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

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0216-x) contains supplementary material, which is available to authorized users

What are the priority research questions for digital agriculture?

There is a need to identify key existing and emerging issues relevant to digitalisation in agricultural production that would benefit from a stronger evidence base and help steer policy formulation. To address this, a prioritisation exercise was undertaken to identify priority research questions concerning digital agriculture in the UK, but with a view to also informing international contexts. The prioritisation exercise uses an established and effective participatory methodology for capturing and ordering a wide range of views. The method involves identifying a large number of participants and eliciting an initial long list of research questions which is reduced and refined in subsequent voting stages to select the top priorities by theme. Participants were selected using purposive sampling and snowballing to represent a number of sectors, organisations, companies and disciplines across the UK. They were each invited to submit up to 10 questions according to certain criteria, and this resulted in 195 questions from a range of 40 participants (largely from England with some representation from Scotland and Wales). Preliminary analysis and clustering of these questions through iterative analysis identified seven themes as follows: data governance; data management; enabling use of data and technologies; understanding benefits and uptake of data and technologies; optimising data and technologies for performance; impacts of digital agriculture; and new collaborative arrangements. Subsequent stages of voting, using an online ranking exercise and a participant workshop for in-depth discussion, refined the questions to a total of 27 priority research questions categorised into 15 gold, 7 silver and 5 bronze, across the 7 themes. The questions significantly enrich and extend previous clustering and agenda setting using literature sources, and provide a range of new perspectives. The analysis highlights the interconnectedness of themes and questions, and proposes two nexus for future research: the different dimensions of value, and the social and institutional arrangements to support digitalisation in agriculture. These emphasise the importance of interdisciplinarity and transdisciplinarity, and the need to tackle the binary nature of current analytical frames. These new insights are equally relevant to contexts outside the UK. This paper highlights the need for research actions to inform policy, not only instrumentally by strengthening the evidence base, but also conceptually, to prompt new thinking. To our knowledge this methodology has not been previously applied to this topic

Welsh sheep Illumina 50K genotyping results and phylogenetic trees

50K Illumina SNP array data .ped and .map files and complete phylogenetic tree files used in our pape