Population Structure and History of the Welsh Sheep Breeds Determined By Whole Genome SNP Genotyping

One of the most economically important areas within the Welsh agricultural sector is sheep farming. Over generations, selective breeding has generated a number of native sheep breeds, which are presumably adapted to the wide-ranging and challenging landscape of the principality. At present, little is understood about these breeds in terms of their history, genetic diversity and how these contribute to the variety of phenotypes observed. As a first step towards answering these questions, we genotyped 319 individuals from 16 native Welsh sheep breeds using the Illumina OvineSNP50 array. Population structure analyses indicated the existence of four distinct population groups within the Welsh breeds. Our genotyping data were then combined with those from 74 breeds, which were genotyped by the Sheep HapMap project, enabling comparisons of genetic diversity and differentiation between Welsh breeds and breeds worldwide. At lower numbers of assumed populations (K), clustering of Welsh breeds with other UK and Irish breeds was observed, indicating a common origin or high level of interbreeding. At higher K, most Welsh mountain breeds clustered together. The Welsh Lleyn breed clustered with the Irish Galway, confirming historical records of a common origin of these breeds in the 18th century. More generally, our results confirm the relations between Welsh breeds and other European breeds, which had been suggested by historical records. These results will be used to design experimental populations for association mapping, genomic selection and genome scans for signatures of selection, thereby potentially benefiting future Welsh sheep breeding programmes.