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Characterization of Sheath Rot Pathogens from Major Rice-Growing

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Characterization of Sheath Rot Pathogens from Major Rice-Growing Promotor: Prof. Dr. Ir. Monica Höfte Laboratory of Phytopathology Department of Crop Protection Faculty of Bioscience Engineering Ghent University Co-Promoter: Dr. Ir. Obedi I. Nyamangyoku Department of Crop Science School of agriculture, Rural Development and Agricultural Economics College of Agriculture, Animal Science and Veterinary Medicine University of Rwanda, RWANDA Dean : Prof. Dr. Ir. Marc Van Meirvenne Rector : Prof. Dr. Anne De Paepe ii Ir. Vincent de Paul Bigirimana Characterization of sheath rot pathogens from major rice- growing areas in Rwanda Thesis submitted in fulfilment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences iii Dutch translation of the title: Karakterisatie van pathogenen die “sheath rot” veroorzaken in de belangrijkste rijstgebieden in Rwanda Cover illustration: Some sheath rot disease features: - Left upper side: microscopic picture of the reverse side of Fusarium andiyazi isolate RFNG10 on PDA medium; - Left lower side: microscopic picture of the front side of Fusarium andiyazi isolate RFNG10 isolate on PDA medium; - Center: illustration of rice sheath rot symptoms on a rice plant; - Right side: illustration of a phylogenetic tree of Pseudomonas isolates associated with rice sheath rot symptoms in Rwanda and the Philippines. This work was financially supported by a PhD grant from the Belgian Technical Cooperation (BTC) (reference number: 10RWA/0018). Additional funding was provided by the Ghent University. Cite as: BIGIRIMANA V.P. 2016. Characterisation of sheath rot pathogens from major rice-growing areas in Rwanda. PhD thesis, Ghent University, Belgium. ISBN Number: 978-90-5989-904-9 The author and the Promoters give the authorization to consult and to copy parts of this work for personal use only. Every other use is subject to the copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. iv Members of the jury Prof. Dr. Ir. Kris VERHEYEN (Chairman) Forest & Nature Laboratory Department of Forest and Water Management Faculty of Bioscience Engineering, Ghent University, BELGIUM Prof. Dr. Ir. Tina KYNDT (Secretary) Epigenetics & Defense Research Group Department of Molecular Biotechnology Faculty of Bioscience Engineering, Ghent University, BELGIUM Prof. Dr. Ir. Monica HOFTE (Promoter) Laboratory of Phytopathology Department of Crop Protection Faculty of Bioscience engineering, Ghent University, BELGIUM Dr. Ir. Obedi I. NYAMANGYOKU (Co-Promoter) Department of Crop Science School of agriculture, Rural Development and Agricultural Economics College of Agriculture, Animal Science and Veterinary Medicine University of Rwanda, RWANDA Prof. Dr. Ir. Kris AUDENAERT Department of Applied Biosciences Faculty of Bioscience Engineering, Ghent University, BELGIUM Dr. Ir. Joseph BIGIRIMANA Eastern and Southern Africa Regional Office International Rice Research Institute (IRRI) and Faculty of Agricultural Sciences University of Burundi, BURUNDI Dr. Bart COTTYN Crop Protection Plant Sciences Research Unit Institute for Agricultural and Fisheries Research (ILVO), BELGIUM v ACKNOWLEDGMENTS At the end of these doctoral studies, I would like to express my gratitude to many people who contributed in their success. My recognition goes first to my Promoter, Prof. Dr. Ir. Monica HOFTE, professor and Head of the Laboratory of Phytopathology at Ghent University, who guided me in the application for admission, writing the research project, conducting the research work, meeting administrative formalities, and in finalizing these studies. You managed to maintain the scientific rigor in an uncommon scientific research context. Dr. Ir. Obedi Ishibwela NYAMANGYOKU, Senior Lecturer in Plant breeding and Crop physiology at the University of Rwanda, you served as my Co-Promoter. Your knowledge and experience on agriculture and science in general in developing countries and your support in administrative formalities provided me with an invaluable help. My doctoral dissertation is evaluated by a team composed of professors Kris VERHEYEN (Chairman), Tina KYNDT (Secretary), Kris AUDENAERT and Monica HOFTE, from Ghent University and Dr. Ir. Joseph BIGIRIMANA from IRRI and the University of Burundi, Dr. Bart COTTYN from ILVO (You also provided us with Pseudomonas strains from the Philippines) and Dr. Ir. Obedi I. NYAMANGYOKU, from the University of Rwanda. I thank you all for having accepted to take part in the evaluation of my doctoral studies and for the way you guided me in improving the PhD dissertation. It is an honor for me to be a graduate of Ghent University. In my doctoral studies, I interacted with many people from the Laboratory of Phytopathology. I think particularly to Lien B. and Jonas, who helped me in getting familiar with Ghent surroundings and initiated me to the working environment in the Laboratory of Phytopathology. Pauline, in addition to your academic talents, you are also gifted for group animation and designing thought-provoking messages. I commend your initiative of creating a Phytopathology Running Team; having participated twice in the Ghent Ekiden is satisfying for me. Nathalie, I appreciated frank talks that we had. You kept encouraging me in the writing phase. Osvaldo and Zhong, I respect the willingness to help that you were expressing to me. Khuong, thank you for facilitating the continuation of my work in Ghent in 2014-2015, when my scholarship was ending. David, you were guiding the “rice team” when I started my doctoral studies. Your scientific mind is admirable. Kaat, I hope that we will keep in touch about the latest developments on rice sheath rot; thank you for translating the summary in Dutch. Soraya, I like that you know about living conditions in various parts of the world. Ilse, your practical assistance in laboratory manipulations and preparing the manuscript for printing was of capital importance. Bjorn and Nadia, your cooperation was invaluable in smoothly organizing my studies and stays in Ghent. In each of my stays in Ghent, I was sitting in a new office and I realize that worked in all the offices of the laboratory; Cristiana, Ilse and Lisa, I shared with you the office in my last stay and I value your companionship. I also think about all the other staff that I met: Alaa, Andrea, Ellen, Eric, Evelien de W., Evelien van B., Feyisara, Henok, Huang, Jasper, Jing, Jolien C., Jolien D’A., Katrien, Lien T., Lieselotte, Lieve, Maria, Nam, Nga, Njira, Olervis, Olumide, Saman, Sarah, Seifi (Soren), Sewwandi, Silke, Suzane, Zabi. I appreciated the company of all of you when we were taking the lunch or participating in events together. To the whole group, for those who vi graduated and that are now working, I wish you the best in your career and for those who are preparing their degrees, good luck. The Belgian Technical Cooperation (BTC) facilitated my studies. Additional funding was provided by the University of Ghent. From the selection for scholarship, the start of studies and their progression, BTC’s assistance proved capital. I think particularly to their teams in Kigali (John, Salama) and Brussels (Célestin, Nicolas, Françoise, Princia) that made this PhD happen. My studies were conducted in partnership with the University of Rwanda, College of Agriculture Animal Science and Veterinary Medicine (Ex-Higher Institute of Agriculture and Animal Husbandry, ISAE). I appreciate the way I was supported by the various authorities at UR and ex-ISAE (Rectors, Vice-Rectors, Deans, Heads of Departments, Directors, Professionals, Officers) and the personnel in the laboratory work, the regular teaching activities and in meeting administrative obligations. I also think about the colleagues with whom I was working in the Crop Production Department when I started my doctoral studies and those with whom I am working now in the Crop Science Department. I also have in mind colleagues with whom I share lunch and talks in the restaurant at Busogo. I can not forget all the people who contributed in my education at Nemba (now Nemba and Mbuga P. S., Gakenke District), Saint Jean Nkumba and Saint Léon Kabgayi Seminaries, National University of Rwanda (now part of the University of Rwanda), Catholic University of Louvain (UCL), Ex-FUSA Gembloux (now Gemboux ABT, part of the University of Liège). You gave me a strong intellectual base and instilled in me human values without which I would not have furthered studies. In my research, I interacted with many farmers, field technicians, researchers and people working in various institutions. I thank all of them and think particularly to many farmers who allowed me to take sheath rot diseased rice plant samples from their fields. My family accepted my long stays while in Belgium and a very busy schedule in Rwanda. I am very grateful to their support. I think particularly to Isabelle, Audrey and Carmina and also to Antoine, Immaculée, Jeanne d’Arc, Bassilien, Assumpta, François-Xavier, Father Angelo, Alice, Liliane, Epimaque and Benjamin. Théoneste, Béatrice, their children and Agnès who were regularly supporting me in my stays in Belgium. I am cognizant to your efforts. To you all, who contributed in the success of these studies, in one way or another, feel that I am grateful to your support. Vincent de Paul BIGIRIMANA vii Table of contents ACKNOWLEDGMENTS ................................................................................................................ VI LIST OF ABBREVIATIONS ............................................................................................................
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