Stallion fertility is of high economic importance for the horse industry. The discovery of molecular mechanisms affecting fertility will be facilitated by the horse genome assembly and the development of novel tools for analysing complex genetic traits. Genetic markers in candidate genes, such as CRISP3, SPATA1 and INHBA, in breeding stallions have been associated with pregnancy rate per oestrus in mares. This paper reviews candidate autosomal, X and Y genes for stallion fertility, including genes encoding hormones and their receptors of the hypothalamic-pituitary axis, proteins of the seminal plasma, proteins involved in spermatozoa-ovum binding and genes influencing sexual development, as well as Y-specific genes. Their chromosomal location and gene structure are described, based on the horse genome assembly EquCab2.0 and a resource for markers located within or in close vicinity to the candidate genes (including pre-designed primer sequences). The application of genetic markers in improving stallion fertility for breeding and management is discussed.
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