ASSESSMENT OF COFFEE BERRY DISEASE, CHARACTERIZATION OF Colletotrichum kahawae ISOLATES AND EVALUATION OF RESISTANCE IN Coffea arabica COLLECTIONS FROM GIDAME, WESTERN ETHIOPIA MSc. THESIS ZENEBE WUBSHET HORDOFA JANUARY 2019 JIMMA, ETHIOPIA II Assessment of Coffee Berry Disease, Characterization of Colletotrichum kahawae Isolates and Evaluation of Resistance in Coffea arabica Collections from Gidame, Western Ethiopia By: Zenebe Wubshet Hordofa A Thesis Submitted to the Department of Horticulture and Plant Sciences, School of Post Graduate Studies, College of Agriculture and Veterinary Medicine, Jimma University, for the Partial fulfillment of Degree of Master of Science in Agriculture (Plant Pathology) Advisors: 1. Daniel Teshome Lopisso (Ph. D) 2. Weyessa Garedew Terefe (Ph. D) January 2019 Jimma, Ethiopia III I DEDICATION I dedicate this thesis manuscript to my father Wubshet Hordofa. II STATEMENT OF THE AUTHOR The thesis has been submitted for partial fulfillment of the requirement for MSc. Degree in plant pathology at Jimma University. The content of the thesis is the result of my original work except due references found in the text, no material is found which is previously published or written by another person. All sources of materials obtained from other sources have been suitably acknowledged in this thesis. I accept that the copy of my thesis must be lodge with the University Library and subject to the policy and procedure of the Jimma University. The thesis is made available as sources of research and study with the rule of copyright unless period of prohibition has been approved by the Dean of Graduate School. Briefs from the thesis are allowable without special permission provided the accurate manuscript in whole or part may be granted by the Dean of Graduate studies or by the Head of the Department of Plant Science of the Jimma University when in his judgment the proposed use of material is in the interest of the student. In all other occasions and permissions must be obtained from the author ________________ ______________ ______________ Name Signature Date II BIBLOGRAPHY The author Zenebe Wubshet Hordofa was born on May 25, 1990 from his father Wubshet Hordofa and his Mother Zewdnesh Alemu in Amhara Regional State, North Shoa zone, in Deneba Woreda. He completed his elementary, secondary and preparatory school at Anchikorer, Deneba and Debire Birhan schools respectively. He joined Debire Birhan University in 2011 and graduated in BSc. Degree in plant science on June 2013.Then, he was employed by the Ethiopian Institute of Agricultural Research Institute (EIAR) in May 2014 as junior crop protection researcher at Jimma Agricultural Research Center (JARC) and served for 2 years until he joined Jimma University for his MSc study in 2016. IV ACKNOWLEDGEMENTS First of all, I would like to thank almighty God with his mother for all things made possible through my life. My gratitude goes to Jimma University for accepting me to the MSc. program and Horticulture and Plant Science Department for providing me adequate knowledge in the basics of plant pathology which had been my long time desire. My deepest appreciation and gratitude also pies to my major advisor Dr. Daniel Teshome who accepted me as his advisehappily and supervised my work very closely with very critical comments, patience, positive and constructive remarks, I am very thankful for his great and unlimited support, I am also deeply indebted to Dr. Weyessa Garedew to welcome me as co-advisor and his critical support and encouragement throughout my study. I would like to thank both of my advisors for their assistance, guidance and comments since the inception of this research project until the final thesis write up, supported me to acquire skill and knowledge. Thank you both of you for giving me the opportunity to learn from you and work with you. I acknowledge Ethiopian Institute of Agricultural Research for giving me this chance and for the financial support. My thanks also qoes to Jimma Agricultural Research Center staff members especially the plant pathology laboratory staff for their unnosoued help during laboratory works. My special thanks also go to Mr. Dereje Amare, Wondmagegn G/Tsadk and Negasa Dechassa for their strong collaboration and encouragement throughout the whole thesis work. Finally, I can’t leave without acknowledging the assistance of my parents who lifted me to go up in my enlightenment and development. Finally, the efforts of all other individuals who weredirectly or indirectly involved in my thesis work are really acknowledged. V ACRONYMS AND ABBRIVATIONS ABT Attached Berry Test ANOVA Analysis of Variance CPS Coffee Production System CRD Complete Random Design CSA Central Statistical Agency DAI Days After Inoculation DBT Detached Berry Test DI Disease Incidence DMRT Duncan’s Multiple Range Test DPI Days Post Inoculation ECX Ethiopian Commodity Exchange FAO Food and Agricultural Organization GARSc Gera Agricultural Research Sub Center GPS Geographic Positioning System HAI Hours After Inoculation ICC International Coffee Council ICO International Coffee Organization ITC International Trade Center JARC Jimma Agricultural Research Center PDA Potato Dextrose Agar PSI Percent Severity Index RGB Red Green Blue SAS Statistical Analysis System SDW Sterilized Distilled Water USDA United State Department of Agriculture VI TABLE OF CONTENTS Pages DEDICATION ................................................................................................................. I STATEMENT OF THE AUTHOR................................................................................ II BIBLOGRAPHY .......................................................................................................... IV ACKNOWLEDGEMENTS........................................................................................... V ACRONYMS AND ABBRIVATIONS ......................................................................... VI TABLE OF CONTENTS ............................................................................................ VII LIST OF TABLES ........................................................................................................ IX LIST OF FIGURES ....................................................................................................... X LIST OF TABLES IN THE APPENDIX ..................................................................... XI ABSTRACT ................................................................................................................ XII 1. INTRODUCTION ...................................................................................................... 1 2. LITERATURE REVIEW ........................................................................................... 4 2.1. Importance of coffee in Ethiopian economy ............................................................ 4 2.2. Productivity and production systems of coffee in Ethiopia ...................................... 4 2.3. Major constraints of coffee production in Ethiopia ................................................. 6 2.3.1. Occurrence and distribution of CBD................................................................. 6 2.3.2. Taxonomic classification of C. kahawae ........................................................... 8 2.3.3. Epidemiology and Disease symptoms .............................................................. 8 2.3.4. Biology of C. kahawae ................................................................................... 10 2.3.5. Cultural and morphological characteristics ..................................................... 11 2.3.6. Variation in virulence of C. kahawae isolate. .................................................. 12 2.3.7. Selection for CBD resistance in C. arabica .................................................... 13 2.3.8. CBD management options .............................................................................. 15 3. MATERIALS AND METHODS .............................................................................. 20 3.1. Description of the study area ................................................................................ 20 3.2. Assessment of CBD in farmers’ field .................................................................... 21 3.3. Sample collection and fungal isolation ................................................................. 22 3.4. Isolation and identification of C. kahawae isolates................................................ 23 3.5. Morphological characterization of C. kahawae isolates ......................................... 24 3.5.1. Macroscopic characterization ......................................................................... 24 3.5.2. Microscopic characterization .......................................................................... 24 VII 3.6. Determination of virulence in C. kahawae isolates ............................................... 25 3.6.1. Inoculum preparation and inoculation ............................................................ 25 3.6.2. Data collection ............................................................................................... 26 3.7. Evaluation of Gidame coffee accessions for resistance against CBD under field conditions, attached berry test ............................................................................. 27 3.8. Evaluation of Gidame coffee accessions for resistance against C. kahawae under laboratory conditions, detached berry test...........................................................