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Genetic Distinctiveness of the Herdwick Sheep Breed and Two Other Locally Adapted Hill Breeds of the UK

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Genetic Distinctiveness of the Herdwick Sheep Breed and Two Other Locally Adapted Hill Breeds of the UK Genetic Distinctiveness of the Herdwick Sheep Breed and Two Other Locally Adapted Hill Breeds of the UK Dianna Bowles1,2*, Amanda Carson2, Peter Isaac3 1 Department of Biology, University of York, York, United Kingdom, 2 The Sheep Trust, registered charity 1094514, University of York, York, United Kingdom, 3 IDna Genetics Ltd, Norwich Research Park, Norwich, United Kingdom 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. Citation: Bowles D, Carson A, Isaac P (2014) Genetic Distinctiveness of the Herdwick Sheep Breed and Two Other Locally Adapted Hill Breeds of the UK. PLoS ONE 9(1): e87823. doi:10.1371/journal.pone.0087823 Editor: William Barendse, CSIRO, Australia Received September 3, 2013; Accepted December 30, 2013; Published January 29, 2014 Copyright: ß 2014 Bowles et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The funding for this research was in part provided by the University of York to DB and in part by The Sheep Trust Charity. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: PI is employed by a commercial company (IDna Genetics Ltd). This does not alter the authors’ adherence to all of the PLOS ONE policies on sharing data and materials. * E-mail: [email protected] Introduction also recognized to be at risk, but for the reason that they are highly concentrated in specific geographical regions to which they are The genetics and conservation of locally adapted livestock adapted [8]. breeds is attracting considerable interest currently [1–3]. This Amongst these locally adapted breeds are the hill breeds of the interest arises in part from the significant contribution of the northern uplands. These typically are farmed on Disadvantaged or breeds to food security in marginal land areas of the world Severely Disadvantaged Areas for agricultural production [9] and unsuitable for other means of agricultural production. Also, the are characterized by their ability to thrive in the harsh ability of the breeds to adapt and thrive under what are often environments of mountains and moorlands, rearing lambs on harsh environmental conditions implies they may have adaptive low inputs of feed and management. fitness traits that could become increasingly useful to the future The endangerment of breeds such as these was first recognized sustainability of mainstream agriculture. in the UK during the Foot and Mouth Disease (FMD) epidemic of Of importance to the global and national conservation strategies 2001 which started in the northwest of England and dispropor- of these breeds is their genetic characterization, confirmation that tionately affected livestock farmed in that region. Losses to the they are genetically distinctive and an assessment of the Herdwick sheep breed were of particular concern, which led to the biodiversity each breed may contribute to future trait selection setting up of the first national gene bank for sheep and a [4–6]. government commitment to survey the level of geographical In this context, the UK has a substantial number of native sheep concentration that existed amongst commercially farmed regional breeds [7]. Many of these are now numerically scarce and largely breeds. Working with Sheep Breeder Associations (SBAs) and maintained in small numbers by breeders committed to conser- more than 1000 breeders, individual flocks of 12 regional breeds vation of rare, endangered livestock. There is however another were geo-referenced [8]. The data showed certain of these category of native sheep breeds that are not rare, are commercially ‘Heritage’ breeds were indeed extremely concentrated with for farmed and continue to exist in tens of thousands [7]. These are example, up to 95% of the Herdwicks numbering some 47 000 PLOS ONE | www.plosone.org 1 January 2014 | Volume 9 | Issue 1 | e87823 Genetic Distinctiveness of Sheep Breeds animals, tightly clustered within 23 km of the breed’s mean centre There have been studies specifically focused on geographical in the Lake District National Park. proximate breeds elsewhere in Europe, including such as those of A significant issue for prioritising conservation strategies is Northern Spain [20,21], Northern Europe, the Baltic and the whether breeds concentrated in proximate geographical regions Volga region of the Russian Federation [22–24]. and locally adapted to very similar environmental conditions are We have used a combination of approaches to study the genetic genetically distinctive. We have selected three breeds from the distinctiveness of the Herdwick, Rough Fell and Dalesbred. Each northern uplands to explore this possibility. Their distribution is approach has been used widely in previous studies of sheep breeds illustrated in Figure 1, together with an image of a typical ram across the world, revealing new information about the history of from each breed. The Herdwick is an iconic image of the Lake sheep domestication, relatedness of populations and increasingly, District; Rough Fells are farmed in partially overlapping regions in the genes encoding interesting phenotypes and important produc- Cumbria to the east of the Herdwicks and the distribution of the tion traits in livestock [16–18,22,25–29]. Dalesbred is to the south and further east into Lancashire and In total, our results show a considerable level of genetic Yorkshire. In each region, the sheep breed continues to be valued distinctiveness amongst the three northern hill breeds. We provide for its cultural heritage and contribution to local economic evidence that the Herdwick has retained characteristics of a sustainability [10–12]. primitive genome and together with Rough Fell and Dalesbred There have been no previous molecular genetic analyses of can be distinguished from one another and other UK breeds these three breeds. Large scale European studies by the Econogene studied previously. The findings emphasise the importance of Consortium and others [13–16] involved some UK breeds, conservation strategies to protect their genetic resources. including the Exmoor Horn and Welsh Mountain shown subsequently to be geographically concentrated [8]. Isolated Materials and Methods Scottish Island populations have also been studied in global Materials, ethics statement and sampling surveys, including the numerically scarce breed of the Soay, and Our study has involved analyzing equal numbers of registered those in the Hebrides, Faeroe and Orkney [15,17–19]. breeding males (rams) from each breed. Through collaboration with the respective Sheep Breeders Associations (SBAs) and individual breeders we were able to ensure samples were each obtained from different commercial flocks of known provenance and breeders who could confirm the familial origins and unrelatedness of the rams selected. Typically, a ram will sire up to 150 progeny of lambs each year over 6 to 10 years, compared to a ewe that will produce up to two offspring per year over a shorter breeding life. As a consequence, rams contribute a major genetic resource to the breed but represent a potential risk to diversity as they form only a numerically small fraction of the total population. Also, such as for the Herdwick breed, not all SBAs register females, so that animals conforming to breed standard phenotypes are only formally recorded if they are males, and sampling from a flock may lead to many related animals. None of the
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