An evaluation of the genetic relationships between the Hill Dartmoor and the registered Dartmoor Pony Breed

The Dartmoor National Park is home to ponies free-living alongside cattle and sheep. In 2015, Natural England requested evidence supporting the claimed value of these ponies to the biodiversity, tradition and culture of Dartmoor. No evidence existed of whether the Hill Dartmoors are sufficiently distinct from the eleven other recognised pony breeds native to the UK and Ireland. Preliminary data from a small collection of Hill Dartmoors using genetic analysis suggested that they could be distinguished genetically from the registered Dartmoor breed. We subsequently suggested that we be supplied samples from as broad a cohort of the Hill Dartmoors as possible (25 animals per herd across five herds) for a more conclusive assessment. In actuality, due to time constraints at roundups, we were supplied 105 Hill Dartmoor samples and a further 16 registered Dartmoors (to supplement our existing data). These animals were tested for genetic variation across 15 highly variable simple sequence repeat (SSR) sites and 172 single nucleotide polymorphisms (SNPs). The results were compared to a body of data obtained from previous work at IBERS including the Welsh Section A-D, the free-living Carneddau Hill Pony and other mixed groups of pedigree and non-pedigree UK ponies (Winton et al., 2013). Results of genetic analysis show that, whilst genetically closer to the registered Dartmoor than to other breeds, shows a genetic distinctiveness that enables assignment of most animals to a Hill Dartmoor grouping when employing SNP markers. When using SSR markers, the lower resolution means that ~50% of the animals are misassigned to other breeds, however misassignment of Hill Dartmoors as registered Dartmoors (or vice versa) is rare. We note that high levels of misassignment are also seen in other breeds when employing SSR markers and that, in some cases, misassignment is due to a small number of herds known to have historically bred with Shetland to produce ponies ideal in size and temperament for use as pit ponies. The Hill Dartmoor is, as might be expected for a free-living population, much more genetically diverse than the other breeds we examined (the Carneddau, whilst also free-living, are a small population of <300 animals and show signs of inbreeding). We would argue that the presence of a common genetic signature across the population despite this adds to the case for recognising the Hill Dartmoor as a separate group to the registered Dartmoor. We also detect a number of SNP markers displaying significant differences in allele frequency between the two groups, some of which are hypothetically linked to trait differences (although further work is required to state this definitively).