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Addis Ababa University Addis Ababa Ethiopia July, 2020 Phylogenetic Relationships among Indigenous and Introduced Bamboo Species and Genetic Diversity Study of Ethiopian Lowland Bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] Using cpDNA Genes ( matK , ndhF and rps16 ) and ISSR Markers Oumer Abdie Oumer Addis Ababa University Addis Ababa Ethiopia July, 2020 Phylogenetic Relationships among Indigenous and Introduced Bamboo Species and Genetic Diversity Study of Ethiopian Lowland Bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] Using cpDNA Genes ( matK , ndhF and rps16 ) and ISSR Markers Oumer Abdie Oumer A Dissertation Submitted to Department of Microbial, Cellular and Molecular Biology in Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology (Applied Genetics) Addis Ababa University Addis Ababa Ethiopia July, 2020 DECLARATION I declare that this Dissertation entitled “Phylogenetic Relationships among Indigenous and Introduced Bamboo Species and Genetic Diversity Study of Ethiopian Lowland Bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] Using cpDNA Genes ( matK , ndhF and rps16 ) and ISSR Markers” submitted for the Degree of Doctor of Philosophy (PhD) in Biology (Applied Genetics) to the School of Graduate Studies, Addis Ababa University, is my original work and its composition has never been submitted elsewhere for any other award. All sources of materials used for the Dissertation have been duly acknowledged. Name: Oumer Abdie Signature: . Date: 20- July-2020 . i ACKNOWLEDGMENT .( ْٱﻟ َﺤ ْﻤﺪ ُ ِ ﱠ @ ِ َ ﺭ ِّ ﺏ ْٱﻟ َٰﻌ َﻠ ِﻤ َﻴﻦ ) First and for most, I would like to thank the Almighty I am highly indebted to eIpress my deepest and genuine appreciation and than.s to my supervisors0 the late Dr. Jifle Dagne, Dr. Tileye Feyissa and Dr. Jassahun Tesfaye for their eIcellent guiding, follow4up and support. Lithout the encouragement and guidance, the completion of this wor. on this form may not have been possible. NeIt, I would also li.e to owe my special than.s to Pa.istani supervisor Dr. Muhammad Meeshan Nyder from Biochemistry, Molecular Biology and Biotechnology BMBB) Lab., Department of Biosciences, faculty of Sciences, C1MSATS ,niversity Islamabad C,I), Islamabad, Pa.istan, for inviting me to BMBB laboratory as a Oisiting PhD Scholar via The Lorld Academy of Science 4 C1MSATS ,niversity Islamabad the then C1MSATS Institute of Information Technology) TLAS4CIIT) scholarships and for his advice on phylogenetics study. I eItend my deepest ac.nowledgments to different institutions that have provided financial support0 Department of Microbial, Cellular and Molecular Biology MCMB) of Addis Ababa ,niversity AA,), Assosa ,niversity AS,), TLAS4CIIT scholarships, training the neIt generation of scientists provided by Carnegie Cooperation of New Por. CCNP) through the Regional ,niversities Forum for Capacity Building in Agriculture R,F1R,M), International Networ. for Bamboo and Rattan INBAR) head quarter and East Africa Regional 1ffice. I am than.ful to Ethiopian Biodiversity Institute EBI) for providing bamboo seeds and eIport permit and Central Ethiopia Environment and Forest Research Center CE4EFRC) for providing cars to collect samples from 1rmoia, Gambella and South nations nationalities and peoples SNNPs) region for this study. I am also grateful to former Department Nead of MCMB Dr. Gurja B., stream supervisor Dr. Dereje B., current Department Nead Dr. Adey F., former Department Nead of BMBB Dr. Teyab 5. and all department staff members of MCMB for their retireless support and advice. Dr. Solange ,., the former manager for Partnerships and Business Management PBM) at R,F1R,M and currently deputy director general in charge of Animal Resources Research ii and Technology Transfer at Rwanda Agriculture and Animal Resources Development Board RAB), 5ayaraman D., project manager INBAR global programme East Africa Regional 1ffice, Ernest N. A., project manager Inter Africa Bamboo Development Programme INBAR Lest Africa Regional 1ffice, Dr. Abeje E., former CE4EFRC director and Dagnew P., former program leader for non4timber forest products at CE4EFRC must be duly ac.nowledged for their contribution to get research funds. I would li.e to than. also my colleagues Dr. Mohammed A., Dr. Fe.adu G., Mr. Mulu.en B., Ms. Nawi N. Mr. Asmamaw A., Mr. Amare E., and Pa.istani friends Sana B. A., M. Shoiab and M. Shafiq as well as many more others for their friendly advice and support. Last but not least, my family beloved mother Medina Me.at, brothers and sisters) deserves special than.s for their all sided support. My wife Nawa Al.adir, my son M. Amin and daughter Naniyah for their patience, encouragement and giving hope at all times of this study period. 1umer Abdie iii TABLE OF CONTENTS DECLARATION......................................................................................................................... i ACKNOWLEDGMENT ........................................................................................................... ii TABLE OF CONTENTS ......................................................................................................... iv LIST OF TABLES .................................................................................................................. viii LIST OF FIGURES .................................................................................................................. ix LIST OF APPENDICES ......................................................................................................... xii LIST OF ABBREVIATIONS ................................................................................................ xiii ABSTRACT ............................................................................................................................. xiv CHAPTER ONE .........................................................................................................................1 1. General Introduction ...........................................................................................................1 1.1. Bac.ground ....................................................................................................................1 1.2. Statement of the problem ...............................................................................................S 1.T. Nypothesis ......................................................................................................................7 1.S. 1bjectives .......................................................................................................................8 1.S.1. General 1bjective ...........................................................................................................8 1.S.2. Specific objectives ..................................................................................................8 CHAPTER TWO ........................................................................................................................9 2. Literature Review .................................................................................................................9 2.1. Taxonomy of Bamboo ..........................................................................................................9 2.2. Bamboo Cytogenetics, Ploidy Level and Genome SiWe ...............................................10 2.T. Area Coverage and Geographical Distribution of Bamboo .........................................12 2.T.1. Bamboo Distribution in Africa, Ethiopia and Pa.istan ........................................1T 2.S. Assessment of Phylogenetics and Genetic Diversity Study .........................................15 2.S.1. Chloroplast Genes Based Phylogenetics and Genetic Diversity Study ................18 2.S.2. ISSR Based Phylogenetics, Genetic Diversity and Population Structure Study ..22 2.5. Phylogenetic Tree Construction Methods ....................................................................2T CHAPTER THREE ..................................................................................................................25 3. Phylogenetic Relationships among the Indigenous and Introduced Bamboo Species using cpDNA Genes Sequences ................................................................................................25 T.1. Materials and Methods .................................................................................................25 iv T.1.1. Plant Materials and Sample Collections ...............................................................25 T.1.2. DNA EItraction and Primer Screening .................................................................25 T.1.T. PCR Product Profiling, Sequencing and Alignment .............................................26 T.1.S. Phylogenetics Analyses ........................................................................................27 T.2. Results ..........................................................................................................................29 T.2.1. Chloroplast DNA Sequence Character and Sequence Divergence .......................29 T.2.1.1. GC and AC content analysis ..........................................................................29 T.2.2. Phylogenetic Inference and Relationship..............................................................T1 T.2.2.1. MaIimum Parsimony Method Phylogenetics Tree Construction ..................T1 T.2.2.2. MaIimum Li.elihood Method Phylogenetics Tree Construction .................T2 T.2.2.T. Neighbor45oining Method Phylogenetics Tree Construction ........................TT T.T. Discussion
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