Fungal pathogens in pome fruit orchards and causal agents of postharvest decay postharvest of agents and causal in pome fruit orchards pathogens Fungal Fungal pathogens in pome fruit orchards and causal agents of postharvest decay Marcel Wenneker Marcel Wenneker Marcel Propositions 1. Postharvest diseases should be regarded as complex problems that require systems intervention approaches for their control. (this thesis) 2. Adequate molecular detection of latent infections depends more on adequate sampling protocols than on the sensitivity of the detection technique. (this thesis) 3. Preventing inappropriate data analysis, such as occurs in p-hacking, is important to prevent obstruction of scientific progress. 4. Augmentative biological control conflicts with the objective to stimulate biodiversity. 5. If retailers and food producers are truly concerned about consumer health, they should focus on reducing salt and sugar content of food rather than on pesticide residues and GMOs. 6. The replacement of natural grass by synthetic turf deteriorates defending skills in soccer, especially concerning sliding tackles. Propositions belonging to the thesis, entitled: “Fungal pathogens in pome fruit orchards and causal agents of postharvest decay” Marcel Wenneker Wageningen, 25 February 2019 Fungal pathogens in pome fruit orchards and causal agents of postharvest decay Marcel Wenneker Thesis committee Promotor Prof. Dr B.P.H.J. Thomma Professor of Phytopathology Wageningen University & Research Other members Prof. Dr R.A.A. van der Vlugt, Wageningen University & Research Dr A.D. van Diepeningen, Wageningen University & Research Dr W. van der Werf, Wageningen University & Research Dr G.C.M. van Leeuwen, National Plant Protection Organization, Wageningen This research was conducted under the auspices of the Graduate School Experimental Plant Sciences Fungal pathogens in pome fruit orchards and causal agents of postharvest decay Marcel Wenneker Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus, Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Monday 25th of February 2019 at 4 p.m. in the Aula. Marcel Wenneker Fungal pathogens in pome fruit orchards and causal agents of postharvest decay, 194 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2019) With references, with summaries in Dutch and English ISBN: 978-94-6343-402-7 DOI: https://doi.org/10.18174/468012 Contents Chapter 1 General introduction and outline of the thesis 7 Chapter 2 New and emerging postharvest diseases of pome fruit in the Netherlands 25 Chapter 3 Fibulorhizoctonia psychrophila is the causal agent of lenticel spot on apple and pear fruit in the Netherlands 47 Chapter 4 Dynamics of postharvest pathogens Neofabraea spp. and Cadophora spp. in plant residues in Dutch apple and pear orchards 57 Chapter 5 Development of a method for detection of latent European fruit tree canker (Neonectria ditissima) infections in apple and pear nurseries 83 Chapter 6 Methods for the quantification of resistance of apple genotypes to European fruit tree canker caused by Neonectria ditissima 93 Chapter 7 Identification of Alternaria spp. as causal agent of Dead Flower Buds Disease of Pear (Pyrus communis) in the Netherlands and methods for disease control 129 Chapter 8 General discussion: Latent postharvest pathogens and their management: from single measures to a systems intervention approach 157 Summary 183 Samenvatting 187 Nawoord 191 Curriculum vitae 193 1. General introduction and outline of the thesis CHAPTER 1 8 General introduction and outline of the thesis Introduction The terms ‘pome’ fruit describes a major group of deciduous fruit-bearing tree species originating from the temperate zone of the northern hemisphere. In Europe, apple represents about 50% of total fruit production. Apple (Malus domestica) and pear (Pyrus communis) are the most common species of the pome fruit group in the Netherlands, Chapter 1 Chapter with a total production of 353,000 and 349,000 tons, respectively, in 2014. The main apple and pear cultivars are Elstar and Conference, comprising 40 and 75% of the respective production areas (CBS, 2016). There are a number of major diseases of pome fruit worldwide. Apple scab (Venturia inequalis), powdery mildew (Podosphaera leucotricha), European fruit tree canker (Neonectria ditissima), fire blight (Erwinia amylovora), and fruit rots are the main diseases of apple (McHardy, 1996; Sutton et al., 2014). The main diseases on pears are pear scab (Venturia pirina) and brown spot (Stemphylium vesicarium) (Llorente and Montesinos, 2006; Villalta et al., 2004). Control of fungal diseases in commercial orchards currently depends on multiple applications of various fungicides. The routine fungicide programme used by fruit growers is mainly devoted to the control of apple scab and powdery mildew on apples, and brown spot of pears. Spray schedules with alternating use of active ingredients from several fungicidal groups are common (Manktelow et al., 1996). Several weather-based decision support systems are available for growers to support their decisions on the timing of specific fungicide applications (Holb et al., 2003; Llorente et al., 2000). However, governmental regulations restrict the use of fungicides (European Union, 2009). The increasing demand for fruit without, or with only low, pesticide residues is a reason why alternatives for synthetic fungicides are needed. Integrated Pest Management (IPM) is a pest and disease control strategy that promotes the use of a variety of techniques and methods, including pest and disease resistant cultivars and biological, cultural, and physical control methods. Pesticides are employed in IPM, but only if monitoring, economic thresholds, or disease forecasts indicate a need. Thus, IPM programs in apple and pear are using pesticides more efficiently, but potential problems which cannot be overlooked include pesticide resistance build- up and the continued use of pesticides that are harmful to beneficial arthropods and insects (Desneux et al., 2007; Roubos et al., 2014). The use of specific pesticides instead of broad pesticides, and the reduced pesticide use for control of major pests may lead to an increased importance of minor pests (Damos et al., 2015). Postharvest diseases of pome fruit Fruit are stored in in regular atmosphere (RA) for short-term storage and in controlled atmosphere (CA) for long-term storage until packing. Pome fruit may remain for up to 12 months in storage, during which time fruit rot diseases may develop (Fig. 1). Despite the 9 CHAPTER 1 use of fungicides and improved storage technologies, postharvest fruit rot diseases still remain an important limiting factor for the long-term storage of apples and pears. Figure 1. Postharvest decay of pears. Postharvest diseases of apple and pear result in significant economic losses during storage, and are caused by a range of fungal pathogens (Sutton et al., 2014). Multiple fungicide treatments before harvest are common to reduce the risk of postharvest diseases (Palm and Kruse, 2012). Owing to the earlier mentioned demand for fruit with a restricted number of chemical residues and low total residue levels, as well as for residue- free fruit (Boccaletti and Nardella, 2000; Magnusson and Cranfield, 2005; Ott, 1990), it is expected that risks of losses by postharvest diseases will further increase. Classification of postharvest diseases of pome fruit Postharvest diseases of pome fruit generally originate from two sources: infections through wounds at harvest or during the fruit handling and packing process, and latent fungal infections that occur in the orchards before harvest. Therefore, the classification of pome fruit diseases due to fungal pathogens is based on their mode of penetration in the fruit: (i) wound pathogens and (ii) latent infections. Wound pathogens All postharvest pathogens on pome fruit are potential wound pathogens. Wounds caused by insects and birds, as well as by physical damage before or during harvest, are an important entrance site for pathogens such as Botrytis cinerea (grey mold), Penicillium expansum (blue mold), Mucor piriformis, and Monilinia fructigena (brown rot) (Snowdon, 10 General introduction and outline of the thesis 1990; Sutton et al., 2014). These pathogens typically cause a rapid decay of fruit in the pre- and postharvest stage. Fungicide applications shortly before harvest and careful handling of fruits during harvest are effective measures to reduce losses by wound pathogens. Latent pathogens Postharvest rots caused by latent pathogens result from infections that occur in the Chapter 1 Chapter orchard but remain quiescent during the growing phase and remain unnoticed at harvest. Development and symptom expression takes place during storage. Common pathogens causing such late postharvest losses are able to infect fruits through lenticels, such as the Colletotrichum acutatum species complex (bitter rot) (Spolti et al., 2012), Neofabraea alba (Soto-Alvear et al., 2013), and Neofabraea perennans (Bull’s eye rot) (Weber, 2009). Other pathogens infect apple cultivars that have an open blossom end (calyx) into the core and cause dry or wet core rot; mainly Alternaria spp. and Fusarium spp. (Niem et al., 2007; Sever et al., 2012). Eye rot and calyx end rot are caused by Neonectria ditissima and Fusarium spp. (Sever et al., 2012; Weber and Dralle,