Thesis on the role of receptor-like protein kinases in wheat resistance to Septoria tritici blotch:

INRAE presentation: The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science.

It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

Cyrille Saintenac (INRAE GDEC, group MDC) and Kostya Kanyuka (NIAB) will co-supervise the PhD Student. The main location of the PhD student will be Clermont-Ferrand but he/she will spend at least six months at NIAB in the UK. INRAE GDEC benefits from the most advanced experimental facilities (technical and experimental platforms) with skills, tools, and world-class modern equipment, which allow for growing crops under controlled conditions (four growth chambers fully equipped to maintain conditions required for optimal Z. tritici infection), broadband genotyping and sequencing approaches and laboratories fully equipped to perform molecular experiments. A wealth of knowledge, tools, expertise and experience on Z. tritici research is also available at NIAB.

The NIAB team has access to multiple field locations across the UK which includes Septoria field nurseries experiencing high natural disease pressure, 18 walk-in plant growth rooms that are ideal for performing infections with wildtype Z. tritici, and cat2-certified, GM-compliant laboratory and plant growth facility for carrying virus-induced gene silencing to assess function of candidate RLKs. The PhD project is part of a national project including twelve private breeding companies. The PhD student will therefore interact with the different companies and present the progress of the project once every year.

Context : Septoria tritici blotch (STB) caused by the hemibiotrophic ascomycete fungus Zymoseptoria tritici represents one of the most important wheat diseases in France, UK, and other wheat production areas. This foliar pathogen induces leaf necrosis that drastically reduces photosynthesis. Losses can reach up to 50% during severe epidemics. In France, this fungus is associated with 5 to 10% harvest losses, which lead to yearly substantial economic losses of 350 to 700 million euros.

STB management strategies rely on fungicides and resistant wheat cultivars. It is striking to see that 70% of annual fungicide usages in EU (one billion euros) are devoted to the control of Z. tritici. However, the efficacy of the two most commonly used fungicides (azoles and strobilurins) against Z. tritici has largely decreased these past few years due to the emergence of resistant isolates. Current disease management strategies are mostly based on a new generation of fungicides, the SDHIs.

However, in 2015, highly resistant isolates to SDHIs were detected in Ireland and are now threatening European wheat production. In this context, breeding for STB-resistant wheat cultivars represents one of the most sustainable options to protect wheat from this devastating disease. It is of high priority for most breeding companies.

Scientific questions : The objective of the PhD project is to analyze the different types of resistance against STB at the seedling and at the adult stages and evaluate the role of RLKs in these different resistances. The ultimate aim is to get insight into the diversity of resistance mechanisms so that appropriate combinations of disease resistance genes could be deployed in new wheat cultivars to provide more efficient disease control.

Question 1 : What is the genetic architecture of adult stage STB resistance in French wheat cultivars ? Every year several STB resistant wheat cultivars are registered to the French national catalogue. However, the genetic basis of their resistance is unknown, which limits subsequent breeding efforts. The objective of this task is to determine the main and most efficient QTL for resistance against STB present in French wheat cultivars.

We have selected thirteen recently registered bread wheat cultivars based on their high level of resistance to STB. The PhD student will identify the STB resistance QTL present in these cultivars by analyzing phenotyping and genotyping data from bi-parental mapping populations developed from the crosses involving these cultivars and those that are highly susceptible to STB.

These populations comprising about 100 to 250 individuals will be phenotyped by breeding companies, Arvalis and NIAB in Septoria nurseries under natural or artificial inoculation and irrigation or no irrigation depending on the STB disease pressure and the environmental conditions at the Septoria nurseries. The PhD student will be involved in the phenotyping of these populations and will perform the QTL analysis and QTL characterization (efficiency and robustness of disease resistance).

Question 2 : Are RLKs the main gene family that confers resistance to STB ?
The first two wheat Stb genes cloned to date encode RLKs. Furthermore, almost all physical intervals spanning the 21 other genetically mapped Stb genes contain RLKs in the reference genome of wheat Chinese Spring.

These data allowed us hypothesize that this gene family plays a major role in wheat resistance to STB. Using phenotyping experiments, comparative genomic, expression data analysis and transient functional candidate gene validation, the PhD student will be able to identify if any of the 21 known Stb genes and the resistance QTL identified in French wheat varieties correspond to RLKs.

Training and skills

Master’s degree/Engineering degree We are seeking for a highly motivated candidate with a background in phytopathology, genetic and bioinformatics. A Master degree in one of these related fields is required.

INRAE’s life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

– up to 30 days of annual leave + 15 days “Reduction of Working Time” (for a full time);
– parenting support: CESU childcare, leisure services;
– skills development systems: training, career advise;
– social support: advice and listening, social assistance and loans;
– holiday and leisure services: holiday vouchers, accommodation at preferential rates;
– sports and cultural activities;
– collective catering.

How to apply

I send my CV and my motivation letter to

Offer reference

  • Contract: PhD position
  • Duration: 3 years
  • Beginning: 02/11/2023
  • Remuneration: 2 044,12 €/month
  • Reference: OT-18504
  • Deadline: 15/09/2023

Centre Clermont-Auvergne-Rhône-Alpes


Contact SAINTENAC Cyrille 0443761389

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