DOI: 10.5061/dryad.z08kprrnm
title: Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom

description: Background: Sheep breeds native to the United Kingdom are noted for high
 breed variability and exhibit a striking diversity of different traits in
 phenotypes and genetic diversity. Some of these traits are highly
 sustainable, such as seasonal wool shedding in the Wiltshire Horn, are
 likely to become more important as pressures on sheep production increase
 in coming decades. Despite their clear importance to the future of sheep
 farming, the genetic diversity of native UK sheep breeds is poorly
 characterised. This increases the risk of losing the ability to select for
 breed-specific traits from native breeds that might be important to the UK
 sheep sector in the future. Here, we use 50K genotyping to perform
 preliminary analysis of breed relationships and genetic diversity within
 native UK sheep breeds, as a first step towards a comprehensive
 characterisation. This study generates novel data for thirteen native UK
 breeds, including 6 on the UK Breeds at Risk (BAR) list, and utilises
 existing data from the publicly available Sheep HapMap dataset to
 investigate population structure, heterozygosity and admixture.
 Results: In this study the commercial breeds exhibited high
 levels of admixture, weaker population structure and had higher
 heterozygosity compared to the other native breeds, which generally tend
 to be more distinct, less admixed, and have lower genetic diversity and
 higher kinship coefficients. Some breeds including the Wiltshire Horn,
 Lincoln Longwool and Ryeland showed very little admixture at all,
 indicating a high level of breed integrity but potentially low genetic
 diversity. Population structure and admixture were strongly influenced by
 sample size and sample provenance – highlighting the need for equal sample
 sizes, sufficient numbers of individuals per breed, and sampling across
 multiple flocks. The genetic profiles both within and between breeds were
 highly complex for UK sheep, reflecting the complexity in the demographic
 history of these breeds. Conclusion: Our results highlight the
 utility of genotyping data for investigating breed diversity and genetic
 structure. They also suggest that routine generation of genotyping data
 would be very useful in informing conservation strategies for rare and
 declining breeds with small populations sizes. We conclude that generating
 genetic resources for the sheep breeds that are native to the UK will help
 preserve the considerable genetic diversity represented by these breeds,
 and safe guard this diversity as a valuable resource for the UK sheep
 sector to utilise in the face of future challenges.
description: # UK Sheep Genotyping - Genotypes, metadata, and workflow
 [https://doi.org/10.5061/dryad.z08kprrnm](https://doi.org/10.5061/dryad.z08kprrnm) ## Description of the data and file structure 1. Title of the dataset: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom 2. Corresponding Author Information.  Corresponding author (manuscript and study information):  Name: Emily Clark  Institution: Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, EH25 9RG Email: [emily.clark@roslin.ac.uk](mailto:emily.clark@roslin.a) Corresponding author (data and code)  Name: Melissa M. Marr Institution: Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, EH25 9RG Email: [mmarr3@ed.ac.uk](mailto:mmarr3@ed.ac.uk) 3. Data files in Plink format *i.* 20210809_0211124_comb_nodups.map & 20210809_0211124_comb_nodups.ped  Genotyped: 2021.  n SNPs: 53123 n samples: 91 Chip Version: OvineSNP50v2_HTS_20032166_A1.bpm *ii.* OVN50KV03_20230327.map  OVN50KV03_20230327.ped Genotyped 2023. n SNPs: 63429 n samples: 48 Chip Version: OvineSNP50v3_HTS_20046264_B1.bpm *iii.* OVN50KV03_20231227.map OVN50KV03_20231227.ped Genotyped 2023.  n SNPs: 63429 n samples: 4 Chip Version: OvineSNP50v3_HTS_20046264_B1.bpm Variable List Family ID: 0 Individual ID: Breed_numericalID OR numericalID_Breed  Paternal ID: 0 Maternal ID: 0 Sex: 0 Phenotype: -9 Genotypes: T G A C Missing genotypes: 0 4. Metadata  i. UKsheep_genotype_meta.xlsx ii. UKsheep_genotyping_workflow.txt. Code, workflow, software.   ## Sharing/Access information Publicly available data from the Sheep HapMap can be downloaded from: * [Ovine SNP50 HapMap Dataset (sheephapmap.org)](https://www.sheephapmap.org/download.php) ## Code/Software Provided in accompanying metadata file: UKsheep_genotyping_workflow.txt