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Making genotyping cheaper and easier (Ref: CTP_FCR_2019_4)

  • Full or part time
    Dr Richard Harrison
    Dr M Loose
  • Application Deadline
    Thursday, February 28, 2019
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

About This PhD Project

Project Description

The Biotechnology and Biological Sciences Research Council (BBSRC ) have awarded a Collaborative Training Partnership (CTP) grant to a consortium led by Berry Gardens Growers Ltd and NIAB EMR. The Collaborative Training Partnership for Fruit Crop Research (www.ctp-fcr.org) focuses on industry led research and development on important fruit crops in the UK.
We are offering an exciting fully funded PhD opportunity on the topic:

“Making genotyping cheaper and easier” (Ref: CTP_FCR_2019_4)

This student is to be registered with University of Nottingham and will be mainly based at NIAB EMR, Kent. The team of supervisors includes Dr Richard Harrison (NIAB EMR) and Dr Matt Loose (University of Nottingham)

The opportunity to capture the full spectrum of genetic variants in any given species is crucial, as this allows accurate classification of individuals and the more accurate linkage of causal variants to phenotypes. There are now a plethora of tools and techniques that allow differential profiling of variant types, from single nucleotide polymorphisms, to DNA base modifications. The challenge is to develop approaches that are easier to execute and analyse.

This studentship will aim to develop both laboratory and bioinformatics techniques to capture the full spectrum of genetic variants using a variety of biological models with modifications of agronomic importance that require the development of specific tests to study non-standard genetic modifications.

The most important eligibility criterion for this funded studentship is residency:

• UK students: If you have been ordinarily resident in the UK for three years you will normally be entitled to apply for a full studentship, covering tuition fees and a maintenance stipend.
• EU students: If you have been ordinarily resident in another EU country (outside the UK) for three years you will normally be able to apply for a tuition fees-only award (without a maintenance stipend). If you have lived in the UK for three years you may be eligible for a full studentship.

This eligibility is unaffected by Brexit. The UK Government has guaranteed EU eligibility for Research Council funding for PhDs beginning before the end of the 2019-20 academic year.

Anyone interested should contact for application form and return the form to before the deadline of 28th February 2019

Background


The opportunity to capture the full spectrum of genetic variants in any given species is crucial, as this allows accurate classification of individuals and the more accurate linkage of causal variants to phenotypes. There are now a plethora of tools and techniques that allow differential profiling of variant types, from single nucleotide polymorphisms, to DNA base modifications. The challenge is to develop approaches that are easier to execute and analyse.

Objectives


This studentship will aim to develop both laboratory and bioinformatics techniques to capture the full spectrum of genetic variants using a variety of biological models with modifications of agronomic importance that require the development of specific tests to study non-standard genetic modifications.

Approaches


The research work will be divided into upto four workpackages (WPs), each with clear deliverables. These may include:
WP1: SNP panel construction- work to identify a low cost method for SNP evaluation using single molecule sequencing
WP2: Epi-allele identification using single molecule sequencing- using Phytophthora fragariae as a model of epiallelic variation
WP3: Structural variant tracking- using Fusarium formae specialis structural rearrangements to identify dynamic genomic rearrangements
WP4: k-mer and signature based identification- reference free approaches of tracking allelic variation using single molecule sequencing.

Benefit to the industry


The research outcome from this work will enable the development of novel genotyping technologies that can be used in breeding, varietal characterization and molecular diagnostics.

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