Molecular and biochemical mechanisms of plant-host rhizosphere manipulation by Rhizoctonia solani for increased virulence to Brassica crop species

Rhizoctonia solani is the most aggressive soil-borne pathogen to oilseed rape (OSR, Brassica napus) during the seedling developmental stage of the crop. The pathogen can reduce crop establishment causing losses of more than £80m in the UK alone. Isolates of R. solani are classified in genetically and biologically diverse anastomosis groups (AGs) based on their ability to fuse and reproduce. Isolates of AG2-1 predominate in UK soils and are most virulent to OSR. The pathogen produces auxins, which contribute to decreased defence response and modify root growth and architecture of the plant host for the benefit of the pathogen.
The aims of this project will be to
i) define molecularly, biochemically, and genetically the function of auxins produced by R. solani for virulence, disease susceptibility and root trait modification
ii) identify auxin candidate genes in R. solani for further functional validation. The overall hypothesis is that specific auxins produced by the pathogen function either as virulence factors or as factors for root growth manipulation and colonisation by R. solani. It is expected that through this project novel functional genetic information will be gained which can be translated from Arabidopsis to OSR to decrease disease susceptibility and/or identify future targets for control of R. solani by chemical or biological means. The project will investigate the following:
1. What is the function of different auxins produced by R. solani for disease susceptibility and root trait modification? To address this question the student will functionally characterise plant pathogen interactions between several isolates of R. solani AG2-1 that produce different auxins using Arabidopsis mutants defective in auxin synthesis, transport and signalling plus mutants defective in flavonoids accumulation and production of reactive oxygen species.
2. What is the genetic or molecular basis of the defence response to R. solani? The student will carry out artificial inoculations with mutants with virulent and avirulent disease phenotypes from 1.
Transcriptomic, metabolomic and pharmacological approaches will be used to identify key candidate genes and signals mediating host defence during plant pathogen interactions. Candidate genes and
signals identified using these approaches will then be further validated by molecular genetic approaches (eg qRT-PCR; hormone profiling) using a number of B. napus genotypes showing varying degrees of resistance to R. solani.
3. Identification and functional validation of candidate genes in R. solani. Selected isolates which produce different quantities and types of auxins in vitro and in planta will be used to investigate, using pharmacological and molecular approaches, the auxin biosynthesis pathway in R.
solani. Orthologue candidate genes of interest will be searched for in sequenced fungal genomes.
The genome of sequenced AGs of R. solani will also be interrogated. CRISPR-CAS9 based genome editing will be used to generate mutants for a few candidate genes in AG2-1 for functional validation.
The student will receive training in several key aspects of molecular biology, plant pathology, functional genomics, bioinformatics, metabolomics and fungal biology, and will acquire specific technical and transferable skills set from their PhD studies to enhance their future scientific career