Harnessing CRISPR Genome Editing to Decode and Engineer Disease Resistance in the Wheat Zymoseptoria tritici Patho-system

Abstract

Zymoseptoria tritici, the cause of Septoria tritici blotch (STB), is a major fungal disease of wheat (Triticum aestivum L.) that has long been a problem in wheat production and causes considerable losses in wheat yields globally. The hemibiotrophic lifestyle of Z. tritici and rapid evolution, genome plasticity and large population size make it difficult to manage the disease and susceptible to breaking deployed resistance mechanisms. Conventional breeding methods, such as quantitative resistance, QTL mapping, marker assisted selection and introgression of resistance genes have been used to improve resistance to STB, but they offer only limited capacity for long-lasting resistance, due to the host's complex genetics and the evolution of the pathogen. However, relatively little is known about the molecular factors that regulate host-pathogen interactions, resulting in limited predictability and durability in resistance. With the advent of the CRISPR/Cas genome editing system, new tools have been developed to dissect gene function and to directly edit genetic elements involved in the virulence of pathogens and the host immune response. This review highlights the use of these CRISPR technologies to reveal molecular determinants of wheat–Z. tritici interactions, the validation of Z. tritici virulence factors, and the engineering of wheat with resistance-related traits. Wheat polyploidy, gene redundancy, transformation efficiency, off-target effects, pathogen adaptation, and regulatory acceptance are significant challenges for wheat resistance strategies in the future. Future resistance strategies will combine CRISPR genome editing with multi-omics technologies, such as genomics, transcriptomics and proteomics, and with the use of AI systems for predicting the optimization of guide RNAs, characterization of the effectors and identification of resistance genes. The combination of CRISPR, computational biology and precision breeding provide next generation tools for developing sustainable wheat resistance to Z. tritici and new fungal threats.

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