Molecular Studies of Equine Cryptorchidism

Cryptorchidism (CO) is a non-lethal phenotypically heterogeneous congenital disorder that negatively impacts equine health and reproduction, and the economy of the horse industry. While it is recognized that CO has a genetic component, very little is known about the underlying genes and mutations. We recently discovered that about 10% of CO horses are homozygous for a large (~200 kb) autosomal deletion that involves genes necessary for dihydrotestosterone metabolism. In order to design qualitative molecular test(s) for the detection of deletion carriers and properly evaluate genotype-phenotype association, a detailed map of the deletion is necessary. Preliminary analysis of the corresponding region in EquCab2 reference genome indicated that the sequence is complex, contains segmental duplications, gaps, and likely miss-assemblies. We are currently reconstructing the reference sequence by long-read (PacBio) sequencing a 400kb BAC tiling path over the deletion and adjacent regions. Also, we generated whole-genome short-read (Illumina) sequences for 2 CO horses carrying the deletion, and for control horses. Sequence analysis confirmed that the 2 CO horses were homozygous for the deletion; that the deletion is larger than anticipated (238kb), and that it involves a gene family with functions in sex hormone metabolism. No such deletion was detected in control horses. However, the large deletion embedded a small common (28kb) CNV which was present in all horses but involved no genes. The sequence information is currently used to demarcate deletion start and end sites and develop a test that can discriminate between homozygous and heterozygous carriers and horses with no deletion.