STATUS AND RELATIVE DISTRIBUTION OF MAIZE STREAK VIRUS IN WESTERN ETHIOPIA M.Sc. THESIS DANIEL KETSELA TIRUNEH JANUARY, 2021 AMBO, ETHIOPIA AMBO UNIVERSITY SCHOOL OF GRADUATE STUDIES COLLEGE OF AGRICULTURE AND VETERINARY SCIENCES DEPARTMENT OF PLANT SCIENCES M.Sc. Thesis Status and Relative Distribution of Maize Streak Virus in Western Ethiopia By Daniel Ketsela Tiruneh A Thesis submitted to the School of Graduate Studies in partial fulfillment of the requirements for the Degree of the Master of Science in Plant Pathology Major Advisor: Berhanu Bekele (PhD) Co-Advisor: Alemu Lencho (PhD) January, 2021 Ambo, Ethiopa APPROVAL SHEET Submitted by _________________________ ________________ _______________ PG Candidate Signature Date Approved by _________________________ _________________ ______________ Main advisor Signature Date __________________________ _________________ _______________ Co-advisor Signature Date __________________________ _________________ _______________ Department Head Signature Date ________________________ __________________ _______________ College/Institute Dean Signature Date ___________________________ ___________________ ______________ Dean, School of Graduate Studies Signature Date I DEDICATION I would like to dedicate this thesis to the memory of my father Ketsela Tiruneh. Let God keep his soul in Heaven. His counsel and vision remains my greatest inspiration to go for the stars. II CERTIFICATION SHEET SCHOOL OF GRADUATE STUDIES AMBO UNIVERSITY As thesis research advisors, we here by certify that we have read and evaluated the thesis prepared by Daniel Ketsela Tiruneh under our guidance, which is entitled Status and Relative Distribution of Maize Streak Virus in Western Ethiopia. We recommend that the thesis be submitted as it fulfills the requirements for the Degree of Master of Science. ________________________ _________________ ______________ Main Advisor Signature Date __________________________ _________________ ______________ Co-advisor Signature Date As members of the Examining Board of the Final M.Sc. open defense, we certify that we have read and evaluated the thesis prepared by Daniel Ketsela and recommended that it is accepted as fulfilling the thesis full requirements for the award of Degree of Master of Science in Plant Pathology _________________________ _________________ _____________ Chairman Signature Date ________________________ _________________ _______________ External Examiner Signature Date _________________________ _________________ _______________ Internal Examiner Signature Date III DECLARATION I declare that, the Status and Relative Distribution of Maize Streak Virus in Western Ethiopia, is my own work, that it has not been submitted for any degree or examination in any other university, and that all the sources I have used or quoted have been indicated and acknowledged by complete references. Name: Daniel Ketsela, Signature: _______________________ Place: Ambo University, Ambo, Ethiopia Date of submission: December, 2020. IV BIOGRAPHY The author, Daniel Ketsela Tiruneh, was born on March 1992 at Gorfo villege in Hageremariam Kesem Woreda, North Shoa zone, Amhara Regional State, Ethiopia from his father, Ketsela Tiruneh and his mother, Ayelech Ymane. He attended his Elementary School education at Gorfo Elementary School and Junior High School education at Bulga Secondary School. He pursued his preparatory school education at Hailemariam Mamo Preparatory School in Debrebirhan town. After that, he was joined Debrebirhan University, College of Natural and Computational Science for his Under Graduate Studies in Applied Biology from October 2010 to 2013. Then, he graduated with BSc Degree in applied Biology on 30 June 2013. After graduation, he has been joined Ethiopian Institute of Agricultural Research (EIAR), Ambo Agricultural Research Center (AmARC) in the department of Agricultural and Nutritional Research Program as a junior researcher. After three years service at Agricultural and Nutritional Research Program he reassigned in Plant pathology program, Virology research department where he served for one year until he joined the graduate studies program of Ambo University, College of Agriculture and Veterinary Sciences, Department of Plant Sciences to pursue a graduate study leading to a Master of Science degree in plant pathology. V ACKNOWLEDGEMENTS First and foremost, I would like to thank my Almighty God for His endowment of Grace, Peace, strength and Health to my life and family. I would like to acknowledge my supervisor Dr.Berhanu Bekele, Senior Researcher of Plant Pathology, for his patience, exceptional guidance and support during the study period. With the deepest gratitude, I wish to thank him for his support in providing reagents like primer, professional expertise and advice from the very planning of this work to its execution and critical review of the manuscript and made it scientifically sound. Without his enlightening guidance and consistent support, I would not have been able to overcome the obstacles I encountered. My heartful thanks go to Dr. Alemu Lencho, Associate Professor of Plant Pathology, My thesis Co-advisor, for his patience and thoughtful guidance throughout my study. With the deepest gratitude, I wish to thank him for his support, professional expertise and advice from the very planning of this work to its execution and critical review of the manuscript and made it scientifically sound. Professor Darren Martin and Oyeniran Kehinde, Department of Molecular and Cell Biology, University of Cape Town, South African, highly acknowledged for their support in running rolling circle amplification (RCA) and sequencing of dozens of MSV isolates from Ethiopia. I would like to extend my gratitude to the Head Department of Plant Sciences, School of Graduate Studies, Ambo University for well-organized and nice facilitations provided during my course work. My deepest gratitude goes to Ethiopian Institute of Agricultural Research (EIAR), Ambo Agricultural Research Center (AmARC) for allowing me MSc study leave and provisions of full financial and material support for this research work. Last, but not least, I am also very grateful to my family and friends for their love, prayers and unwavering support. VI ACRONYMS AND ABBREVIATIONS AmARC Ambo Agricultural Research Center BLAST Basic Local Alignment Search Tool BLASTn Nucliotied Basic Local Alignment Search Tool CIMMYT International Maize and Wheat Improvement Center CSA Central Statistics Agency CTAB Cetyl trimethyl Ammonium Bromide Cp Coat Protein DNA Deoxyribonucleic Acid dNTP Deoxynucleoside triphosphate FAO Food and Agricultural Organization FAOSTAT Food and Agriculture Organization Corporate Statistical Database EIAR Ethiopian Institute of Agricultural Research EDTA Ethylene di-amine tetra acetic acid ICTV International Committee on Taxonomy of Viruses IITA International Institute of Tropical Agriculture ISAAA International Service for the Acquisition of Agri-biotech Applications LIR Large Intergenic Region MP Movement protein NCBI National Center for Biotechnology Information RCA Rolling Circle Amplification RCR Rolling Circle Replication RepA Replication association protein Rep Replication initiation protein SIR Small Intergenic Region TAE Tris Acetate EDTA TE Tris EDTA VII TABLE OF CONTENTES Table of Contents Pages APPROVAL SHEET ....................................................................................................................... I DEDICATION ................................................................................................................................ II CERTIFICATION SHEET ........................................................................................................... III DECLARATION .......................................................................................................................... IV BIOGRAPHY ................................................................................................................................ V ACKNOWLEDGEMENTS .......................................................................................................... VI ACRONYMS AND ABBREVIATIONS .................................................................................... VII TABLE OF CONTENTES ........................................................................................................ VIII LIST OF TABLES ........................................................................................................................ XI LIST OF FIGURES ..................................................................................................................... XII LIST OF APPENDIXS .............................................................................................................. XIV ABSTRACT ................................................................................................................................. XV 1. INTRODUCTION ................................................................................................................... 1 1.1. Statement of the Problem ................................................................................................. 4 1.2. Objectives ......................................................................................................................... 5 1.2.1. General Objective ..................................................................................................... 5 1.2.2. Specific Objectives ..................................................................................................