k-mer-based GWAS reveals a candidate avirulence gene and structural variation in Puccinia triticina linked to gain of Lr20 virulence

Plant pathogens secrete effector proteins into their hosts to promote colonisation. Among these are avirulence (Avr) effectors, which can be recognised by specific host immune receptors, triggering an immune response that prevents pathogen progression. This recognition exerts strong evolutionary pressure on pathogens to alter and/or eliminate Avrgenes to escape recognition. Consequently, understanding Avr gene evolution is critical for developing effective resistance deployment strategies. However, identifying and validating Avr effectors remains a significant challenge, especially for fungal plant pathogens, leading to a limited catalogue of Avr genes. This challenge is particularly pronounced for obligate biotrophic pathogens such as the wheat leaf (brown) rust fungus Puccinia triticina (Pt), where only two Avr genes have been confirmed to date.