Developmental genetics of the world. V.44 /

Cover Page 1
Title Page 4
Copyright Page 5
Contents 6
Contributors to Volume 44 12
Contents of Volumes 34-43 16
Chapter 1: Angiosperm Floral Evolution: Morphological Developmental Framework 23
I. Introduction 24
II. Development: From Floral Primordium to Flower-Contingency of the Primary Morphological Surface 26
III. Evolution: From Simple to Complex Flowers-Contingency of the Developmental Program 28
IV. Floral Organs as Modules, Organ Categories (Organ Identity), and Their Evolution 29
A. Floral Organs as Modules 29
B. Sequence of Evolutionary Origin of Floral Organs 30
C. Ovules 31
D. Carpels 32
E. Stamens 33
F. Perianth Organs 34
G. Bracts and Bracteoles 36
V. Floral Phyllotaxis 37
VI. Floral Symmetry 42
VII. Angiospermy: Carpel Closure and Modes of Sealing 45
VIII. Postgenital Coherence 47
IX. Synorganization 48
A. What is Synorganization? 48
B. Means of Synorganization: Congenital and Postgenital Coherence 51
C. Sites of Synorganization 51
1. Synorganization among organs of the same whorl (organs of the same category) 51
a. Perianth 51
b. Androecium 52
c. Gynoecium 53
2. Synorganization between whorls (organs of diVerent kinds) 56
3. Synorganization between flowers in an inflorescence 57
X. Plasticity of Organ Form in Development Shaped by Floral Architecture or by Contiguous Parts 57
A. Monosymmetry and Synorganization 57
B. Autonomous Shapes and Imprinted Shapes, Positional Effects 58
XI. Architectural Extremes 59
XII. An Innovation of Flexibility: Escape from Constraints of Synorganized Flowers in Core Eudicots-Increase of Stamen Number and Decoupling of Sequence of Initiation of Stamens and Carpels by Ring Meristems 61
XIII. Potential Pitfalls of Generalizations from Model Plants 65
XIV. Conclusions and Questions 67
Acknowledgments 68
References 68
Chapter 2: Recent Developments Regarding the Evolutionary Origin of Flowers 85
I. Introduction 86
II. What Needs to Be Explained for the Origin of the Flower? 93
III. Important Attributes of the Ancestral Flower 96
A. Bisexuality 96
B. The Carpel 97
C. The Stamen 97
D. The Angiosperm Ovule 98
E. Pollen 98
IV. What Should a Theory Do? 99
V. The Anthophyte Theory 100
VI. Molecular Phylogenetic Analyses of Seed Plants Undermine the Anthophyte Theory 101
A. Molecular Phylogenetic Studies Using Nonduplicated Genes 102
B. Molecular Phylogenetic Studies with Duplicated Genes 110
C. Morphological Phylogenetic Analyses 112
VII. The Mostly Male Theory 117
A. The Genesis of the Mostly Male Theory 117
B. New Evidence Regarding The Mostly Male Theory 120
C. LFY Expression and Inferred Function 121
D. Dorsiventrality of the Outer Integument and of the Cupule Wall 125
VIII. Alternatives and Modifications of the Mostly Male Theory 126
IX. Baum and Hileman's Scenario for Flower Origins 129
X. Doyle's Caytonia-Glossopterid Model for the Origin of the Carpel 130
XI. Meyen's Gametoheterotopy Theory (and Krassilov's (1997) Book) 132
XII. Double Fertilization and Friedman and Williams' Modular Scenario 134
XIII. Overall Conclusions 138
Acknowledgments 138
References 138
Chapter 3: Duplication, Diversification, and Comparative Genetics of Angiosperm MADS-Box Genes 151
I. Introduction 152
II. Rationale for Exploring MADS-Box Gene Diversification 153
III. Flower Morphologies Across the Angiosperms 154
A. Fossil Evidence 155
B. What is the Closest Extant Nonangiosperm? 156
C. What Angiosperm is Sister to Other Extant Flowering Plants? 156
IV. Perianth Diversity Across the Major Clades of Angiosperms 157
V. How Did the Genetic Mechanisms Controlling These New Morphologies Evolve? 158
A. Analysis Of Perianth Development In Arabidopsis, A Core Eudicot 159
1. The floral homeotic genes specify organ identity 160
2. Expression of AP3 and PI 161
3. AP3 and PI form protein complexes 162
4. Downstream targets of AP3 and PI 162
B. Conservation and Diversification in Expression and Function Of AP3 and PI Genes in the Angiosperms 163
1. Gene duplication in the AP3 and PI gene lineages 164
2. An exploration of the changing roles of the AP3 and PI lineage genes 165
VI. Evolution of AP3 and PI Function 169
VII. How Do We Functionally Analyze MADS-Box Genes in Nonmodel Species? 170
VIII. Prospects 172
Acknowledgments 173
References 173
Chapter 4: Beyond the ABC-Model: Regulation of Floral Homeotic Genes 185
I. Introduction: The ABC-Model 186
II. Regulators of A-Function 192
A. Regulation of AP1 by Meristem Identity Genes 192
B. Regulation of AP1 by AG 194
III. Regulators of B-Function 195
A. Expression Patterns of B-Function Genes in Arabidopsis 195
B. Activation of B-Function Genes by LFY and AP1 196
C. SCFUFO E3 Ubiquitin Ligases as Regional Activator of B-Function Genes 197
D. Regulation of B-Function by SEP3 199
E. Control of the Inner Boundary of B-Function Gene Expression by Superman 200
F. The Autoregulatory Circuit of AP3/PI 201
G. GA Signaling and Early Bolting in Shortdays Affects AP3/PI Expression 202
IV. Regulators of C-Function 203
A. Positive Regulators of AG 204
1. Regulation of AG expression by LFY and WUS 204
2. Regulation of AG transcript processing by the HUA and HUA ENHANCER proteins 205
3. Regulation of C\u2010function by SEP3 208
B. Negative Regulators of AG 208
1. Negative regulators of AG in vegetative tissues 209
2. AP2 as a repressor of AG in the perianth 210
3. LUG and SEU form a corepressor complex 211
4. BLR mediates repression of AG 212
5. RBE and UFO regulate the boundary of AG expression 213
6. SAP has both positive and negative functions 213
7. Aintegumenta 214
8. C\u2010Function regulators that do not directly regulate AG 215
C. Regulators of AG in the Ovule 215
V. Summary and Perspectives 216
Acknowledgments 218
References 218
Chapter 5: Missing Links: DNA-Binding and Target Gene Specificity of Floral Homeotic Proteins 231
I. Introduction 232
II. Binding of MADS-domain Proteins to DNA 233
III. Learning from Homeodomain Proteins in Animals 236
IV. CArG Galore: What For? 238
V. DNA Bending 239
VI. Does the Protein Concentration Matter? 241
VII. Protein-Protein Interactions: Elective Affinities 243
A. Role of Non-Mads Factors 243
B. Higher order Complexes and their Influence on Target Gene Specificity 245
VIII. Target Genes: Hints for Target Gene Specificity? 249
IX. Evolutionary Implications: Nothing in the MADS World Makes Sense Except in the Light of Target Gene Specificity 250
Acknowledgments 252
References 252
Chapter 6: Genetics of Floral Development in Petunia 259
I. Introduction 260
A. Solanaceae 260
B. The Genus Petunia 260
C. Petunia Flower Characteristics 261
D. Floral Diversity in the Petunia Clade: Pollination Syndromes 261
E. Research on Petunia Flower Development 263
F. Petunia in Molecular Studies 264
G. Floral Development 264
II. The Transition to Flowering 265
III. Meristem Identity Genes: Inflorescence and Flower Architecture 269
A. Petunia Inflorescence Architecture 270
IV. Floral Organ Identity Determination 273
A. The A-Function Genes 274
B. The B-Function Genes 276
1. GLO/PI lineage genes 276
2. DEF/AP3 lineage genes 277
3. PhDEF 278
4. PhTM6: an atypical and interesting B\u2010function gene 278
5. Interactions between the Petunia B\u2010function proteins 279
C. The C-Function Genes 280
D. The D-Function Genes 283
1. Pistil and ovule development in Petunia 283
2. Interacting proteins 285
E. The E-Function Genes 286
V. Conclusions 290
Acknowledgments 292
References 292
Chapter 7: Flower Development: The Antirrhinum Perspective 301
I. Introduction 302
II. The Control of Floral Identity: Where the Differences Begin 303
III. The (A)BC-Model: Past Discoveries and Current Problems 304
A. The A-Function and its Dubious Role in the Control of Perianth Identity: The Relation Between Floral Meristem and Sepal Identity 305
B. The A-Function in the Spatial Control of C-Gene Expression 309
C. Additions to (A): Floral Functions Necessary for Manifestation of the B- and C-Control 313
D. The B-Function Proteins and their Partners in the Making of a Petal 314
E. The C-Function: PLE and FAR Together Control Reproductive Development 316
F. The Link Between the B- And C-Functions in Controlling Floral Determinacy 317
G. A Novel Definition of the (A)-Function in the (A)BC-Model to Recover its Universality 319
IV. Inflorescence and Floral Architecture 320
A. CEN: A Major Influence on Inflorescence Architecture 321
B. Incomposita: Aberrant Prophyll Initiation Impairs Floral Architecture 323
V. Floral Symmetry 325
A. The Players: Mutants With Symmetry Defects and the Genes Involved 325
B. A Possible Mechanism to Control Symmetry 328
C. Floral Asymmetry in Other Species 329
VI. Floral Color, Scent, and Cell Shape: The Skills of Antirrhinum to Attract Pollinators 330
A. Floral Color 331
B. The Production of Scent 331
C. MYB Transcription Factors Control Cell Shape 332
VII. Outlook 334
A. Present and Future Resources 335
B. Antirrhinum for Studying Diversity and Ecology 336
Acknowledgments 337
References 337
Chapter 8: Floral Developmental Genetics of Gerbera (Asteraceae) 345
I. Introduction 346
A. Design of Gerbera Flowers 349
B. Reverse Genetics Tools in Gerbera 351
II. Gerbera MADS-Box Genes 353
A. ABC-Model of Flower Development in Gerbera 354
B. Beyond the ABCs: Subfunctionalization of the Sepallata Genes in Gerbera 359
C. Control of Floral Meristem Fate by SEP Genes 363
III. Gerbera Genomics 365
IV. The Gerbera Capitulum 366
A. Regulation by a Radial Morphogenetic Gradient? 366
B. Some Speculative Models 367
V. Conclusions 369
References 369
Chapter 9: Gene Duplication and Floral Developmental Genetics of Basal Eudicots 375
I. Introduction 376
II. Evolution and Morphology of the Eudicots 376
III. Genetics of Floral Organ Identity in Model Species 379
A. THE ABC-Model and its Elaboration 379
B. The MIKC family of MADS-Box containing genes 381
IV. Gene Duplications Within the Basal Eudicot Grade 384
A. The APETALA3 Lineage 384
B. The APETALA1 Lineage 388
C. The Agamous Lineage 391
D. The Sepallata Subfamily 392
E. Broader Implications 394
V. Gene Duplications in the Early Branches of the Eudicot Radiation: The Ranunculales 395
VI. Summary 397
Acknowledgments 398
References 398
Chapter 10: Genetics of Grass Flower Development 407
I. Introduction 408
II. Grass Floral Morphology 410
III. Genetics of Grass Flower Development 412
A. MADS-Box Genes and Grass Flower Development: Rounding Up the Usual Suspects 412
1. A\u2010class 413
2. B\u2010class 417
3. C\u2010class 419
4. D\u2010class 421
5. E\u2010class 422
B. Thinking Outside of the MADS-Box: How Forward Screens Reveal Non-MADS-Box Genes Important for Grass Floral Patterning 424
IV. Physical Interactions among MADS-Box Proteins: Function and Evolution 426
V. The Grass Family as a Model System for Evo-Devo 430
A. Gene Duplication and Subfunctionalization 431
B. The Evolution of Derived Morphologies 433
C. Synteny and the Grass Family as an Integrated Genetic System 436
VI. Conclusions 437
Acknowledgments 439
References 439
Chapter 11: Developmental Gene Evolution and the Origin of Grass Inflorescence Diversity 447
I. Introduction 448
A. Tools for Evolutionary Developmental Genetics 448
B. The Grass Family 449
C. Grass Inflorescences vs Arabidopsis 450
D. Duplicate Genes, the Raw Material for Evolution of Novel Function 454
II. Methods 456
A. Choice of Genes and Taxa 456
B. Data, Alignment, and Polymerase Chain Reaction Primer Design 456
C. DNA Isolation, PCR, Subcloning, and Sequencing 457
D. Alignment and Phylogenetic Analysis 459
III. Morphological Variation and Molecular Evolution of Genes in Grass Inflorescences 459
A. Formation of Lateral Structures and Noncorrelation of Meristem Fates 459
1. Morphological variation 459
2. KNOTTED1\u2010like genes 460
3. LAX PANICLE1/BARREN STALK1 464
4. MONOCULM1 464
5. Barren Inflorescence2 466
B. Number of Orders of Branching 466
C. Number of Branches at Each Order 467
1. Morphological variation 467
2. RICE CENTRORADIALIS 468
3. RAMOSA1 470
4. ABERRANT PANICLE ORGANIZATION 471
5. Grain Number 1A/CKX2 471
D. Phyllotaxis 472
1. Morphological variation 472
2. CLAVATA\u2010like 473
3. ABPHYL1 475
E. Bracts and Leaves Subtending Branches 476
1. Morphological variation 476
2. LEAFY 476
F. Presence of a Terminal Spikelet 478
G. Elongation of Inflorescence Internodes 479
H. Glumes and Spikelets 479
1. Morphological variation 479
2. FRUITFULL 1/2/3 480
3. BRANCHED SILKLESS1/FRIZZY PANICLE1 483
I. Glume vs Lemma Identity 484
1. Morphological variation 484
2. SEPALLATA genes 485
J. Floret Number 487
1. Morphological variation 487
2. INDETERMINATE SPIKELET1 488
IV. Conclusions 490
Acknowledgments 493
References 494
Chapter 12: Expression of Floral Regulators in Basal Angiosperms and the Origin and Evolution of ABC-Function 505
I. Introduction 506
II. Summary of the ABC-Model 507
A. The ABC\u2010Model. 507
B. The Quartet Model 508
III. Alternatives to the ABC-Model 508
A. The Tulip/Lily Model 509
B. Shifting/Sliding Boundaries 509
C. Fading Borders 510
IV. Expression of Floral Regulators in Basal Angiosperms 511
A. Are Homologs of Arabidopsis A\u2010, B\u2010, and C\u2010Function Genes Present in Basal Angiosperms? 511
B. Where and When are Homologs of the A\u2010, B\u2010, and C\u2010Function Genes of Arabidopsis Expressed? 513
C. AGL6: A Candidate A\u2010Function Gene in Basal Angiosperms 514
V. Correspondence Between Expression Patterns and Floral Morphology 515
VI. New Insights into the Evolution of Novel Floral Structures 516
VII. Derivation of the ABC-Model 517
VIII. Future Directions 518
A. The Role of Gene Duplications 518
B. Transcription Factor Complexes and the Origin of the ABC\u2010Model: Testable Hypotheses 519
IX. Conclusions 520
References 524
Chapter 13: The Molecular Evolutionary Ecology of Plant Development: Flowering Time in Arabidopsis thaliana 529
I. Introduction 530
II. Evolutionary Ecology of Flowering Time 530
III. The Genetic Basis of Environmental Perception in Flowering Time Signaling 534
IV. Quantitative Trait Locus Mapping of Flowering Time Variation 536
V. Isolation of Genes Underlying Flowering Time Variation 538
VI. Microevolution of Flowering Time Loci 540
VII. Summary 543
Acknowledgments 543
References 543
Chapter 14: A Genomics Approach to the Study of Ancient Polyploidy and Floral Developmental Genetics 549
I. Introduction 550
A. Phylogenetic Context 550
B. Genomic Approaches 552
II. Widespread Polyploidy in Angiosperm History 553
III. Implications of Ancient Polyploidy for Comparative Genomics 555
A. Orthologs, Homeologs, and Paralogs 555
B. Characterizing the Fate of Duplicated Genes 556
C. A Gene Family Perspective on Genome Duplications 557
D. Shifts in Selective Constraint 559
IV. Comparative Analyses of Distantly Related Taxa Elucidate Gene Function in Arabidopsis 561
V. Future Prospects: Developing a Gene Family Framework to Characterize Plant Gene and Genome Evolution 563
Acknowledgments 564
References 564
Author Index 573
Subject Index 601