Genetic distinctiveness of the Herdwick sheep breed and two other locally adapted hill breeds of the UK

Abstract

There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits) and PRLR (reproductive performance traits) also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the lentivirus.

Figure 1. The distribution of three locally adapted sheep breeds of the UK uplands and their geographical concentration shown on a composite map using data described in .

Figure 2. Analysis of retrotypes.

The four most common retrovirus events (enJSRV-18, enJSRV-7, enJS5F16, enJSRV-8) were used by Chessa et al to construct a classification scheme based on retrotypes. The pie charts show the relative proportion of retrotypes in each of the three hill breeds in this study. For ease of comparison, the colouring of each retrotype is the same as used in , and pie charts of example breeds from are also illustrated in the Figure.

Figure 3. Analysis of microsatellite data.

The microsatellite data were analysed with Structure; the most likely number of populations to explain the data was for K = 3 (−1525.1). Rough Fell corresponds with cluster 1, Dalesbred with cluster 2 and Herdwick with cluster 3 (all others).