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I MOLECULAR and PHYLOGENETIC DIVERSITY STUDIES of SOME i MOLECULAR AND PHYLOGENETIC DIVERSITY STUDIES OF SOME ACHA (Digitaria spp.)LANDRACES OF THE JOS PLATEAU AND ITS ENVIRONMENTS Davou Dung Nyam B.Sc. M.Sc. (Jos) UJ/2012/PGNS/0323 A thesis in the Department of PLANT SCIENCE AND TECHNOLOGY, Faculty of Natural Sciences,Submitted to the School of Postgraduate Studies, University of Jos, in partial fulfilment of therequirements for the award of the degree of DOCTOR OF PHILOSOPHY in CYTOGENETICS AND PLANT BREEDING of the UNIVERSITY OF JOS JUNE 2017 ii DECLARATION I hereby declare that this work is the product of my research efforts, undertaken under the supervision of Professor Emmanuel Hala Kwon-Ndung, and has not been presented elsewhere for the award of a degree or certificate. All sources have been duly distinguished and appropriately acknowledged. -------------------------------------------------------- Davou Dung Nyam (B.Sc, M.Sc) UJ/2012/PGNS/0323 iii CERTIFICATION This is to certify that this thesis has been examined and approved forthe award of the degree of DOCTOR OF PHILOSOPHYinCYTOGENETICS AND PLANT BREEDING of the University of Jos _______________________________________ ___________________ PROF. EMMANUEL HALA KWON-NDUNG Date Supervisor ___________________________ __________________ DR. PONCHANG A. WUYEP Date Head of Department ___________________________ __________________ PROF. (MRS) GEORGINA S. MWANSAT Date Dean, Faculty of Natural Sciences ____________________________ ___________________ PROF. NUHU A. GWORGWOR Date Internal Examiner ____________________________ ____________________ PROF. GODFREY AKPAN IWO Date External Examiner DEDICATION iv This Thesis is dedicated to my wife Margaret Davou Nyam (CHOM DD) and all the children (Paul-Mado, Nerat-Dagwi, Yongrat, Kim-Zadok and John-Suga & Hwelleng, Kim,Juliet and Dorcas) God has blessed us with. v ACKNOWLEDGEMENTS I am indeed, very grateful to Prof.Emmanuel Hala Kwon-Ndung for not only accepting to take over the supervision of this work after the retirement of my first supervisor, Prof. Onyekwere P. Ifenkwe, but also believing in me and pushing me to the successful completion of this work. Your interest and continued encouragement, advice and positive criticisms at various stages of the study which has made the preparation of this thesis possible, is highly appreciated. Prof. Onyekwere P. Ifenkwe, you had desired to graduate me before your retirement from active service but this could not be. Nevertheless, I remain truly grateful for your kind understanding of the predicaments that militated against me and all the encouragements I received from you. I particularly want to acknowledge the support and encouragement of Dr. Ponchang A. Wuyep, HOD of the Department of Plant Science and Technology. I am indeed very grateful to the Dean of Natural Sciences, Prof. Georgina S. Mwansat, for her interest, concern and push. I sincerely register my profound gratitude to Prof. Dana‟an A. Dakul, the immediate past Dean for his concern and continued encouragement which has in no small measure propelled this work to its logical conclusion..I particularly want to acknowledge the support, encouragement and excellent criticisms and contributions of the workby Prof. Bashir A. Ajala and Dr. Ahmed D. Ali.My big brother, Da Dr.Michael D. Sila-Gyang, words indeed, cannot express my appreciation for your selfless contributions in diverse ways to the success of this work.I am also very grateful to Dr. Marta Vicente Crespo of the Institute of Biomedical Research, Kampala International University, Ishaka, Uganda for her valuable training sessions during my visit to her laboratory.I had also, received a lot of encouragement from Dr. Bitrus Yakubu, Dr. Luka Pam, Ms. Anvou D. Jambol (my teacher in the lab), Mrs. Dinchi Davouand all the other staff of the Department of Biotechnology, National Veterinary Research Institute (NVRI), Vom. Thank you very much. vi I sincerely appreciate the efforts of my late parents, Da Chief Anthony D. Nyam and Ngo Vou D. Nyam for their parental role in my life. I could not have had better parents. Rest in perfect peace with the Lord.My mother, Ngo Vou D. Nyam; thank you for being a loving and caring mother to your children. Even though you did not go to school, you truly appreciated the value of education and did everything possible to ensure we were properly educated. My sincere appreciation to all my siblings, for the love, respect and encouragement. May the good Lord continue to keep us together. I love you all! My fine wife, Margaret D. Nyam, my „CHOMDD‟, I cannot thank you enough for your concern, support and encouragement are beyond imagination. Our children, I thank you all for being my very loving and wonderful children. The good Lord bless and keep you. I love you all! My special appreciation goes to the academic and non- academic staff of the Department of Plant Science and Technology University of Jos. I am very grateful to the University of Jos authority for its financial support and sponsorship of this study. I salute and appreciate the entire staff of the School of Postgraduate Studies for your kind advice and suggestions towards the successful compilation of this study. I extend my profound gratitude to Mr. Gimba Mohammed who helped with the statistical analyses and to Mrs. Bamijoko O. Oroye (Mama Tosin) who aided in formatting the various chapters of the thesis. Thank you. My praises and thanksgiving to my Lord and Saviour, JESUS CHRIST for His Mercies concerning me that has endured forever. Thank you for the people you have sent my way in the course of this work. TABLE OF CONTENTS CONTENT PAGE TITLE PAGE - - - - - - - - - i DECLARATION- - - - - - - - - ii CERTIFICATION - - - - - - - - iii vii DEDICATION - - - - - - - - iv ACKNOWLEDGEMENTS - - - - - - - v TABLE OF CONTENTS - - - - - - - vii LIST OF TABLES - - - - - - - - x LIST OF FIGURES - - - - - - - - xii LIST OF PLATES - - - - - - - - xiii LIST OF ABBREVIATIONS AND SMBOLS- - - - - xiv LIST OF APPENDICES - - - - - - - xvi ABSTRACT - - - - - - - - - xvii CHAPTER ONE INTRODUCTION 1.1 BACKGROUND OF THE STUDY - - - - - 1 1.2 STATEMENT OF THE PROBLEM - - - - - 4 1.3 JUSTIFICATION - - - - - - - 5 1.4 AIM - - - - - - - - - 5 1.5 SPECIFIC OBJECTIVES - - - - - - 5 1.6 HYPOTHESES - - - - - - - 6 1.7 SCOPE OF THE STUDY - - - - - - 6 CHAPTER TWO LITERATURE REVIEW 2.1 BOTANY OF THE CROP - - - - - - 8 2.2 ORIGIN AND DOMESTICATION - - - - - 13 2.3 CULTIVATION AND PRODUCTION - - - - 13 2.4 USES - - - - - - - - - 15 2.5 CROP ECOLOGY, AGRICULTURAL PRACTICES AND SEED SYSTEM - - - - - - - 15 2.6 COMPOSITION - - - - - - - 20 2.7 CHALLENGES OF ACHA PRODUCTION - - - - 23 viii 2.8 PHYLOGENETIC STUDIES - - - - - - 24 2.8.1 Molecular Phylogenetics - - - - - - 25 2.8.2 Techniques and Applications - - - - - - 25 2.8.3 Characteristics and Assumptions of Molecular Systematics - - 28 2.8.4 Isozymes - - - - - - - - 31 2.8.5 Amplified Fragment Length Polymorphism (AFLP) - - 32 2.8.6 Random Amplified Polymorphic DNA (RAPD) - - - 35 2.8.7 Single Sequence Repeat (SSR) - - - - - 35 CHAPTER THREE MATERIALS AND METHODS 3.1 FIELD WORK - - - - - - 37 3.1.1 Location and Description of Experimental Site - - - 37 3.1.2 Source of Planting Materials - - - - - - 37 3.1.3 Experimental Treatments and Layout/Design- - - - 37 3.1.5 Cultural Practices - - - - - - - 40 3.1.6 Field Observations/Data Collection - - -- - - 40 3.1.7 Data Analysis - - - - - - - - 41 3.2 LABORATORY WORK - - - - - - 42 3.2.1 Germination and Seedling Development - - - - 42 3.2.2 DNA Extraction - - - - - - - 42 3.2.3 Agarose Gel Electrophoresis - - - - - - 43 3.2.4 Amplification - - - - - - - - 44 CHAPTER FOUR RESULTS 4.1 MORPHOLOGICAL CHARACTERISTICS - - - 47 4.1.1 Plant Height - - - - - - - - 47 4.1.2 Stem Girth - - - - - - - - 49 4.1.3 Leaf Length - - - - - - - - 49 4.1.4 Leaf Width - - - - - - - - 52 4.1.5 Number of Days to 75% Maturity- - - - - - 54 4.1.6 1000 Seed Weight - - - - - - - 54 4.2 CORRELATION - - - - - - - 57 4.3 PRINCIPAL COMPONENT ANALYSIS (PCA) - - - 61 4.4 GENETIC RELATEDNESS OF ACCESSIONS - - - 66 4.5 MOLECULAR ANALYSIS - - - - - - 82 CHAPTER FIVE DISCUSSION 5.1 MORPHOLOGICAL CHARACTERISTICS- - - - 102 5.1.1 Plant height - - - - - - - - 102 5.1.2 Stem girth - - - - - - - - 104 5.1.3 Leaf length - - - - - - - - 105 5.1.4 Leaf width - - - - - - - - 105 ix 5.1.5 Number of days to 75% Maturity - - - - - 105 5.1.6 1000 seed weight - - - - - - - 106 5.2 CORRELATION ANALYSES - - - - - 106 5.3 PRINCIPAL COMPONENT ANALYSIS (PCA) - - - 106 5.4 MOLECUAR ANALYSIS - - - - - - 108 CHAPTER SIX SUMMARY OF FINDINGS, CONCLUSION AND RECOMMENDATIONS 6.1 SUMMARY OF FINDINGS - - - - - - 111 6.2 CONCLUSION - - - - - - - 113 6.3 RECOMMENDATIONS - - - - - - 114 6.4 LIMITATIONS OF THE STUDY - - - - - 115 6.5 SUGGESTIONS FOR FURTHER STUDY - - - - 115 6.6 CONTRIBUTION TO KNOWLEDGE - - - - 115 REFERENCES - - - - - - - 117 x LIST OF TABLES TABLE PAGE 1 List of Acha Accessions used in the Study - - - - 37 2 List of Selected Specific Microsatellite Primers Used - - - - 45 3 Mean Height (cm)and combined Mean of 30 Accessions of Acha (Digitaria spp.) Grown in 2012, 2013 and 2014 Rainy Seasons at Binkan Near Jos- - - - - - - - 48 4 Mean Stem Girth (cm)and Combined Mean of 30 Accessions of Acha (Digitaria spp.)Grown in 2012, 2013 and 2014 Rainy Seasons at Binkan Near Jos - - - - - - - - 50 5 Mean Leaf Length (cm) and Combined Mean of 30 Accessions of Acha (Digitaria spp.) Grown in 2012, 2013 and 2014 Rainy Seasons at Binkan Near Jos - - - - - - - - - 51 6. Mean Leaf Width (cm) and Combined Mean of 30 Accessions of Acha (Digitaria spp.)
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