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Protecting the Australian Capsicum Industry from Incursions of Colletotrichum Pathogens

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Protecting the Australian Capsicum Industry from Incursions of Colletotrichum Pathogens Protecting the Australian Capsicum industry from incursions of Colletotrichum pathogens Dilani Danushika De Silva ORCID identifier 0000-0003-4294-6665 Submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy Faculty of Veterinary and Agricultural Sciences The University of Melbourne January 2019 1 2 Declaration I declare that this thesis comprises only my original work towards the degree of Doctor of Philosophy. Due acknowledgement has been made in the text to all other material used. This thesis does not exceed 100,000 words and complies with the stipulations set out for the degree of Doctor of Philosophy by the University of Melbourne. Dilani De Silva January 2019 i Acknowledgements I am truly grateful to my supervisor Professor Paul Taylor for his immense support during my PhD, his knowledge, patience and enthusiasm was key for my success. Your passion and knowledge on plant pathology has always inspired me to do more. I appreciate your time and the effort you put in to help me with my research as well as taking the time to understand and help me cope during the most difficult times of my life. This achievement would not have been possible without your guidance and encouragement. I am blessed to have a supervisor like you and I could not have imagined having a better advisor for my PhD study. I sincerely thank Dr. Peter Ades whose great advice, your vast knowledge in statistical analysis, insightful comments and encouragement is what incented me to widen my research to various perspectives. I extend my gratitude to my external supervisor Professor Pedro Crous for his invaluable contribution in taxonomy and phylogenetic studies of my research. Most importantly for his guidance, support and giving me the opportunity to work with Phytopathology research team at the The Westerdijk Fungal Biodiversity Institute, Netherlands. I am grateful to both of you for your time, patience, expertise and especially the scholarly input in preparing, and publishing manuscripts. A big thank to Dr. Ewald Groenewald for his great knowledge in phylogenetics, invaluable input into the analysis and influential assistance in my publications. Most importantly for his generous support and kind advice given when I needed it the most. My appreciation extends to all the members of the group and Ms. Mieke Starink-Willemse and Arien van Iperen for excellent technical support. I would like to thank Dr. Helen Billman-Jacobe, Prof. Glenn Browning and Dr. Ken Snibson of my advisory committee for their support, guidance and direction on improving my PhD project. I thank our lab manager, Carolyn Selway and the laboratory technical officer Martin Ji for their continuous support and assistance throughout my candidature. Dr. Roger Shivas, Australia, Dr. Andi Nasruddin, Indonesia, Dr. Orarat Mongkolporn, Thailand, Dr Nalika Ranathunge, Sri Lanka and World Vegetable Center AVDRC, Taiwan are greatly acknowledged for the collaboration and providing specimens for the project. ii I am lucky to be surrounded by good friends throughout my PhD journey. A special thankyou goes to Dr. Niloofar Vaghefi and Dr. Eden Tongson for their mentoring and guidance, Dr. Jiang Chang, Dr. Veradina Dharjono, Dr. Baki Bhuiyan, Dr. Azin Moslemi for great friendship and endless support on this challenging but exciting journey. Also, to the young generation of our group Aruni Alahakoon, Ruvini Lelwala, Sophia Callaghan and Mee-Yung Shin, you guys are the best! None of this would be possible if not for The University of Melbourne and I gratefully acknowledge the financial support from the Melbourne International Research Scholarship (MIRS) and Melbourne International Fee Remission Scholarship (MIFRS) awarded by the University of Melbourne. I would like to extend my gratitude to my first university, University of Peradeniya, Sri Lanka where I did my honours degree, which gave the foundation for my higher studies. I am pleased to express my appreciation to all my beloved teachers at the University, and Prof. Adikaram and Dr. Charmalie Abayasekara for their inspirational guidance towards Plant pathology. I am truly grateful to my family I would never have come this far without you. I am truly grateful to my loving parents Mr & Mrs. De Silva, for the sacrifices they have made on my behalf. They have given me the blessing, encouragement and the strength to make this journey a success. Words would never say how grateful I am to both of you. Warm regards to my brothers and sister for supporting me throughout my life. Last, but certainly not least my loving, supportive, encouraging and patient husband Upendra for being there for me, in each and every moment. You were always there at times I thought that it is impossible to continue, you helped me to keep things in perspective. I appreciate my son, my little boy Yuvain for his unconditional love and patience during my PhD. I consider myself the luckiest to have such a lovely and caring family, standing beside me with their love and unconditional support. iii Abstract Anthracnose of chili (Capsicum annuum) causes serious production loss globally wherever chili plants are grown especially in the subtropical and tropical regions of Asia and Australia. Anthracnose is caused by a complex of Colletotrichum species that are one of the most important groups of plant pathogenic fungi throughout the world. Currently 24 Colletotrichum spp. have been identified as causing anthracnose of chili globally with some species capable of causing disease in other plant species such as tropical fruits. The distribution of these species is quite uneven and the status of the taxonomy of Colletotrichum spp. in most countries in Asia and Australia remains uncertain. The Australian horticultural industry is at risk of infection by exotic Colletotrichum spp. entering from Asia. In this thesis, multigene phylogenetics combined with description of morphological characters were used to study the taxonomy and phylogeny of Colletotrichum species associated with chili anthracnose in Australia and Asia. A detached Capsicum fruit bioassay was optimised to assess the pathogenicity of isolates of C. scovillei one of the most important pathogens causing anthracnose. Pathogenicity and aggressiveness of all the identified species were evaluated in the detached fruit bioassay and PCR-based diagnostic assays were developed to detect C. scovillei. In Australia, five Colletotrichum species causing anthracnose of chili were identified with C. truncatum being the most prevalent. Colletotrichum cairnsense sp. nov was described as a new species while C. queenslandicum, C. simmondsii and C. siamense were recorded for the first time as pathogens of chili in Australia. Pathogenicity assay confirmed that the new species C. cairnsense was highly aggressive and showed symptoms in both wound and non-wound inoculated fruits. Whereas, C. siamense was moderately aggressive on fruits inoculated with both methods and the other two species were only pathogenic and mildly aggressive on wound inoculated fruits. In Indonesia, Malaysia, Sri Lanka, Thailand and Taiwan, eight known Colletotrichum species were identified being C. endophyticum, C. fructicola, C. karsti, C. plurivorum, C. scovillei, C. siamense, C. tropicale and C. truncatum. In addition, three new Colletotrichum species were described as C. javanense sp. nov., C. makassarense sp. nov. and C. tainanense sp. nov. from West Java (Indonesia); Makassar, South Sulawesi (Indonesia); and Tainan (Taiwan), respectively. This was also the first report of C. siamense causing anthracnose of Capsicum annuum in iv Indonesia and Sri Lanka and also the first report of C. fructicola infecting chili in Taiwan and Thailand and C. plurivorum in Malaysia and Thailand. Colletotrichum truncatum, C. scovillei and C. siamense were the most commonly isolated species. Development of a detached Capsicum fruit bioassay to determine the pathogenicity of a diverse geographical range of isolates of C. scovillei showed that the interaction of fruit maturity, host genotype and inoculation method affected infection and lesion development. On Ca. annuum Bangchang fruit, wounded prior to inoculation, pathogenicity was consistent regardless of fruit maturity. In contrast, in the non-wound fruit bioassay there was variability in pathogenicity with some isolates unable to infect and those that did infect being variable in their aggressiveness. On the resistant genotype, Ca. chinense PBC932, pathogenicity was dependent on the inoculation method and maturity stage of the fruit. In addition, lack of correlation in pathogenicity of isolates between the two Capsicum genotypes for both inoculation methods and fruit maturity variables indicated that there was host specialization which made it difficult to predict pathogenicity of isolates in one host environment or testing condition from pathogenicity in the other. All the Colletotrichum species from Asia caused symptoms of anthracnose on wounded fruit of Ca. annuum genotype Bangchang at both maturity stages but there were large differences in severity of the symptoms. Pathogenicity assay showed that C. javanense and C. scovillei were highly aggressive, especially when inoculated on non-wounded fruit, compared to all other species. Capsicum chinense genotype PBC932 was mostly resistant to anthracnose and all the species induced smaller lesions at different host conditions. Several pathotypes were identified within multiple isolates of C. scovillei and C. siamense, the two most frequently identified and pathogenic
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