DISTRIBUTION OF MAIZE LETHAL NECROSIS DISEASE, ITS CAUSAL VIRUSES AND ALTERNATIVE HOSTS IN THE NORTH - CENTRAL REGIONS OF TANZANIA BY ALLAN MARIKI B.SC HORTICULTURE (SUA) 2013/HD02/1994T A DISSERTATION SUBMITTED TO THE DIRECTORATE OF RESEARCH AND GRADUATE TRAINING IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE AWARD OF THE MASTER OF SCIENCE IN CROP SCIENCE DEGREE OF MAKERERE UNIVERSITY MAY, 2017 DECLARATION i ACKNOWLEDGMENTS The Innovative Agricultural Research Initiative (iAGRI) is acknowledged for providing the full scholarship that allowed me to pursue a Master of Science in Crop Science degree at Makerere University. I also acknowledge the support for laboratory and field research work offered to me through the USAID funded Africa Research in Sustainable Intensification for the next Generation (Africa RISING) project in East and Southern Africa that is led by the International Institute of Tropical Agriculture (IITA). The support of my employer, the Ministry of Agriculture, Food and Cooperatives in Tanzania is also appreciated for granting me a two-year study leave to pursue the postgraduate degree. I am most grateful to my academic supervisor(s), Dr. Mildred Ochwo-Ssemakula, a Lecturer at the School of Agricultural Sciences, Makerere University, Uganda, for the invaluable advice and support that helped me overcome the challenges I faced during the course of studying for the Master of Science degree. I would like to express my gratitude to Dr. Lava Kumar, Head of the Germplasm Health Unit and Virologist at IITA-Ibadan, for his understanding, tireless guidance and facilities that allowed me to work and pursue my studies. I also appreciate the assistance, advice and valuable interaction with members of the Virology and Molecular Diagnostics Units at IITA-Ibadan, especially Mrs. Patricia Ogunsanya and Mr. Adedamola Oresanya, who I worked with closely in the laboratory in a pleasant atmosphere and aided me every bit in sample analysis. I am thankful for the support from the Selian Agriculture Research Institute (SARI) in Arusha, Tanzania, especially Dr. January Mafuru, Mr. Heri Kitenge and Mrs. Salome Munisii, for providing accommodation and allowing me to use facilities in the Pathology Laboratory for virus indexing. In a special way, I greatly appreciate my wife Haikaema Mboya and sons, Livingstone Mariki and Lucas Mariki, for the care, support, and undiminished love during my study period; and for the tolerance of my longtime friendship with the computer. ii TABLE OF CONTENTS DECLARATION ............................................................................................................................. i ACKNOWLEDGMENTS .............................................................................................................. ii TABLE OF CONTENTS ............................................................................................................... iii LIST OF FIGURES ........................................................................................................................ v LIST OF TABLES ......................................................................................................................... vi LIST OF PLATES ........................................................................................................................ vii LIST OF APPENDICES .............................................................................................................. viii LIST OF ACRONYMS AND ABBREVIATIONS ...................................................................... ix LIST OF SYMBOLS/UNITS ........................................................................................................ xi ABSTRACT .................................................................................................................................. xii CHAPTER ONE :INTRODUCTION ............................................................................................. 1 1.1 Background ...................................................................................................................... 1 1.1.1 Importance, global production and uses of maize ........................................................... 1 1.1.2 Production and constraints to maize production in Tanzania .......................................... 1 1.2 Problem statement ............................................................................................................ 2 1.3 Justification ...................................................................................................................... 3 1.4 Objectives of the study..................................................................................................... 3 1.4.1 General objective ............................................................................................................. 3 1.4.2 Specific objectives ........................................................................................................... 3 1.5 Hypothesis........................................................................................................................ 4 CHAPTER TWO: LITERATURE REVIEW ................................................................................. 5 2.1 Origin, classification and biology of maize ..................................................................... 5 2.2 Ecology and agronomy of maize ..................................................................................... 5 2.3 Maize lethal necrosis disease ........................................................................................... 6 2.3.1 History of MLN disease ................................................................................................... 6 2.3.2 Genomic organization of causal agents of MLN ............................................................. 7 2.3.3 Transmission of MLN viruses ....................................................................................... 10 2.3.4 MLN Disease symptoms ................................................................................................ 12 2.3.5 Host plants of MLN causing viruses .............................................................................. 13 iii 2.4 Disease management ...................................................................................................... 13 2.5 Methods used to identify MLN causing viruses ............................................................ 14 2.5.1 Serological tests ............................................................................................................. 14 2.5.2 Molecular tests ............................................................................................................... 15 2.6 Section summary ............................................................................................................ 18 CHAPTER THREE: MATERIALS AND METHODS ............................................................... 20 3.1 Location and geographical description of the study area ............................................... 20 3.2 Surveys ........................................................................................................................... 21 3.3 Laboratory analyses ....................................................................................................... 23 3.3.1 Serological identification in ELISA............................................................................... 23 3.3.2 Virus detection by reverse transcription polymerase chain reaction (RT-PCR) ............ 24 3.3.3 Nucleotide sequencing and phylogenetic analysis ......................................................... 25 CHAPTER FOUR: RESULTS ..................................................................................................... 28 4.1 Incidence and severity of MLN disease ......................................................................... 28 4.1.1 Based on symptoms and laboratory analysis ................................................................. 28 4.1.2 Cropping systems ........................................................................................................... 31 4.1.3 Cultivated varieties ........................................................................................................ 31 4.1.4 Alternative hosts for MCMV and SCMV ...................................................................... 32 4.2 Viruses detected on ELISA ............................................................................................ 33 4.3 Viruses detected on RT-PCR ......................................................................................... 34 4.4 Nucleotide sequencing and BLAST analyses ................................................................ 37 4.4.1 MCMV ........................................................................................................................... 37 4.4.2 SCMV ............................................................................................................................ 42 4.5 Phylogenetic analysis ..................................................................................................... 49 CHAPTER FIVE: DISCUSSIONS, CONCLUSIONS AND RECOMMENDATIONS ............. 55 5.1 Discussions .................................................................................................................... 55 5.2 Conclusions ...................................................................................................................