Exploring the prevalence and molecular basis of tomato leaf mould caused by Fulvia fulva on disease-resistant tomato cultivars in commercial New Zealand glasshouses : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Breeding at Massey University, Palmerston North, New Zealand

Abstract

Leaf mould disease, caused by the fungus Fulvia fulva (formerly Cladosporium fulvum), can significantly reduce tomato yields in commercial glasshouses. Protection against this disease has predominantly been based on the introgression of one or two Cf resistance genes from wild tomato species. For example, most resistant cultivars contain the Cf-9 locus, which harbours the resistance genes Cf-9B and Cf-9C. In all cases, these Cf genes encode immune receptors that recognise specific virulence factors of F. fulva called effectors. Unfortunately, however, resistance conferred by Cf genes can be overcome through mutation or deletion of the genes encoding the recognised effectors. This has led to the global emergence of F. fulva strains capable of overcoming all deployed Cf genes. As such, currently deployed Cf genes no longer provide reliable control against leaf mould disease. Recently, wild tomato plants with one or more of 10 new Cf resistance genes were identified, suggesting that these genes could be stacked in commercial tomato cultivars through breeding to provide durable resistance. However, before these Cf genes can be introduced into commercial tomato cultivars, it must first be determined whether they have already been overcome by F. fulva through mutation of the corresponding effector genes. In the current study, I aimed to address this knowledge gap by investigating F. fulva strains present in commercial tomato glasshouses across New Zealand. Specifically, this project sought to determine the prevalence of leaf mould on various cultivars currently grown in the country, particularly those carrying Cf-derived resistance genes (including cultivars marketed as “Ff:A–E”, which harbour the Cf-9 locus). Initial glasshouse observations revealed apparent leaf mould symptoms on cultivars previously considered to be resistant. Establishing whether these cultivars remain protected, or whether their resistance genes have been widely overcome, is essential for informing future breeding programmes. To address this aim, a field survey was conducted across 20 tomato growing sites in New Zealand, encompassing mostly commercial glasshouses, during which leaf mould-infected samples were collected, for the most part, from tomato cultivars considered to be resistant. Leaf mould was recorded on all four resistant cultivars sampled, indicating that these cultivars did not remain reliably protected under the conditions encountered, though confirming this pattern nationally would require wider scrutiny across more cultivars and locations. F. fulva was isolated from three samples (one from a resistant cultivar and two from F. fulva collections), visually characterised, stored, and prepared for genomic DNA extraction. The three isolates spanning a temporal range (collected in the 1980s, 2022 and 2025) were whole-genome sequenced, and the coding sequences of 20 known avirulence (Avr) and extracellular protein (Ecp) effector genes were reconstructed and compared against published reference alleles to identify mutations, truncations and gene-loss events. The effector repertoire was largely conserved, with changes concentrated in the Avr genes: a mutation profile consistent with the predicted evasion of several deployed Cf genes. In contrast, the effectors recognised by the recently identified resistances were largely intact across all isolates, indicating that these new Cf genes are predicted to remain effective and represent viable candidates for deployment. Together, these findings provide a first genomic assessment of the current status of leaf mould resistance in commercially grown tomato cultivars in New Zealand. By clarifying which Cf resistance genes appear to have been overcome and which are predicted to remain effective, this research supports evidence-based cultivar deployment, reduces the risk of resistance breakdown, and strengthens Integrated Pest Management (IPM) strategies within the New Zealand tomato industry.