University of Dundee

China Scholarship Council PhD programme - Using state-of-the-art genomics and genetics to clone functional disease resistance genes in potato

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.

Supervisors - Dr Ingo Hein and Prof John Jones (James Hutton Institute)

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 potato cyst nematodes (PCN) 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 PCN and potato. PCN species Globodera rostochiensis and G. pallida are widespread in the UK and are economically significant threats to global crop production. PCN has significant impact on potato seed production 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 PCN that determine recognition in the plants and therefore resistance. We have coined these novel methods RenSeq [1] and PenSeq [2].  PenSeq in PCN has been established following the successful adaptation from P. infestans (Kyriakos et al., under review). 

1. 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.   

2. 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 oomycets. New Phytologist.DOI:10.1111/nph.1544