A preliminary examination of the genetic variation within and between the Improvement Society herds of Welsh Mountain ponies

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Abstract

In order to understand the within and between herd diversity in the Upland Hill ponies of Wales and their relationships to their pedigree relatives and other native pony breeds a preliminary examination of a small sample of animals from a group of upland herds was carried out between 2014 and 2015.
Samples of DNA were obtained from 16 herds of Welsh Mountain Ponies from the Upland Improvement Societies. Around 130 animals were tested for genetic variation at 17 highly variable sites, 172 single base pair polymorphisms and by sequencing across 540 base pairs of the mitochondrial Control Region. These results were compared to a body of data obtained from Welsh Section A-D, and the Carneddau population and mixed groups of pedigree and non-pedigree UK ponies.
We have established that, while clearly related to the pedigree Section-A animals, it is possible to perform a genetic assignment of unknown Upland animals to their correct herd of origin in the majority of cases, and that the native Upland animals can be distinguished from several common ‘pony crosses’ of the sort that might be found ‘abandoned’ on Welsh common land.
We would argue that despite the presence of Upland blood-lines in the pedigree animals there are unique patterns of mitochondrial diversity within some upland herds that argues for there being a long term local stability to these populations. Our findings suggest that further work is required to ascertain to what extent the upland populations retain a unique genetic signature of Natural Selection in situ, and whether it is possible to exploit this, if present, to understand the particular adaptive complexes that make the Welsh Hill pony unique.