University of Dundee

EASTBIO: Molecular characterisation of plant disease resistance genes through novel Next-Generation Sequencing applications

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership This opportunity is open to UK and EU nationals.

Applicants should apply by completing the EASTBIO application form (downloadable from the EASTBIO website) and e-mail to Candidates should also include their academic transcripts and ensure that they ask their referees to send completed references to Applicants may wish to explain their motivation for joining the EASTBIO training programme.

Supervisors: Dr Ingo Hein (UoD) and Dr Micha Bayer (JHI)

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 a virulence 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 [1-2] and PenSeq.

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 oomycetes. New Phytologist.DOI:10.1111/nph.15441

3.Jupe F., Witek K., Verweij W., Sliwka J., Pritchard L., Etherington G.J., Maclean D., Cock P.J., Leggett R.M., Bryan G.J., Milne L., Hein I.*and Jones D.J.* (2013) Resistance gene enrichment sequencing (RenSeq) enables re-annotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating.