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China Scholarship Council - Molecular characterisation of plant disease resistance genes through novel Next-Generation Sequencing applications

  • Full or part time
  • Application Deadline
    Wednesday, January 15, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

The School of Life Sciences at the University of Dundee, joint with the China Scholarship Council (CSC), is proud to be able to offer a scholarship programme for postgraduate research students. The scholarship covers all tuition fees and research fees and provides living expenses and one return flight ticket to successful candidates. There are up to 5 scholarships of 4 years duration available.

Project Description

This PhD project will provide comprehensive training for the successful candidate in potato genetics (diploid and tetraploid) as well as plant-pathogen genomics/co-evolution. The student will generate and analyse state-of-the-art Next Generation Sequencing (NGS) data for the genetic mapping and the cloning of resistances effective against the late blight pathogen Phytophthora infestans in established segregating populations. In addition, the student will characterise the mode-of-action of already isolated functional resistance genes and their variants through cell-biological assays including report genes, pull-downs, confocal imaging, and effector recognition.
The student will have the opportunity to develop NGS techniques with a focus on high-molecular DNA sequencing through Oxford Nanopore MinION.

The student will be a full member of the Dundee Effector Consortium (DEC), which unites more than 50 researchers on all aspects (including computational genetics/genomics) of plant-pathogen co-evolution. DEC will provide a forum to gain experience in communicating results in a friendly environment and receiving critical but constructive feedback on progress and direction of the PhD.
General Background: The data analyses will be focused on studying the interaction between Phytophthora infestans and potato. The oomycete pathogen P. infestans is a widespread and economically significant threat to global crop production. Phytophthora species are very destructive and can adapt rapidly to new selection pressures imposed by modern agriculture. On a molecular level pathogen avirulence or virulence to naturally occurring or deployed host disease resistances is determined by effectors. The effector recognition-based inducible plant defense response is often governed by nucleotide-binding, leucine-rich repeat (NLR) disease resistance proteins.
We have successfully developed target enrichment sequencing for potato NLRs as well as pathogen effectors from P. infestans that determine recognition in the plants and therefore resistance. We have coined these novel methods RenSeq [1] and PenSeq [2].

Funding Notes

In order to be eligible for these awards applicants must:

Be a Chinese national
Meet the requirements of the CSC – please see their website
Hold an unconditional offer to study for a PhD at the University of Dundee and meet our English language requirements
Have completed bachelors or masters degree before the agreed start of PhD study.

References

Armstrong M.R., Vossen J., Lim T.Y., Hutten R.C.B., Xu J., Strachan S.M., Harrower B., Champouret N., Gilroy E.M. and Hein I.* (2018) Tracking disease resistance deployment in potato breeding by enrichment sequencing. Plant Biotechnol J. doi: 10.1111/pbi.12997. 

Thilliez G.J.A., Armstrong M.R., Lim T.Y., Baker K., Jouet A., Ward B., van Oosterhout C., Jones J.D.G, Huitema E., Birch P.R.J and Hein I* (2018). Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. New Phytologist.DOI:10.1111/nph.15441

How good is research at University of Dundee in Biological Sciences?

FTE Category A staff submitted: 73.20

Research output data provided by the Research Excellence Framework (REF)

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