Understanding a Recessive Embryo-Lethal Genotype in Australian Thoroughbred Horses

Summary

This project addresses an emerging issue in Australian Thoroughbred breeding: a highly prevalent recessive gene variant, LY49B, which appears to cause early embryonic loss when inherited from both parents. Around 50% of Thoroughbreds are carriers, but the reason for this high frequency is unclear.

When two LY49B carriers are mated, there is a 25% chance of producing a non-viable embryo, reducing per-cycle pregnancy rates compared to non-carrier or mixed matings. At the national herd level, this may contribute to a 6.25% drop in per-cycle pregnancy rates — potentially explaining recent anecdotal reports of declining fertility by breeders. Typically, such variants are eliminated naturally through evolutionary pressure on reproductive efficiency. However, the increasing frequency of LY49B suggests that selection for certain pedigree lines may be inadvertently allowing this gene to persist in the breeding population.

This project will assess the impact of LY49B variants on embryo development. The findings will guide breeders in deciding whether to avoid carrier-to-carrier matings to improve pregnancy rates, or simply manage expectations – recognising that such matings will require more covers to achieve pregnancy and will therefore incur higher veterinary and transport costs. The results will also lay the foundation for a genetic screening tool. Because the development of such a test requires robust gene characterisation, this project will generate the essential knowledge required to meet standards for commercial test development.

Program

Thoroughbred Horses

Research Organisation

The University of Newcastle

Objective Summary

As above