Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. The genetic architecture of the divaricate growth form: A QTL mapping approach in Sophora (Fabaceae) . A thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology At Massey University, Manawatu, New Zealand Kay Margaret Pilkington RPQY II Abstract Divarication is a plant growth form described, in its simplest form, as a tree or shrub with interlaced branches, wide branch angles and small, widely spaced, leaves giving the appearance of a densely tangled shrub. The frequency of this growth form is a unique feature in the New Zealand flora that is present in ~ QP% of the woody plant species, a much higher frequency than that of other regional floras. While several hypotheses have been developed to explain why this growth form has evolved multiple times within New Zealand, to our knowledge, no work has addressed the genetic basis of the divaricating form. Sophora is one of several genera in New Zealand that possesses divaricate species. Among the factors making this an ideal system for a genetic investigation of divarication is an existing FR population formed from reciprocal crosses between the divaricating S. prostrata and the non-divaricating S. tetraptera . Using this segregating population and newly developed molecular markers, the first linkage maps for Sophora were generated, providing a new genetic resource in Sophora . These linkage maps allowed for quantitative trait locus (QTL) mapping for traits associated with the divaricate form in the segregating population. Multiple QTL were mapped to seven of the divaricate traits with many QTL co-locating for multiple traits, indicating that the divaricate growth form is genetically controlled by many loci, potentially including pleiotropic loci, that each contribute to the overall divaricate phenotype in Sophora . The strigolactone biosynthesis and perception pathway is a good candidate for involvement in control of the divaricate form based on mutant phenotypes in Pisum that display similarities to the divaricate growth form, such as increased branching, shorter plant height and smaller leaves. QTL, for multiple traits, were mapped to two candidate genes investigated, RMSU and RMSX . An amino acid replacement was identified in RMS, III in S. prostrata, and was predicted to be deleterious suggesting RMS may be non- functional in S. prostrata. These results support RMSU as a strong candidate gene for future work on divarication. This study is the first to investigate the genetic architecture of the divaricate growth form and contributes to further understanding of this unique feature in the New Zealand flora and of plant architecture generally. IV Acknowledgments Throughout the research and writing of this thesis, I have received a great amount of support and assistance. I would first like to express my sincere gratitude to my supervisor, Dr. Vaughan Symonds, for the invaluable knowledge, patience and guidance in undertaking the research and writing of this thesis. I am also grateful to my co- supervisors, Dr. Jennifer Tate, for the insightful comments, encouragement and guidance and, Dr. Peter Heenen, for the support, knowledge and care of the plants at the study site. My sincere thanks also go to the Massey Graduate Scholarship and Heseltine Trust Scholarship for the funding that enabled me to undertake this research. Without this support, I would not have been able to take this opportunity. I would like to thank my fellow labmates and colleagues for all the support and willingness to help me. I would especially like to thank Sofie and Jacob for the help with collecting and measuring of plants and Lesley from the Massey Horticultural Units for the continuous care of the growing plants and seedlings. Likewise, my sincere thanks to the lab technician, Prashant, for the help and knowledge in the lab. Also, I would like to thank all the administrative staff that in one way or another helped and supported me during my PhD study. In addition, I would like to thank my parents for their support and counsel during the course of my PhD. Finally, my thanks to family and friends for the wonderful support and fun you provided throughout this time. V Table of Contents ABSTRACT ................................................................................................................. III ACKNOWLEDGMENTS .............................................................................................. V LIST OF FIGURES .......................................................................................................X LIST OF TABLES ....................................................................................................... XII LIST OF APPENDICIES ........................................................................................... XIV Q CHAPTER ONE - INTRODUCTION .......................................................................Q Q.Q PLANT ARCHITECTURE ............................................................................................... Q U.U.U Woody plant architectures .................................................................................. W Q.R DEFINING DIVARICATION ...........................................................................................V Q.S HYPOTHESES FOR ORIGIN OF DIVARICATION : ............................................................. U.W.U Moa Browsing Hypothesis .................................................................................. UU U.W.V Climate Hypothesis ............................................................................................. UW U.W.W Alterative Hypotheses ......................................................................................... U[ Q.T HETEROBLASTY ....................................................................................................... U] Q.U THE GENETICS OF DIVARICATE TRAITS ...................................................................... RQ U.Y.U Apical dominance ............................................................................................... VU U.Y.V The Strigolactone Pathway ................................................................................VX U.Y.W Other candidate genes for divaricate traits .......................................................V] Q.V QUANTITATIVE GENETICS ........................................................................................ SS U.Z.U Populations for QTL mapping ........................................................................... WW U.Z.V Linkage maps ..................................................................................................... WY U.Z.W Quantitative trait analysis ................................................................................. W\ Q.W SOPHORA ............................................................................................................... TP U.[.U An important resource re-discovered................................................................ XZ U.[.V Sophora as a model for divarication .................................................................. X[ Q.X OBJECTIVES ............................................................................................................ TX Q.Y THESIS STRUCTURE ................................................................................................. TX Q.QP REFERENCES ........................................................................................................... UP Q.QQ APPENDIX ............................................................................................................... VT R CHAPTER TWO – PHENOTYPING OF THE LINCOLN SOPHORA FR................ VW R.Q ABSTRACT ................................................................................................................ VW R.R INTRODUCTION ...................................................................................................... VY R.S MATERIALS AND METHODS ..................................................................................... WR V.W.U Study site ............................................................................................................ [V V.W.V Phenotyping trial................................................................................................ [X V.W.W Phenotyping of Lincoln F V .................................................................................. [Y V.W.X Phenotyping analysis ......................................................................................... [Z R.T RESULTS .................................................................................................................. WX V.X.U Parents and F U ..................................................................................................... [\ V.X.V Divaricate Trait Variation ................................................................................. [] VI V.X.W Divaricate Trait Correlation.............................................................................. \V V.X.X Cross Direction Effects ....................................................................................... \Y R.U DISCUSSION ............................................................................................................. YQ V.Y.U Divaricate