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Assessment of Genetic Relationship Between Six Populations of Welsh Mountain Sheep Using Microsatellite Markers

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Assessment of Genetic Relationship Between Six Populations of Welsh Mountain Sheep Using Microsatellite Markers This publication is made freely available under ______ __ open access. AUTHOR(S): TITLE: YEAR: Publisher citation: OpenAIR citation: Publisher copyright statement: This is the ______________________ version of an article originally published by ____________________________ in __________________________________________________________________________________________ (ISSN _________; eISSN __________). OpenAIR takedown statement: Section 6 of the “Repository policy for OpenAIR @ RGU” (available from http://www.rgu.ac.uk/staff-and-current- students/library/library-policies/repository-policies) provides guidance on the criteria under which RGU will consider withdrawing material from OpenAIR. If you believe that this item is subject to any of these criteria, or for any other reason should not be held on OpenAIR, then please contact [email protected] with the details of the item and the nature of your complaint. This publication is distributed under a CC ____________ license. ____________________________________________________ Original Paper Czech J. Anim. Sci., 60, 2015 (5): 216–223 doi: 10.17221/8171-CJAS Assessment of genetic relationship between six populations of Welsh Mountain sheep using microsatellite markers K.M. Huson, W. Haresign, M.J. Hegarty, T.M. Blackmore, C. Morgan, N.R. McEwan Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, United Kingdom ABSTRACT: This study investigated the genetic relationship between 6 populations of Welsh Mountain sheep: 5 phenotypic breed-types within the Welsh Mountain (WM) sheep breed, which have each been bred in spe- cific geographic areas of Wales, and the Black Welsh Mountain sheep breed. Based on DNA analysis using 8 microsatellite markers, observed heterozygosity levels were similar to those expected in livestock populations subjected to selective breeding (0.530–0.664), and all but one population showed evidence of inbreeding. Using Bayesian cluster and Neighbor-joining analyses, the Black Welsh Mountain sheep were identified as being the outlier group, and the remaining groups could be categorized into five distinct sub-populations, which reflects the geographical separation seen between these populations. Keywords: sheep; interbreed relationship; population biology; phylogeography INTRODUCTION specific environment, is thought to have contrib- uted to some degree of genetic isolation of breed The native Welsh Mountain (WM) sheep are types relative to the general WM flock. Historic typically a small and hardy breed and account for reference was made to different “local varieties” of the largest proportion of the estimated 4.3 mil- WM sheep by Wood (1937) in his report on sheep lion breeding ewes in Wales, kept across almost management in Great Britain, and subsequently 15 000 sheep holdings (Hybu Cig Cymru 2014). They by Duckham (1963). Wood clearly distinguishes have been bred to survive in some of the harsher between the “South Walien” type Welsh Mountain environments and climates in the UK, including (likely to be the origins of the Nelson/South Wales areas of relatively poor-quality pasture. Due to the type known today) and the WM sheep observed topology of Wales, with clearly defined geographical in other areas. He also identifies that the Welsh features (e.g. Snowdonia, the Cambrian Mountains, Mountain Pedigree flock at this time was mainly the Brecon Beacons) several different breed types kept in the lowland areas, and suggests that these of WM sheep exist across Wales, largely restricted sheep are distinct from their upland relatives and to their respective specific local geographic areas, no longer suited to life in the hills. where the breed type was historically developed In general, most of the WM sheep are predomi- prior to more recent significant movements of nantly white fleeced, although one example exists livestock around the country (Carson et al. 2009). of a black fleeced breed (the Black WM breed), There is a belief that local breed types are best with a conformation very similar to the other WM suited to the region they originate from, and that sheep types except for its black fleece colour. In breed types will thrive less well when not in their this example, the black fleece colour is known to native area. This belief, suggesting that each local be caused by an allele which is dominant to the breed or breed type is selectively adapted to its white allele (Roberts and White 1930), unlike most 216 Czech J. Anim. Sci., 60, 2015 (5): 216–223 Original Paper doi: 10.17221/8171-CJAS other breeds where black colouration is recessive if there is any genetic basis for the suggestion that to the white one. local breed types are continuing to persist in spe- Detailed population data for individual WM breed cific geographic areas, and if the different types types are not consistently recorded. Figures for WM of WM sheep identified are genetically distinct, sheep stated in the DEFRA report estimate the UK how the populations are related to each other. population at around 1.9 million breeding ewes, and this figure will consist largely of the North Wales MATERIAL AND METHODS (NW) Mountain type along with smaller local WM breed types such as the Tregaron type. Statistics Sample collection. In addition to the Black WM on the UK sheep population available from DEFRA breed, five further breed types were included in (2003) estimate the UK population of Nelson/South this study: the Tregaron type, Llandovery White- Wales (SW) Mountain type breeding ewes to be face type, the NW Mountain type, the Nelson around 73 500 and the Black WM sheep to have 8060 (SW Mountain) type, and the Pedigree Welsh breeding ewes. Both the Llandovery Whiteface and Mountain section. Black WM sheep are registered as “at risk” with the For each breed type, buccal swab DNA samples UK Rare Breed Survival Trust, meeting the criteria for were collected from 3–5 farms and 4 sheep per an “at risk” population with less than 10 000 breed- farm were used for analysis. In order to obtain ing ewes registered (DEFRA 2014). representative samples for each breed type, DNA Genetic diversity within farm livestock is needed was collected from different flocks, and efforts were to ensure adaption to changing production require- made to avoid sample collection from closely related ments and environments, and to allow continued individuals within each flock. Sample collection breed improvements (Groeneveld et al. 2010). It is was performed on-farm using Catch-AllTM Sample ® also essential to maintain genetic diversity to avoid Collection Swabs (EPICENTRE Biotechnologies, the negative effects of inbreeding on production Madison, USA) by rubbing the swab against each and health traits (Notter 1999; McParland et al. of the sheep’s cheeks approximately 20 times. 2007; Carrillo and Siewerdt 2010). Human man- The swabs were frozen and were stored at –80°C agement influences selection and mating decisions until required. in domesticated livestock, and examples exist of DNA isolation. DNA extraction from buccal using animals (generally sires) from other breeds samples was harvested using a BuccalAmpTM DNA ® or types as a way of introducing desired traits, and Extraction Kit (EPICENTRE Biotechnologies) in so doing, genetic diversity within the breed. according to the manufacturer’s instructions and A number of studies have been conducted into the samples were stored at –20°C until DNA purifi- genetic diversity of farm livestock (e.g. SanCristobal cation. DNA was then purified using a Qiagen ® et al. 2006; Granevitze et al. 2007; Medugorac et DNeasy Plant Kit (Qiagen, Crawley, UK), fol- al. 2009) including European sheep breeds (e.g. lowing the Plant Tissue Mini Protocol, as per the Arranz et al. 2001; Dalvit et al. 2008; Ligda et al. manufacturer’s instructions from the AW1 buffer 2009), but British breeds have generally not been incubation onwards, with an additional 60 s cen- included in these analyses. Examples of investiga- trifugation step at 14 000 g of the minispin column tions including hill breeds, or breeds selected for after the AW2 wash, and 30 µl of buffer AE used relatively harsh conditions, from the UK include for each elution. DNA was then quantified using Lawson-Handley et al. (2007) and Bowles et al. a ThermoScientific NanoDrop 1000 spectropho- (2014), with the former including an example of tometer (Thermo Fisher Scientific, Wilmington, a Welsh breed – the Llanwenog. The only other USA), and ND-1000 software (Version 3.17, 2006) example of inclusion of a Welsh breed in an in- on the nucleic acid setting. A DNA concentration vestigation was the North American population of of ≥ 4.0 ng/μl was deemed sufficient to use for Black WM sheep (Blackburn et al. 2011), although PCR. Samples which fell below this were purified these sheep may no longer be directly comparable again. Eluted DNA from extractions was stored to the population still found in Wales. at –20°C until required. The current study investigates the extent of ge- Primer selection and PCR conditions. Eight mi- netic diversity between the different types of WM crosatellite markers were identified from a ranked sheep using microsatellite markers, to determine list of recommended markers for use in sheep popu- 217 Original Paper Czech J. Anim. Sci., 60, 2015 (5): 216–223 doi: 10.17221/8171-CJAS lation genetics studies published by the ISAG/FAO The DNA was amplified in a G-Storm GS1 Thermal advisory group on animal genetic diversity as part Cycler (Gene Technologies Ltd., Braintree, UK).
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