CENTROMERE FUNCTION AND EVOLUTION IN MAIZE (ZEA MAYS) A Dissertation Presented to the Faculty of the Graduate School University of Missouri – Columbia In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy By JONATHAN CARL LAMB Dr. James A. Birchler, Dissertation Supervisor DECEMBER 2006 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled CENTROMERE FUNCTION AND EVOLUTION IN MAIZE (ZEA MAYS) presented by Jonathan Carl Lamb, a candidate for the degree of doctor of philosophy of Biological Sciences, and hereby certify that, in their opinion, it is worthy of acceptance. Professor James A. Birchler Professor Kathleen J. Newton Professor Karen C. Cone Professor Emmanuel Liscum Professor Perry Gustafson ACKNOWLEDGEMENTS My mentor, Dr. James A. Birchler, has provided an environment in which creativity and collaboration can thrive. The opportunities and freedom that have been presented to me in Dr. Birchler's laboratory have truly been exceptional. At one point he told me that publications were the currency of the academic world. Continuing that metaphor, I do not believe that the pay could have been better in any other laboratory or institution in the world. Nor could I have grown and improved my abilities at the same rate in any other situation. He is truly a kind and wise friend and I will be proud to acknowledge his influence throughout the rest of my scientific career. The bulk of the research presented in this dissertation was conducted in collaboration with others. I have benefited greatly through these interactions. The community of maize researchers embodies the ideals of collegiality. The willingness of others, from undergraduates to senior scientists, to discuss their ideas and listen to mine has let me feel included in the great scientific endeavor. Of course, I have worked more closely with some. Accordingly, I am grateful to the coauthors on the various publications I have contributed to, especially Drs. Akio Kato and Fangpu Han. Dr. Kato developed the technique I used most and taught it to me thoroughly. Dr. Han is endlessly finding more interesting things to study and has shared it all with me. ii TABLE OF CONTENTS ACKNOWLEDGEMENTS................................................................................................ ii TABLE OF CONTENTS...................................................................................................iii ABSTRACT........................................................................................................................ v CHAPTERS ........................................................................................................................ 1 1. INTRODUCTION ...................................................................................................... 1 The role of DNA sequence in centromere formation.................................................. 2 References:................................................................................................................ 11 What’s in a centromere? ........................................................................................... 13 References................................................................................................................. 24 Figure ........................................................................................................................ 26 2. CHROMOSOME PAINTING USING REPETITIVE DNA SEQUENCES AS PROBES FOR SOMATIC CHROMOSOME IDENTIFICATION IN MAIZE.... 27 Abstract..................................................................................................................... 29 Introduction............................................................................................................... 30 Materials and Methods.............................................................................................. 32 Results....................................................................................................................... 38 Discussion................................................................................................................. 42 References................................................................................................................. 46 Table ......................................................................................................................... 48 Figures....................................................................................................................... 49 3. SEQUENCES ASSOCIATED WITH A CHROMOSOME CENTROMERES ARE PRESENT THROUGHOUT THE MAIZE B CHROMOSOME................................. 53 Abstract:.................................................................................................................... 54 Introduction............................................................................................................... 55 Materials and Methods.............................................................................................. 58 Results:...................................................................................................................... 61 Discussion................................................................................................................. 71 Conclusion ................................................................................................................ 78 Acknowledgements................................................................................................... 79 References................................................................................................................. 80 Table ......................................................................................................................... 83 Figures....................................................................................................................... 84 4. MOLECULAR AND FUNCTIONAL DISSECTION OF THE MAIZE B CHROMOSOME CENTROMERE.............................................................................. 93 Abstract..................................................................................................................... 95 Introduction............................................................................................................... 96 Results....................................................................................................................... 99 Discussion............................................................................................................... 106 Materials and Methods............................................................................................ 110 Acknowledgements................................................................................................. 112 References............................................................................................................... 113 Tables...................................................................................................................... 117 Figures..................................................................................................................... 119 5. HIGH FREQUENCY OF CENTROMERE INACTIVATION RESULTING IN STABLE DICENTRIC CHROMOSOMES OF MAIZE ........................................... 129 iii Abstract................................................................................................................... 130 Introduction............................................................................................................. 131 Results..................................................................................................................... 132 Discussion............................................................................................................... 139 Materials and Methods............................................................................................ 142 Acknowledgements................................................................................................. 143 References............................................................................................................... 144 Figures..................................................................................................................... 145 6. RETROELEMENT GENOME PAINTING: CYTOLOGICAL VISUALIZATION OF RETROELEMENT EXPANSIONS IN THE GENERA ZEA AND TRIPSACUM ..................................................................................................................................... 157 Abstract................................................................................................................... 159 Introduction............................................................................................................. 160 Materials and Methods............................................................................................ 162 Results..................................................................................................................... 167 Discussion............................................................................................................... 178 Acknowledgements................................................................................................. 189 References............................................................................................................... 190 Table ......................................................................................................................