The first whole genome sequence of a UK native pony breed is giving new hope for the survival of the Exmoor pony.

The availability of the breed’s full gene sequence as a result of the whole genome sequencing by Dr Sarah Blott at the University of Nottingham is described by Rare Breeds Survival Trust (RBST) and partners as a “quantum leap” in understanding the Exmoor Pony’s genetic make-up.

The RBST says the advance opens up important new possibilities for the work to save the rare breed from extinction.

“Up until now, genetic analysis to further the conservation of native livestock and especially equine breeds has been restricted to examining a much smaller set of genes,” said RBST Trustee Professor Tim Morris. “But thanks to this comprehensive genomic analysis, undertaken over several years and representing the 2.7 billion DNA base pairs in the genome, we can now see the Exmoor pony breed’s whole genetic picture for the first time.

“This is a quantum leap in genetic understanding, which can be used to improve the breed’s prospects for survival long into the future, opening up new possibilities in managing genetic diversity, in identifying conditions which could put the breed’s future at risk, and in ascertaining whether changes in herds are down to genetics or environmental factors.”

The whole genome has never before been analysed for equine breed conservation in the UK, but has now become a more viable prospect thanks to scientific advances and costs coming down. The only other equine breeds for which complete genomes currently exist are the thoroughbred and the Mongolian pony.

The Exmoor pony whole genome analysis was commissioned by RBST, Exmoor National Park Authority and the Exmoor Pony Society, with support and assistance from the University of Nottingham and local individuals. Hair samples were taken from both semi-wild and domesticated ponies around Britain in early 2021, after selection via the breed’s stud book to ensure a truly representative sample for study. 15 of these samples have been aligned with a further core reference sample to provide a unique and highly representative Exmoor Pony whole genome.

“This is an incredibly important advance in the fight for the Exmoor pony breed’s survival,” said RBST Chief Executive Christopher Price. “We are thrilled with the success of this very ambitious project, made possible through the dedication and expertise of Dr Sarah Blott at the University of Nottingham in navigating this technically and logistically challenging project during the disruption of the pandemic.

“The Exmoor pony is irreplaceable, it is part of our national heritage but it also has an important role in environmental land management today and in the future. This genomic analysis is a major landmark in underpinning the breed’s future and we hope that this work will serve as a model for similar whole genomic analyses of other rare breeds of livestock and equines.”

All the Exmoor ponies on the moor are owned by moorland farmers with specific grazing rights, who monitor the herds at key stages of the breeding cycle.

David Wallace, Vice Chairman of the Exmoor Pony Society and co-owner with his wife Emma of the moor bred Anchor herd, said the society was “delighted” to have part-funded the Genome Project.

“The resulting information will assist in the future health and welfare of this rare native breed and allow the society to carry out further research,” he said. “Quality scientific information together with good equine management go hand-in-hand.”

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