“Survival for the fittest of a species is the total sum effect of accumulated variation produced in each generation better adapted to the environment” Charles Darwin (1809-1882) i Promotors: Prof. Dr. ir. Geert Haesaert Department of Applied Bioscience Engineering, Faculty of Bioscience Engineering, Ghent University, Belgium Prof. Dr. Godelieve Gheysen Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium Chairman of examination committee Prof. dr. Colin Janssen Department of Applied Ecology & Environmental Biology, Ghent University Members of the reading committee Prof. dr. ir. Patrick Van Damme Faculty of Bioscience Engineering, Ghent University Prof. Dr. ir. Monica Höfte Faculty of Bioscience Engineering, Ghent University Dr. ir. Bart Cottyn Instituut voor Landbouwen Visserijonderzoek (ILVO) Dr. Danny Vereecke Department of Plant Production University College Ghent Prof. Dr. Sabastian Masaert Unite de phytopathology, Gembloux Dean: Prof. Dr. ir. Marc Van Meirvenne Rector: Prof. Dr. Anne De Paepe ii Kennedy Chepkurui Pkania Genetic diversity of cotton and bacterial blight (Xanthomonas citri pv. malvacearum) prevalence in Western Kenya Thesis submitted in fulfillment of the requirement for the degree of Doctor (PhD) of Applied Biological Sciences: Agricultural Sciences iii Dutch translation of the title: Genetische diversiteit van katoen en ras specificiteit van Xanthomonas citri pv. malvacearum in West Kenia Illustration on the cover: Cotton field ready for harvest Please refer to this work as follows: Pkania C.K. (2016). Genetic diversity of cotton and bacterial blight (Xanthomonas citri pv. malvacearum) prevalence in Western Kenya. PhD Thesis, Ghent University, Belgium ISBN-number: 978-90-5989-924-7 The research was financially supported by Moi University VLIR–UOS (Flemish Interuniversity Council - department for University Cooperation for Development) project activity funds 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 ACKNOWLEDGEMENT In 2010, I arrived at Ghent University to enroll for my PhD studies and as I come close to its completion. I would not have reached this level without the contribution of the many people who held my hand in this tremendous journey and have had so much influence to the work. I would like to express my sincere gratitude to my doctoral promoter Prof. Dr. ir. Geert Haesaert for the incredible guidance you provided throughout my doctoral study at the Department of Applied Bioscience Engineering, Faculty of Bioscience Engineering, Ghent University, Belgium. The many consultations you accorded me to ensure that nothing went wrong during my study stay surely I have no words to express it but accept my sincere appreciation that without your expert guidance this journey would have surely been tough. I also wish to thank my co-promoter Prof. Dr. Godelieve Gheysen for your valuable suggestions, useful comments and expert advice throughout project formulation; implementation to this final stage of thesis submission, surely this work would not have been possible without you. The constant availability and guidance whenever an issue arose provided me enormous opportunity to proceed with the research in a focused manner throughout the period. Sincere gratitude goes to Prof. Dr. ir. Kris Audenaert for the unlimited access you accorded me on the many issues especially many molecular applications, statistical and review work of my study that enabled me to undertake successful molecular work despite my previous limited experience. You were always ready to troubleshoot for me whenever I got stuck and your guidance on data analysis will forever be remembered. I greatly thank ir. Jolien Venneman for everything we have gone through together in the course of my study. We met the first time as a Master’s thesis student on research travel grant to Kenya. I was lucky to supervise a very hardworking student who adapted very fast to the new environment. I remember the field work we carried out together in hot tropical conditions when temperature exceeded 30°C and an almost 100% humidity but you never complained but you always remained focused on the objective. The field evaluations, sample collection in Kenya and laboratory work in Ghent and tropical greenhouse in Melle. The manner in which we worked together will forever remain in my mind based on commitment that you put in to ensure all went well. The academic partnership that has existed from the first day we met is unmatched. I cannot enumerate all but overall thanks for everything and I trust the future holds a lot of hope for you in the academic field and my prayer is that God almighty will bless you abundantly. v Special thanks to all my colleagues at Faculty of Bioscience Engineering, Department of Applied Biological Science Ghent University; Prof. Dr. Geert Baert, Dr. ir. Frank Wesbrouck, Jolien Miclotte, Sophy Aschoot, Marelke, Boris, etc.; the friendly environment was just wonderful for academic growth. The long list of people who assisted me can not be exhausted without mentioning the following people who helped me in many ways at the University of Eldoret (UOE), Kenya: Dr. O.K. Kiplagat HOD Biotechnology department at UOE - Kenya, VLIR–UOS AGBIO Team leader Dr. Florence Wamunga and all team members: Prof. Dr. Okalebo, Prof. Dr. Auma, Dr. Ngode, Prof. Dr. Gohole, Dr. Nekesa, Mr. Katloi, Mr. Rugut, Mr. Njira, Mrs. Njoroge, and Mrs. Emmy Chepkoech to mention only a few and all UOE community for the conducive environment you provided for my study. I will not forget my friend and colleague Mr. Moses Kiniga (Field Officer Biotechnology Department UOE) for your effort to ensure that the greenhouse and experimental fields were well-maintained even in my absence, thanks very much and may God bless you. Special thanks I wish to extend to my parents; my dad Mr. John T. Kiboi, and Mum Mrs. Rebecca N. Pkania for the value of education you accorded me despite not having the formal education. The Christian upbringing and focused approach to life you always inculcate on me since my childhood has played a tremendous role in my academic life. I will not forget my whole extended family for which I can not mention everyone: brothers, sisters, cousins and friends. All of you have made me what I am. I wish to pay special tribute to my dear family: my dear wife Eunice K. Pkania, children: Delphine, Newton, Madeleine, Iverson, and Herbert, your cousins Winnie, Yvonne and Aunt Millie. To my wife Mrs. Eunice K. Pkania, your constant love, encouragement and support will be remembered forever. My dear Eunice, you have been a major inspiration playing both roles as mother and father for our kids to an extent they seem to have not even felt my absence during my stay in Belgium. This study would not have been completed without you. To my children and entire household my prayer to the Lord almighty is that He will shower special blessings on you for the respect and discipline you displayed throughout. You remain my dream and motivation for what the future hold and my prayers are always upon you. Last but not least, special thanks go to Moi University VLIR–UOS project for awarding me the scholarship to undertake my doctoral studies at Ghent University and University of Eldoret (UOE) on sandwich. vi Finally, my very sincere thanks go to the “Almighty Father” in heaven for bringing me this far in life. Lord almighty you have guided my destiny since my childhood and I believe I would not have reached this level without you and I pray that you’ll continue to guide me in all future endeavours. Thank you all and God bless. vii TABLE OF CONTENTS ACKNOWLEDGEMENT ............................................................................................................................ v LIST OF ABBREVIATIONS ....................................................................................................... xii CHAPTER 1 ................................................................................................................................... 1 INTRODUCTION, PROBLEM STATEMENT, OBJECTIVES AND OUTLINE ................................. 1 1.1. INTRODUCTION ........................................................................................................................ 2 1.2. PROBLEM STATEMENT AND JUSTIFICATION ................................................................... 5 1.3. RESEARCH OBJECTIVES ......................................................................................................... 8 1.4. THESIS OUTLINE ....................................................................................................................... 9 CHAPTER 2: LITERATURE REVIEW ...................................................................................... 11 BIOLOGY OF COTTON, GENETIC DIVERSITY AND BACTERIAL BLIGHT DISEASE ............ 11 2.1 ORIGIN AND PRE-HISTORIC COTTON UTILISATION ...................................................... 11 2.2 TAXONOMY AND DISTRIBUTION OF COTTON ............................................................... 11 2.2.1 Taxonomy and evolution of the commercial Gossypium species ....................................... 11 2.2.2 Current production and geographical distribution .............................................................. 13 2.3 BIOLOGY OF COTTON ..........................................................................................................