Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom

Background Sheep breeds native to the United Kingdom exhibit a striking diversity of different traits. Some of these
traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, and are likely to become more
important as pressures on sheep production increase in coming decades. Despite their clear importance to the future
of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk
of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep
sector in the future. Here, we use 50 K genotyping to perform preliminary analysis of breed relationships and genetic
diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including six on the UK Breeds at Risk (BAR) list, and utilises existing data
from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture.
Results In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had
higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed,
and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln
Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially
low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample
provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep,
reflecting the complexity in the demographic history of these breeds.
Conclusion Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure.
They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies
for rare and declining breeds with small population sizes. We conclude that generating genetic resources for the sheep
breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds,
and safe-guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.