Zymoseptoria tritici show local differences in within-field diversity and effector variation

Zymoseptoria tritici is a cosmopolitan hemibiotrophic wheat pathogen with a high mutation rate and a mixed reproduction system, leading to challenges in traditional farming management. For successful integration of pest management, especially for early diagnostics of new aggressive or fungicide-resistant lineages, it is critical to understand population diversity in the field. We look at whole-genome sequence data for three datasets to differentiate within field diversity in fields of similar size: one dataset from a newly sampled field population from the United Kingdom and two publicly available datasets from fields from the United States and Switzerland. Inspection of population structure and diversity features, such as minor allele frequency distribution and clonality, show no within-field structure, the most abundant SNPs are present in low frequency, and European fields have higher clonality. Knowing that effectors play particularly important roles in (a)virulence, we specifically assess effector diversity characteristics. Whereas on a whole-genome scale, we can see separation of the populations at the regional scale, we do not find such separation for the effectors. Moreover, we find that multiple effector haplotypes can be found interspersed within the field and even occur within what has been considered clonal isolates or isolates from a single lesion. Our analyses highlight that within-field Z. tritici diversity is higher than previously reported. Our finding that multiple effector haplotypes can be found within a single lesion might explain the large resistance gene-breaking potential of Z. tritici.