Characterizing the Flax Core Collection for Earliness and Canopy Traits

.................................................................................................................. ii ACKNOWLEDGMENTS ............................................................................................ iv LIST OF TABLES ........................................................................................................ ix LIST OF FIGURES ...................................................................................................... xi LIST OF ABBREVIATIONS .................................................................................... xiii CHAPTER 1 .................................................................................................................. 1 1. Introduction ................................................................................................................ 1 CHAPTER 2 .................................................................................................................. 4 2. Literature review ........................................................................................................ 4 2.1 Flax production and area ........................................................................................................................... 4 2.2 Centre of origin and domestication ........................................................................................................ 4 2.3 Flax cultivar genetic diversity .................................................................................................................. 5 2.4 Leaf canopy studies in flax ....................................................................................................................... 7 2.5 Early maturity in flax .................................................................................................................................. 8 2.5.1 Importance of early maturity in flax ......................................................................................... 8 2.5.2 Photoperiod sensitivity and photoperiod insensitivity in flax .......................................... 8 2.5.3 Theories of flowering .................................................................................................................... 8 2.6 Association mapping in flax ..................................................................................................................... 9 2.6.1 Concepts of association mapping and linkage disequilibrium ..................................... 10 2.6.2 Resolution of association mapping ........................................................................................ 10 2.6.3 Association mapping population ............................................................................................ 10 2.6.4 Marker-assisted selection .......................................................................................................... 11 2.7 Path analysis in flax .................................................................................................................................. 11 2.8 Objectives .................................................................................................................................................... 12 2.9 Hypothesis ................................................................................................................................................... 13 CHAPTER 3 ................................................................................................................ 14 3. Characterization of early and late flowering accessions under controlled growth chamber environments and field performance ............................................................. 14 3.1 Abstract ........................................................................................................................................................ 14 3.2 Introduction ................................................................................................................................................. 14 3.3 Materials and Methods ............................................................................................................................ 16 vii 3.3.1 Collections and experimental setup ....................................................................................... 16 3.3.2 Data collection .............................................................................................................................. 18 3.3.3 Statistical models and data analyses ...................................................................................... 19 3.4 Results ........................................................................................................................................................... 20 3.4.1 Growth chamber analyses ......................................................................................................... 20 3.4.2 Field analyses ................................................................................................................................ 26 3.4.3 Growth chamber versus field performance ......................................................................... 29 3.5 Discussion .................................................................................................................................................... 31 CHAPTER 4 ................................................................................................................ 33 4. Association mapping of canopy traits and plant branching in the flax core collection ...................................................................................................................................... 33 4.1 Abstract ........................................................................................................................................................ 33 4.2 Introduction ................................................................................................................................................. 33 4.3 Material and Methods .............................................................................................................................. 35 4.3.1 Mapping Population .................................................................................................................... 35 4.3.2 Phenotypic Evaluation ............................................................................................................... 35 4.3.3 Canopy Traits ................................................................................................................................ 36 4.3.4 Plant Branching ............................................................................................................................ 37 4.3.5 Genotyping ..................................................................................................................................... 38 4.4 Data Analysis ............................................................................................................................................. 39 4.4.1 Phenotypic Data ........................................................................................................................... 39 4.4.2 Analysis of Population Structure and Kinship ................................................................... 40 4.4.3 Association analysis .................................................................................................................... 40 4.5 Results ........................................................................................................................................................... 41 4.5.1 Phenotypic variation ................................................................................................................... 41 4.5.2 Population Structure and Kinship .......................................................................................... 42 4.5.3 Model comparison and marker-trait association ............................................................... 45 4.6 Discussion .................................................................................................................................................... 49 CHAPTER 5 ................................................................................................................ 52 5. The relationship between crop phenology, canopy, branching characteristics and seed yield of the core collection through structural equation modeling ...................... 52 5.1 Abstract ........................................................................................................................................................ 52 5.2 Introduction ................................................................................................................................................. 52 5.3 Material and Methods .............................................................................................................................. 54 5.3.1 Experiment material and design ............................................................................................. 55 5.3.2 SEM software ................................................................................................................................ 55 5.3.3 The initial model development ................................................................................................ 55 5.3.4 Composite Variables ................................................................................................................... 57 5.3.5 Evaluating Model and modification ...................................................................................... 58 5.4 Agronomic Interpretation ....................................................................................................................... 61