Exploring Gene Diversity in Wheat-zymoseptoria

**Exploring gene diversity in wheat-Zymoseptoria tritici interactions as a path to improved Septoria tritici blotch control**:

- Réf **ABG-125661**
- Sujet de Thèse- 04/09/2024- Autre financement public- INRAE- Lieu de travail- Clermont-Ferrand - Auvergne-Rhône-Alpes - France- Intitulé du sujet- Exploring gene diversity in wheat-Zymoseptoria tritici interactions as a path to improved Septoria tritici blotch control- Champs scientifiques- Biologie

**Description du sujet**:
**Context**
- Septoria tritici blotch (STB), caused by the fungal pathogen _Zymoseptoria tritici_, is one of the most devastating diseases in France and Europe. This pathogen induces leaf necrosis, reducing photosynthesis and yield by an average of 1.5 tons per hectare per year. In the current agro-ecological context, sustainable management of STB primarily involves implementing integrated pest management (IPM) strategies, with the use of resistant wheat cultivars as the main pillar.- To date, 23 _Stb_ genes and over 300 QTL conferring resistance to _Z. tritici_ have been mapped on the wheat genome. Three _Stb_ genes - _Stb6_, _Stb15_, and _Stb16q_ - have been cloned. These genes encode receptor-like protein kinases anchored at the plasma membrane, which detect the presence of the pathogen extracellularly. In the early 2000s, it was shown that resistance mediated by the _Stb6_ gene follows a gene-for-gene interaction with the corresponding avirulence gene from _Z. tritici_, _AvrStb6_. More recently, similar interactions have been observed for other _Stb/AvrStb_ genes, raising questions about the universality of this interaction model. On the pathogen side, four _AvrStb_ genes have been cloned: _Avr3D1_, _AvrStb6_, _AvrStb9_, and _AvrStb20q_. The exact mechanism (direct or indirect) by which AvrStb proteins are recognized by Stb proteins is currently unknown. A wide number of haplotypes has already been described for these _AvrStb_ genes that mediate varying efficiencies of resistance against the same _Stb_ alleles. On the other side, genetic diversity on _Stb_ genes has been revealed with for instance 22 different alleles of _Stb6_ described in the literature but only one known to confer resistance. While the impact of _AvrStb_ diversity on the outcome of the interaction has been investigated, the effect of diversity of _Stb_ alleles has not been as thoroughly studied, limiting the available alleles for breeding resistant cultivars and understanding the Stb/AvrStb recognition.- The population of _Z. tritici_ is genetically very diverse, with several million haplotypes per hectare of wheat. This pathogen undergoes several cycles of sexual reproduction per year, allowing it to evolve rapidly and potentially overcome resistant wheat cultivars. To mitigate this, one proposed strategy is to diversify resistances and deploy them with a faster turnover based on the frequency of corresponding avirulence genes in the natural fungal population. This strategy requires a thorough understanding of the diversity of Stb/AvrStb interactions, the mechanisms of recognition between wheat and _Z. tritici_, and comprehensive data on the number, distribution, and frequency of _AvrStb_ genes in the natural population of _Z. tritici_. To this end, the PhD project will be divided in two main objectives:
**1-Identification of new alleles of wheat **_Stb_** genes involved in resistance**

The objective of this task is to thoroughly evaluate the genetic diversity of the _Stb_ genes, identify alleles involved in wheat resistance to STB, and unravel the specificity of their interaction with the corresponding _AvrStb_ genes. The PhD student will investigate the allelic diversity of the wheat genes _Stb6_ and _Stb9_, two of our current model genes. A large collection of several hundred wheat accessions, primarily landraces, will be selected in collaboration with our local biological resource center from the ten thousand accessions that have been recently genotyped. These landraces will be chosen from the 11 clades used to retrace the evolutionary history of wheat. The extracellular domain of these two genes involved in pathogen recognition will be sequenced using new sequencing technologies available at the Gentyane platform. Phylogenetic relationships between the different haplotypes and their evolution through wheat migration routes will be analyzed.

Once the allelic diversity is identified, the PhD student will evaluate the resistance efficiency of each _Stb_ allele (both those documented in the literature and those identified in this project) against different alleles of the corresponding _AvrStb_ genes. At least 10 _Z. tritici_ isolates, known to carry different _AvrStb_ alleles that are widely represented in the _Z. tritici_ French population, will be used to phenotype wheat accessions carrying the different allelic versions of _Stb_. _Stb_ alleles identified as potentially conferring resistance according to the phenotyping assays will be functionally valida