Transcriptional, microscopic and macroscopic investigations into monogenic and polygenic interactions of tomato and powdery mildew Chengwei Li Promotor: Prof. dr. R. G. F. Visser Hoogleraar in de Plantenveredeling, Wageningen Universiteit Co-promotor: Dr. ir. A. B. Bonnema Onderzoeker, Laboratorium voor Plantenveredeling Promotiecommissie: Prof. dr. ir. P.J.G.M. de Wit, Wageningen Universiteit Prof. dr. T. Bisseling, Wageningen Universiteit Prof. dr. X. Zhang, Chinese Academy of Agricultural Sciences Dr. G. vanden Ackervecken, Universiteit van Utrecht Dit onderzoek is uitgevoerd binnen de onderzoeksschool Experimental Plant Sciences en de onderzoekschool van de Chinese Academy of Agricultural Sciences Transcriptional, microscopic and macroscopic investigations into monogenic and polygenic interactions of tomato and powdery mildew Chengwei Li Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof. dr. M. J. Kropff, in het openbaar te verdedigen op maandag 3 oktober 2005 des middags om half twee in de Aula CIP-DATA Koninklijke bibliotheek, Den Haag Li C. Transcriptional, microscopic and macroscopic investigations into monogenic and polygenic interactions of tomato and powdery mildew Thesis Wageningen University (2005), the Netherlands. - with references- with summary in English, Chinese and Dutch. Laboratory of Plant Breeding, P.O. Box 386, 6700 AJ, Wageningen, NL ISBN : 90-8504-307-7 Keywords: basal defense, cDNA-AFLP, differentially expressed transcript fragment (DE-TDF), extra-haustorial matrix, fast hypersensitive response (HR), histology, monogenic resistance, Near Isogenic Line (NIL), papilla formation, polygenic resistance, powdery mildew ( Oidium neolycopersici ), RT-PCR, slow HR, tomato (Solanum lycopersicum ), vesicle. Contents Chapter 1 General introduction 1 Chapter 2 Tomato defense to the powdery mildew fungus: 19 differences in expression of genes in susceptible, monogenic- and polygenic resistance responses are mainly in timing Chapter 3 Transcript profiling of genes involved in powdery mildew 37 induced defense responses in tomato mediated by papilla formation, fast or slow hypersensitive responses Chapter 4 Tomato defense against powdery mildew: quantitative 57 resistance is mainly mediated by the hypersensitive response Chapter 5 Transcriptome investigations of powdery mildew 73 challenged tomato lines carrying different combinations of resistance QTLs Chapter 6 General discussion 95 Summary (English) 107 Summary (Chinese) 111 Summary (Dutch) 115 Acknowledgements 119 Curriculum vitae 123 List of publications 125 Education statement 127 Chapter 1 General introduction Crop production needs to be increased more than two-fold to satisfy the increasing demands of high-quality food for an increasing human population and enough feed for livestock. Besides the development of high-yielding cultivars, protecting crops from damage by weeds, animal pests and pathogens is another major sustainable way for producing enough good-quality food and feed (Oerke et al., 2004). Worldwide, crop losses due to plant diseases have steadily increased to 12-15% annually (Food and Agriculture Organization, 1993; Oerke et al., 2004). Therefore, the fight against plant diseases is among the most important issues to guarantee a sufficient global food supply. Plant-biotrophic fungus interaction Of infectious plant diseases, fungal diseases, which include all white and true rusts, smuts, needle casts, leaf curls, mildew, sooty molds and etc, represent the great majority, an estimated two-thirds (Holliday, 1998). The parasitic fungi can be divided into biotrophs that need a living host to complete their life cycle and necrotrophs that kill the host and absorb nutrients from the dead tissue. In order to feed on their hosts, many but not all biotrophic fungi have the ability to differentiate special interfacial structures, so-called haustoria (Schulze and Panstruga, 2003). The interaction between the plant and biotrophic fungus is compatible (susceptible, from the plant side) or incompatible (resistant, from the plant side). An incompatible interaction between plant and biotroph results in the arrest of the growth of the biotroph at different infection stages and often is associated with programmed death of host cells (hypersensitive response, HR). By contrast, during the compatible interaction certain biotrophs establish haustoria within living plant cells for nutrient uptake and reprogram the host’s metabolism to favor their own without causing host cell death (Panstruga, 2002). For a long time, the majority of research on the plant-biotrophic fungus interaction has been focused on plant resistance to the pathogen. On the contrary, little attention is paid to plant susceptibility to biotrophic fungi. As for resistances, nonhost resistance is considered as one of the ideal resistance types to achieve durable resistance although little milestone progress has been made (Mysore and Ryu, 2004). Host resistances, which are among the hottest topics in plant pathology, are monogenic (dominant and recessive) or polygenic resistances, depending on the genetic control of the resistance. Below, details and comparisons between susceptibility and resistance, nonhost and host resistance, monogenic and polygenic resistance, and dominant and recessive resistance of plants to biotrophic fungi are described. Susceptibility and resistance Biotrophic fungi need to be successful in all the infection stages to finish their life cycle, including spore deposition, spore germination and germ tube development, finding a stoma, stoma recognition and appressorium formation, stoma penetration/cell wall Chapter 1 penetration, haustorium formation, colonization and sporulation (Niks and Rubiales, 2002). However, it should be mentioned that the above-described infection stages are relevant for many different plant-biotrophic fungus interactions, while individual interactions may need only some of these infection stages, for example stomata recognition, which is not necessary for powdery mildew. Plants can virtually arrest biotrophic fungal growth at any of these infection stages, however, so far the plant resistances to biotrophs, which are selected by breeders and/or studied by researchers, are mainly associated with the following infection stages: cell wall penetration and stages after haustorium formation. At the prehaustorial stage, plants can react with papilla formation, and at the posthaustorial stage, plants can initiate an HR. Resistances based on papilla formation are well exemplified by mlo-mediated resistance against the barley powdery mildew fungus in barley (Hückelhoven et al., 1999) and ol2 -mediated resistance to tomato powdery mildew in tomato (Bai et al., 2005). However, to our knowledge, there are few other good examples of resistance associated with papilla formation. More frequently, HR accompanies the plant resistance to biotrophic fungi, by arresting the fungal growth at the posthaustorial stage (Parker, 2002). Most of these disease resistances fit the classic “gene-for-gene” model (Flor, 1971). Hm1 from maize, the first R gene cloned through transposon tagging, is a resistance gene to the fungal pathogen Cochiobolus carbonum (Johal and Briggs, 1992). Hm1 encodes a NADPH-dependent reductase unlike the later isolated R genes and the mechanism does not involve interaction via an Avr gene. Martin et al (1993) successfully isolated the tomato Pto gene , encoding a serine/threonine kinase, which renders tomato resistant to a bacterial pathogen ( Pseudomonas syringae pv tomato ) expressing the Avr-Pto gene. It is the first case of cloning an R gene by using map-based cloning. Cf-9 is the first cloned R gene, mediating resistance to a fungal pathogen (Cladosporium fulvum ) that fits the gene-for-gene model (Jones et al., 1994); C. fulvum belongs to the semi-biotrophic extra-cellular fungi without haustoria that enter the leaf via stomata. Cloned R genes against biotrophic intracellular fungi with haustoria include mlo , Mla, Mla6, RPW8.1 and RPW8.2 (reviewed by Hammond-Kosack and Parker, 2003). So far, more than 50 R genes have been cloned (Coaker et al., 2005) and most of them share homologous domains, like leucine rich repeats, nucleotide binding sites, kinase domains and etc. The R genes cloned in the past 10 years greatly increased our knowledge on plant disease resistance. However, we should also pay attention to the other side of the coin: “plant disease susceptibility”. Screening natural populations or induced mutant libraries resulted in the identification of recessively inherited R genes against different biotrophic fungi, such as Barley mlo (Büschges et al. 1997), tomato ol-2 (Ciccarese et al., 2000), and Arabidopsis pmr genes (Vogel and Somerville, 2000; Vogel et al., 2002; Nishimura et al., 2003). Because the resistances mediated by mlo , pmr6 and ol-2 are not associated with the constitutive expression of know defense markers (Panstruga, 2002; Vogel et al., 2002; This thesis), it is plausible to assume that the dominant counterparts to these genes could be the candidates of host genes required for susceptibility to the pathogen or involve some uncharacterized host defense pathways. Studies of the cloned pmr4, pmr6 and mlo genes support the assumption that the host proteins MLO, PMR6 and PMR4 are located and functional at the extrahaustorial membrane, the extrahaustorial matrix and the plant 2 Chapter 1 cell wall at sites of infection, respectively (Figure 1). In contrast to