landscape is complex and that the reference genome might have mis-assemblies in the region. Currently, re-sequencing of the CNV region in chromosome 29 is in progress. The goal is to improve the assembly and annotation of the AKR1C-region and develop a diagnostic test for detecting mutation carriers. The biomedical importance of the findings will potentially extend to other domestic animals and humans.