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Masters Dissertation MAKERERE UNIVERSITY INCIDENCE AND MOLECULAR VARIABILITY OF CASSAVA BROWN STREAK DISEASE IN RWANDA Jeanine UMFUYISONI BSc in Biology, Option: Biotechnology (University of Rwanda) A THESIS SUBMITTED TO THE DIRECTORATE OF RESEARCH AND GRADUATE TRAINING IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE AWARD OF A MASTER OF SCIENCE DEGREE IN CROP SCIENCE (CROP PROTECTION) OF MAKERERE UNIVERSITY May 2018 DECLARATION I hereby declare that the work in this report is my own and has never been submitted to any other university Signed: Date 24 October 2018. Jeanine Umfuyisoni MSc. Crop Science This report has been submitted with the approval of the university supervisor Signed Date 3rd October 2018. Assoc. Prof. Jeninah Karungi Tumutegyereize Department of Agricultural Production College of Agricultural and Environmental Sciences School of Agricultural Production Makerere University This report has been submitted with my approval as a supervisor Signed Date 3rd October 2018 Dr. Peter Sseruwagi Mikocheni agriculture Research institute P.O Box 6226 Dar-es-Salaam,Tanzania i DEDICATION To my wonderful husband Richard Manishimwe and my lovely son Rickson Béni Ishimwe, for their constant support, encouragement, love, patience and prayers during my study period. The pursuit for my goals would not be possible without you. ii ACKNOWLEDGEMENT I would never have been able to finish my dissertation without the guidance of Almighty God. Thank you for keeping me strong and healthy throughout my academic endeavour. Thank you for giving me other people to whom I owe my deepest gratitude for their support. I am grateful to the Rwanda Agriculture Board specifically Mrs Marie Claire Kanyange, the Cassava Disease Diagnostic Project country team leader and the whole Cassava Program team for selecting me as one of project beneficiaries (student). My gratitude goes to Bill and Melinda Gates Foundation for funding the project “Cassava Disease Diagnostics” through Mikocheni Agricultural Research Institute (MARI) from which I got the full fund for my studies. I would like to sincerely thank my supervisors Associate Professor Jeninah T. Karungi from Makerere University and Dr. Peter Sseruwagi from MARI for their guidance, patience and understanding during my studies. Despite their many other academic and professional commitments, they were able to provide their time for scientific advices, knowledge, many insightful discussions and suggestions. I would like to thank Dr. Joseph Ndunguru, Dr. Fred Tairo, Dr. Laura Boykin and Dr. Mildred O. Ssemakula for useful guidance, constructive criticism, supervision and providing me an excellent atmosphere for doing my course work and research. Thank you for sourcing my molecular laboratory work at NaccRI and your support in Bioinformatic linkage analysis to Western Australia University. Special thanks to my husband my son and my sister (Claire Uwineza) for your patience, practical and emotional support. I thank you for sticking by my side when I was in need. May almighty God bless you abundantly. Lastly I would like to express my sincerely appreciations to my friends and colleagues Andrew Mtonga, Veneranda Ngazi and Brenda Muga for inspiring my effort despite enormous work pressure we faced together. iii TABLE OF CONTENTS DECLARATION ..................................................................................................................................... i ACKNOWLEDGEMENT ..................................................................................................................... iii TABLE OF CONTENTS ....................................................................................................................... iv LIST OF FIGURES .............................................................................................................................. vii LIST OF TABLE ................................................................................................................................. viii ABSTRACT ........................................................................................................................................... ix CHAPTER ONE ..................................................................................................................................... 1 1.0 INTRODUCTION ................................................................................................................... 1 1.1 Background ................................................................................................................................... 1 1.2 Problem statement ......................................................................................................................... 2 1.3 Justification ................................................................................................................................... 3 1.4 Objectives ..................................................................................................................................... 4 1.4.1 Main objective .................................................................................................................. 4 1.4.2 Specific objectives ............................................................................................................ 4 1.4.3 Hypotheses ........................................................................................................................ 4 CHAPTER TWO .................................................................................................................................... 5 2.0 LITERATURE REVIEW ................................................................................................................. 5 2.1 Ecology and Agronomy of cassava ............................................................................................... 5 2.2 Viruses and virus diseases of cassava in Africa ............................................................................ 5 2.3 CBSVs of cassava ......................................................................................................................... 6 2.3.1 History of CBSVs in Africa ....................................................................................................... 6 2.3.2 Genetic diversity of CBSV and UCBSV .......................................................................... 7 2.3.3 Symptomology of cassava brown streak disease .............................................................. 7 2.3.4 Cassava brown streak viruses transmission ...................................................................... 9 2.3.5 Host range of Cassava brown streak viruses .................................................................. 10 2.3.6 Diagnosis and Detection ................................................................................................. 10 2.3.7 Economical damage of Cassava brown streak viruses ................................................... 11 2.3.8 Management of Cassava brown streak disease ............................................................... 11 CHAPTER THREE .............................................................................................................................. 14 iv 3.0 INCIDENCE AND SEVERITY OF CASSAVA BROWN STREAK DISEASE IN MAJOR CASSAVA GROWING DISTRICTS OF RWANDA ......................................................................... 14 3.1 Introduction ................................................................................................................................. 14 3.2 Study areas .................................................................................................................................. 14 3.2.1 Sampling procedure ........................................................................................................ 15 3.2.2 Data Analysis .................................................................................................................. 16 3.3 Results ................................................................................................................................ 17 3.3.2 Cassava brown streak disease Severity ........................................................................... 18 3.3.3 Whitefly abundance ........................................................................................................ 18 3.4 Discussion ................................................................................................................................... 19 CHAPTER FOUR ................................................................................................................................. 22 4.0 MOLECULAR VARIABILITY OF ISOLATES OF CBSVs INFECTING CASSAVA IN RWANDA............................................................................................................................................. 22 4.1 Introduction ................................................................................................................................. 22 4.2 Detection of cassava brown streak viruses in collected samples ................................................ 22 4.2.1 Sample collection ............................................................................................................ 22 4.2.2 Nucleic acid extraction ................................................................................................... 22 4.2.4 PCR Amplification ........................................................................................................
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