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Evaluating the contribution of transposons to agricultural domestication. PhD Biosciences (SWBio DTP)

  • Full or part time
  • Application Deadline
    Monday, December 02, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Lead Supervisor
Dr Alex Hayward, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors
- Dr Pablo Orozco Ter Wengel, School of Biosciences, Cardiff University
- Professor Chris Bass, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Location: University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE

Programme Overview

The South West Biosciences Doctoral Training Partnership (SWBio DTP) is led by the University of Bristol, together with the Universities of Bath, Cardiff and Exeter, alongside Rothamsted Research. This partnership also includes the following collaborative partners; Marine Biological Association (MBA), Plymouth Marine Laboratory (PML), Swansea University, UCB Pharma, University of the West of England (UWE) and SETsquared Bristol.

These institutions represent a distinctive group of bioscience research staff and students, with established international, national and regional networks, and widely recognised research excellence. As research leaders, we have a strong track record in advancing knowledge through high-quality research and teaching, in partnership with industry and the government.

For more information about the programme structure, please visit https://www.swbio.ac.uk/programme/

Funding for 2020/21

These studentships are available to UK and EU nationals who have established UK residency (EU nationals must have ordinarily lived in the UK throughout the three years preceding the start of the studentship).

The four core universities (Bath, Bristol, Cardiff and Exeter) have a very limited number of fully-funded four year studentships for EU students who do not meet the residency requirements (1-2 studentships per university)*. Please contact the relevant university for more information.

*These are not available for CASE DTP studentships or Standard DTP studentships with a collaborative partner

Project Description
Vertebrates and transposons share an ancient co-evolutionary history. Indeed, the whole of vertebrate evolution has occurred within the context of transposoninteractions, since the origin of transposons is believed to significantly predate the origin of the vertebrates. Consequently, vertebrate genomes typically contain very large proportions of both active transposons and mutatedtransposon remnants (e.g. transposons account for ~50% oftotal genome content in humans).

Until recently, transposons were largely considered to be ‘junk DNA’ that littered the host genome. While active elements were known to cause insertional mutagenesis, there was very little appreciation that transposons played a meaningful role in host evolution. However, since the genomics revolution, it has become apparent that transposons are highly important players in the evolution of host genomic complexity, playing key regulatory roles as well as directly contributing protein coding sequence as raw material for novel host functions.

Given an abundance of high quality genomes from across vertebrate phylogeny, we are now in a powerful position to learn more about the intricacies by which transposons are harnessed by host genomes during evolution. This offers great potential for developing novel applications across arrange of important areas in biology.

This project will address the exciting question of the contribution of transposons to agricultural domestication, using a detailed comparative genomics analysis of important livestock breeds and their wild ancestors. In this project, genomic data from a large number of agriculturally important livestock species, will be complemented with data from high and low producing breeds and wild ancestral species, to perform cutting-edge 4 / 15 bioinformatic analyses of transposon content, integration history, and interactions with host gene ontology. This will provide a new and detailed picture of transposon activity and the contribution of transposons during domestication. Of particular interest will be transposon involvement in genomic regions linked to production traits, and regions identified to contain transposon hotspots, where nested insertions have provided the substrate for evolutionary processes such as adaptive walks and the expression of new host phenotypes.

This cross-disciplinary project will involve training at several prestigious universities, including cutting-edge bioinformatic and phylogenetic approaches at Exeter (DrAlex Hayward, University of Exeter), and population genomics and livestock genomics at Cardiff (Dr PabloOrozco terWengel). The project will provide highly novel insights into the genetic architecture and evolutionary basis of domestication, with considerable potential for applications in agriculture, to increase the resilience and sustainability of livestock production systems.

Eligibility
To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria which is in line with UKRI guidelines see the following webpage for further details https://www.swbio.ac.uk/programme/eligibility/.

A fully-funded four year SWBio DTP studentship will cover:

• a stipend* at the standard UKRI rate; currently £15,009 per annum for 2019-2020
• research and training costs
• tuition fees (at the standard UKRI rate)
• additional funds to support fieldwork, conferences and a 3-month internship

Funding Notes

SWBio DTP funded studentship available for September 2020 entry. The studentship will provide funding of fees and a stipend which is currently £15,009 per annum for 2019-20, on a full time basis.

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