Effectors as tools for controlling scab disease of apple

Apple is an important crop worldwide. One of the most devastating diseases of apple is scab, or black spot, caused by the fungal pathogen Venturia inaequalis (Bowen et al., 2011). Scab disease is primarily controlled through extensive fungicide application. However, with growing evidence of fungicide resistance in the V. inaequalis population, as well as increased public concern over fungicide residues on fruit and in the environment, alternative control strategies are required. Resistance breeding remains the most sustainable alternative.

Like other microbial pathogens, V. inaequalis secretes a collection of virulence factors, termed effector proteins, to the plant–pathogen interface. These effectors function to promote host colonization. In certain cultivars and wild accessions of apple, however, specific effectors of this fungus are recognized as invasion patterns (IPs) by cognate host IP receptors (IPRs) to give IP-triggered responses (IPTRs) (Cook et al., 2015). Such IPTRs, including the hypersensitive response (HR), a localized form of cell death, render the pathogen avirulent and the plant resistant. To evade the above-mentioned recognition events, it is assumed that V. inaequalis must delete, modify or suppress the genes encoding recognized effectors. Any such action, however, will depend on the associated fitness cost (or degree of lost virulence) to the pathogen.

The overall aim of this research is to identify and functionally characterise effectors from V. inaequalis that (a) are recognized as IPs by IPRs (i.e. trigger an HR) in apple, and (b) are important virulence factors (i.e. are unlikely to be deleted, modified or suppressed to avoid recognition by cognate IPRs). This research will enhance our fundamental understanding of the V. inaequalis–apple pathosystem and will directly inform scab resistance breeding programmes. The specific objectives of this research are to:

(1) Identify effector candidates from V. inaequalis (phenotyped New Zealand isolate MNH120) using a combined bioinformatic and transcriptome sequencing (RNA-Seq) approach (Mesarich et al., 2014). For this objective, the MNH120 genome sequence and protein catalogue are available.

(2) Screen apple for HR-associated recognition of V. inaequalis effector candidates identified in (1) using methodologies based on protein infiltration. In excess of 500 apple varieties, including domesticated cultivars and wild accessions are available for infiltration at The New Zealand Institute for Plant and Food Research Limited.

(3) Determine which recognized effectors in (2) are important virulence factors of V. inaequalis using strategies based on gene deletion/overexpression, in planta protein localization (fluorescent reporter–candidate effector protein fusions), in planta protein pull-downs, and plant immune system suppression assays (in Nicotiana benthamiana using Agrobacterium tumefaciens-mediated transient expression assays).

(4) Predict the durability of potential resistances identified in (2) by studying natural polymorphism levels in recognized effector candidates across the V. inaequalis population. An extensive collection of V. inaequalis isolates from New Zealand and around the world is available for investigation at The New Zealand Institute for Plant and Food Research Limited.

Applicants should have a strong interest in molecular plant–microbe interactions, and a first or upper second class B.Sc.(Hons) or M.Sc. degree in Molecular Plant Pathology, Plant Molecular Biology, Molecular Microbiology, Genetics, or related disciplines. Experience in microscopy, plant pathology, fungal biology, proteomics, and genomics/transcriptomics would be an advantage.

Massey University is a leading New Zealand University for postgraduate study, and is one of the QS-ranked top 30 Universities in the world for Agriculture. The supervisory team will include Dr. Carl Mesarich (Primary Supervisor; Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand), Dr. Joanna Bowen (Co-supervisor; The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand), and Prof. Rosie Bradshaw (Co-supervisor; Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand). The scheduled start date for the Ph.D. project is June 2017.

To apply, please send a curriculum vitae, motivation letter and contact details (preferably email addresses) of at least two academic referees to Dr. Carl Mesarich ([Email Address Removed]) before the closing date (November 18, 2016). Shortlisted applicants will be interviewed by Skype or telephone between the 21st and 25th of November, 2016.

Informal inquiries can be directed to Dr. Carl Mesarich ([Email Address Removed]).