Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

Abstract

Background: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project.

Results: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise F ST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825.

Conclusions: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.

Fig. 1

Clustering of Welsh and worldwide sheep breeds based on multi-dimensional scaling of genotype data. Individuals are shown in the context of the International Sheep Genome Consortium HapMap data set of 74 breeds [11]

Fig. 2

Phylogeny of 18 native Welsh sheep breeds and their most closely related European breeds. Welsh breeds are shown in red, European in grey, Australian/New Zealand in yellow, Scottish in blue, English in yellow and Irish in green. An Indian Garole individual was used to provide an outgroup (no. 13). 1) Llanwenog, 2) Clun Forrest, 3) Black Headed Mutton, 4) Beulah, 5) Kerry Hill, 6) Welsh Hardy Speckled Faced, 7) Hill Radnor, 8) Black Welsh Mountain, 9) Balwen, 10) Badger Faced, 11) Boreray, 12) Soay, 13) Indian Garole - Outgroup, 14) Scottish Blackface, 15) Brecknock Hill Cheviot, 16) Llandovery White Faced, 17) Talybont Welsh Mountain, 18) Improved Welsh Mountain, 19) South Wales Welsh Mountain, 20) Hill Flock Welsh Mountain, 21) Dolgellau Welsh Mountain, 22) Tregaron Welsh Mountain, 23) Lleyn, 24) Galway, 25) German Texel, 26) New Zealand Texel, 27) Scottish Texel, 28) Australian Coopworth, 29) Border Leicester, 30) New Zealand Romney, 31) Wiltshire. Breed names shown in bold correspond to the adjacent breed images

Fig. 3

Model-based clustering of 18 native Welsh sheep breeds and their most closely related European breeds. Analysis was performed using the program STRUCTURE, with K representing the assumed number of populations

Fig. 4

Clustering of individuals from 18 native Welsh sheep breeds based on multi-dimensional scaling analysis of genotype data. The image shows a plot of the first two components, revealing clustering of a central group of mountain breeds

Fig. 5

Demographic inference for three individual sheep of different native Welsh breeds. The breeds used were the Dolgellau Welsh Mountain (DWM1), Tregaron Welsh Mountain (TWM1) and Welsh Hardy Speckled Faced (WHSF1). In each demographic plot, a standard mutation rate of 1×10⁻⁸ has been scaled by the appropriate false negative error rate for each animal (Additional file 11: Table S3). Demographic trends were inferred using the HHn method (see Methods)