In 2022 the Eriskay Pony Society (EPS) set up a project with the Medical Technologies Innovation Facility (MTIF) at Nottingham Trent University (NTU) to investigate the genomics of the Eriskay Pony population. This was funded by a generous grant from the Horserace Betting Levy Board along with a contribution from the Society’s own funds.
The project goal was to understand the genetic makeup of the Eriskay pony and establish its relationship, or otherwise, to other native pony breeds. NTU were also asked to evaluate the current pedigree-based breeding programme (SPARKS) to see whether it was fit for purpose or whether future breeding advice should be based on genomics.
NTU were provided with a set of 103 hair samples from Eriskay Ponies distributed throughout the UK, around 25% of the population, which they used to extract DNA following user-developed guidelines for purifying total DNA from nails, hair, or feathers. Data from these samples was then gathered using a microarray chip used for genotyping designed to detect and analyse genetic variations across the horse genome. These variations can be used to gain knowledge about physical traits, diseases, and genetic diversity within horse populations, and which are useful for researchers and breeding organisations alike.
NTU used the data to analyse breed genetic diversity, incorporating data from 31 other equine breeds, and this revealed that the Eriskay Pony is a genetically unique breed with no relationships with any of the other horse and pony breeds it was screened against.
In particular, mitochondrial DNA studies and haplotype determination indicated that the Highland and Eriskay ponies do not share haplotype, and that the Highland Pony does not exhibit the rare da_4E Y chromosome haplotype of the Eriskay Pony. This evidence points to the fact that the Eriskay and the Highland are genetically different breeds.
The study showed the good correlation between pedigree and genomic metrics providing reassurance that the current breed advisory system is valid and there are signs that using SPARKS is having a positive effect on managing inbreeding and improving the Effective Population Size (Ne).
The study also identified 9 female mtDNA haplotypes, of which 3 are most prevalent, and EPS has been advised to identify the haplotypes of the current female breeding population and ensure that animals representing the less frequent haplotypes are bred from so that their genetics are not lost to the population.
The results of this study will now be used by the Society’s Breed Conservation Committee to form an updated breeding programme and to work on identifying the most appropriate ponies to encourage breeders to use in 2025.
Steve McMinn, Chair of the Eriskay Pony Society said ‘’We are very grateful to HBLB for its support in funding this project, to Dr Robert Reisel, Dr Andy Dell and Daniela Eberl of MTIF at NTU for the investigation and analysis, and to all the owners who submitted hair samples from their ponies which allowed such a significant part of the population to be included. This study has given us a huge amount of information on which to base our future plans as well as providing us with the genomic data we can use to monitor the effects of our breed advisory scheme’’
NOTE: This work has not been published in a peer-reviewed publication yet but it is currently under review following scientific good publication practice guidelines.
THE ERISKAY PONY SOCIETY 