HORSE Sport Ireland has commenced the transition of DNA analysis services from Microsatellite (MS) to Single Nucleotide Polymorphism (SNP) technology with Weatherbys Scientific (WS).

WS has been providing DNA parentage testing using MS technology to the Thoroughbred and Sport Horse industry for more than 20 years. MS technology has limited application and is primarily used for parentage verification purposes only.

Advancements in DNA analyses over the last 20 years and the introduction of SNP technology has extended the suite of DNA applications, which were previously unavailable with MS. Since 2009, many livestock breeding programmes have adopted SNP technology to produce genomic breeding values (gEBVs) which have an increased reliability over traditional methods that used pedigree alone and can enhance breed/farm management decisions.

Furthermore, SNPs can be used for calculating inbreeding (improved mating decision making), parentage assignment (including filling gaps in pedigrees) and determining breed composition. With this technology, we can also test for genetic diseases (e.g., Fragile Foal Syndrome) and can even predict coat colour.

The MS technology ‘marks’ approximately 10-20 areas on the genome, however the SNPs technology applied in this project will mark 50,000 areas of the genome. It is estimated that WS process 1,500 – 2000 samples per week using MS, on the SNPs technology approximately samples 20,000 per week would be processed.

Breeders will immediately benefit from the transition, where results for the above applications could be collated from the one sample if required.

The MS technology is underpinned by an old technology, which is approaching end of life, sourcing certain replacement parts is proving challenging and a contributor to disruption in service delivery.

It is worth noting, that equines are the only remaining species on the microsatellite platform. To facilitate the transition to SNPs, breeding stock (stallions and mares) would require genotyping on the new technology, which would be time consuming under normal circumstances, as resampling of these animals would be required.

Dr Rebecca Weld, General Manager of Weatherbys Scientific

Data-led decisions

However, Horse Sport Ireland owns the archive of samples stored in WS and therefore will be able to analyse existing and verified samples, without the need of resampling. The project will provide a ‘reference library’ of DNA for which to roll out all DNA analysis research and services in the future.

Implementation of the SNPs DNA analysis will allow HSI to integrate data collated through previous and future schemes.

To date, the Horse Sport Ireland X-ray screening scheme has collated several 100 sets of mare and filly X-rays, this anonymised data can be used for preliminary investigation into the relationship between bony abnormalities and their genetic markers in the Irish herd.

There is currently no existing data concerning the prevalence of osteochondrosis and bony abnormalities in the Irish mare herd.

Should this link be established, this valuable information could be used to support earlier identification of abnormalities, act as an aid for breeder decision making and mitigating the impact of heritable conditions in the Irish herd.