Identification of new functional resistance genes against P. infestans in Solanaceae species

  • Pauline S. M. Van Weymers

Student thesis: Doctoral ThesisDoctor of Philosophy


Pests and pathogens represent a serious and continuing threat to potato and tomato production worldwide. In this thesis, I have developed a new NB-LRRs probe library accounting for the recent improved annotations of both potato and tomato (Jupe et al., 2013 and Andolfo et al., 2014). The probe library was successfully used to map a late blight resistance in the diploid potato population B3C1HP. Using bulked-segregant resistance gene enrichment and sequencing (RenSeq) analysis in this population, which segregated 1:1 for the phenotype, the resistance was mapped to the lower end of chromosome 9. Furthermore, I developed a novel diagnostic tool, dRenSeq, to screen existing germplasm collection for the presence or absence of known, already characterised disease resistance genes, to prioritise novel resistances for research and breeding. dRenSeq was applied successfully on a set of S. okadae accessions as a proof of concept. The tomato late blight resistance gene Rpi-Ph3 was another focal point in this work, and the use of RenSeq was envisaged to identify Rpi-Ph3. However, another team published the gene (Zhang et al., 2014) and efforts were redirected towards the development of PCR markers to aid marker-assisted selection in breeding programs and to identify the cognate avirulence gene, Avr-Ph3. In addition, the new probe library was assessed in silico to evaluate if it would have enabled the identification of Rpi-Ph3 and homologous sequences. The identification of Avr-Ph3 was established through a large effector screen in an association panel of tomato accessions, co-infiltrations with Rpi-Ph3 in the model Solanaceae plant Nicotiana benthamiana and pathogen assays. The effector screen required the prior establishment of a robust transient expression system in tomato.
Date of Award2016
Original languageEnglish
SponsorsUnited States Department of Agriculture
SupervisorPaul Birch (Supervisor), Ingo Hein (Supervisor) & David Cooke (Supervisor)


  • Phytophthora infestans
  • Effector
  • Resistance
  • Solanaceae
  • Omics

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