Appropriate sampling to aid on-farm assessments of the haplotype composition of Zymoseptoria tritici populations

Abstract

Background: Zymoseptoria tritici causes Septoria tritici blotch (STB), which is the biggest threat to wheat in the UK. Azole fungicides have been used since the 1980s to control STB, but resistance to these chemicals is now widespread. The main resistance mechanism is based on the accumulation of CYP51 mutations, with 33 mutations reported. Hence, farmers need an accurate estimate of the haplotype composition of Z. tritici populations to develop effective fungicide treatments and resistance management.

Results: Isolates from Z. tritici lesions were collected from three fields across three commercial farms using two sampling approaches. Analysis of the isolate sequences revealed that the number of distinct haplotypes and the haplotype composition of the most dominant haplotypes varied only between and not within farms. Conventional W-shaped and point sampling both found the same percentage of distinct haplotypes and frequencies of the six most dominant haplotypes.

Conclusion: The results from this survey suggest that farm-resistance-management strategies should be based on farm-specific rather than national data, and that sampling within a single field is sufficient. W-shaped sampling is often recommended in sampling approaches, but this survey finds no evidence of this approach being more appropriate for detecting a greater percentage of distinct haplotypes which may aid the discovery of potential new resistance threats. © 2024 Fera Science Ltd. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Keywords: CYP51; Zymoseptoria tritici; azole; fungicide resistance; haplotype.

Figure 1

Minimum spanning haplotype network for Zymoseptoria tritici representing the haplotype distribution between farms (green = Louth; purple = Salisbury; red = Dorset) amongst all isolates that were successfully sequenced. Each circle depicts a unique haplotype and the size of each circle is proportional to the number of isolates of that haplotype. CYP51 amino acid mutations are denoted by the hatch marks across lines connecting haplotypes with each hatch mark representing a mutation.

Figure 2

Minimum spanning haplotype network for Zymoseptoria tritici representing the haplotype distribution between farms (green = Louth; purple = Salisbury; red = Dorset) amongst all isolates that were successfully sequenced after collection using (a) the H sampling method (point sampling at two locations within a field) and (b) the W sampling method (conventional W‐shaped sampling). Each circle depicts a unique haplotype and the size of each circle is proportional to the number of isolates of that haplotype. CYP51 amino acid mutations are denoted by the hatch marks across lines connecting haplotypes with each hatch mark representing a mutation.

Figure 3

PCA of the principal components (PC) that explain the most variability between samples related to (a) haplotype composition and (b) relative haplotype presence by farm for the six most common haplotypes. Proportion of variability explained by each axis is presented in brackets within the axis label. Red circles = Dorset; Green triangles = Louth and Blue squares = Salisbury.