Plant Roots: The Hidden Half, Fourth Edition

Plant Roots......Page 3
Contents......Page 5
Preface to the Fourth Edition......Page 9
Editors......Page 11
Contributors......Page 13
I. The Evolution and Genomics of Roots......Page 18
II. Roots in the Fossil Record......Page 19
3. Rhizoids......Page 20
4. Branches with Uniquely Rooting Function......Page 21
1. Horsetails......Page 22
2. Clubmosses......Page 23
4. Progymnosperms......Page 24
A. Root Origins......Page 25
D. Mycorrhizae: An Early Symbiosis......Page 26
E. Roots, Soils, and Early Phanerozoic Ecosystems......Page 27
IV. Leading Topics, Gaps, and the Future......Page 28
References......Page 29
I. Introduction: The Genomic Sequencing Revolution in Plants......Page 33
B. Quantitative and Association Genetic Approaches......Page 34
III. Comparative Genomics and Genetics......Page 35
A. Ancient Plants......Page 36
B. Sequencing Plants of Agronomic Importance......Page 37
IV. Arabidopsis Root as a Model Organ......Page 38
A. Transcriptional Profiling in Developmental Time......Page 40
B. Transcriptional Profiling at Cell Type Resolution......Page 41
VI. Transcriptional Responses Link Development and Stress Responses in Root Cell Types......Page 42
VII. Identification of Novel Regulatory Modules from High-Resolution Transcriptional Data......Page 44
B. Proteomic and Metabolomic Analysis......Page 45
IX. Conclusions and Perspectives......Page 46
References......Page 47
II. Root Structure......Page 50
II. Anatomical Coordinates......Page 51
III. Definition of the Term “Meristem?......Page 52
V. Root System......Page 53
VI. Structure of the RAM......Page 54
VIII. Control of Meristem Size......Page 58
IX. Changes in the Patterning of the Meristem......Page 60
X. Importance of the QC in Maintaining Root Growth......Page 61
XI. Reformation and Maintenance of a QC......Page 64
XII. Stem Cell in the Root Meristem......Page 65
XIII. Stem Cell Niche Concept in the Root......Page 66
XIV. Importance of Cell Signaling in Root Growth......Page 68
References......Page 71
II. Arabidopsis Root Postembryonic Growth and Development......Page 77
B. Arabidopsis Genes Controlling Root Epidermal Cell-Fate Specification......Page 79
D. Chromatin Modifications Influence Root Epidermal Cell-Fate Specification......Page 82
E. Molecular Model of Position-Dependent Epidermal Patterning......Page 83
V. Conclusion and Future Directions......Page 84
References......Page 85
I. Introduction......Page 87
2. Anatomy and Histochemical Detection......Page 88
2. Anatomy and Histochemical Detection......Page 89
2. Anatomy and Histochemical Detection......Page 90
A. Early Development and Permeability......Page 91
C. Viability......Page 93
A. Three States of Development......Page 95
b. Multiseriate......Page 96
3. Molecular Mechanisms That May Regulate Exodermal Development......Page 97
1. Radial Movement of Ions and Water......Page 98
a. Ion Movement......Page 99
2. Drought and Salt Resistance......Page 100
V. Concluding Remarks......Page 101
References......Page 102
A. Short Guide to Lateral Root Development......Page 107
A. Pericycle: A Complex Tissue......Page 108
B. Regulation of Lateral Root Spacing......Page 109
C. Lateral Root Initiation......Page 111
D. Organogenesis: Shaping of the New Primordium......Page 112
F. Meristem Activation and Maintenance......Page 114
References......Page 115
I. Introduction: Why Study Vascular Development?......Page 120
II. Formation of the Vascular Cylinder during Embryogenesis......Page 121
A. Cambium......Page 123
IV. Hormonal Signaling Establishes the Radial Vascular Pattern......Page 124
A. Two-Component Cytokinin Signaling Specifies Protoxylem versus Procambial Cell Fate......Page 125
C. Auxin Signaling Promotes AHP6 Expression and Protoxylem Identity in the Correct Position......Page 126
D. Mutually Inhibitory Interaction between Auxin and Cytokinin Specifies the Radial Vascular Pattern......Page 127
B. SHR and MicroRNA Movement Act Non-Cell-Autonomously to Restrict HD-ZIP Expression......Page 128
B. VND7 Forms a Heterodimer with VNI2, Which Inhibits Upregulation of VND7 Targets......Page 130
B. CLE Peptides Regulate Xylem Differentiation by Modulating Cytokinin Signaling......Page 131
IX. Cytokinin Signaling Controls the Secondary Growth of Cambial Cells......Page 133
X. Putting the Pattern Together......Page 134
References......Page 135
II. Scope of This Review......Page 138
III. Secondary Growth: An Introduction......Page 139
IV. Root and Shoot Cambia Are Alike......Page 141
B. Breaking the Rules......Page 142
VI. Cytoskeletal Considerations of the Secondary Vascular System......Page 144
2. Dividing Cells......Page 145
a. Biphasic Fiber Growth......Page 146
b. Bipolar Tip Growth......Page 147
b. Bordered Pits......Page 148
C. Seasonal Cycle of Cambial Activity-Dormancy......Page 149
D. Continuity, Coordination, and Communication......Page 150
VII. Where Next? Ascendancy of Arabidopsis? Or the Tyranny of Thale Cress?......Page 151
References......Page 152
I. Introduction......Page 157
II. Initiation of CRs Occurs from a Ground Meristem inside the Stem......Page 159
III. Initiation of CR Is Regulated by Auxin and Cytokinins and by Specific Transcription Factors......Page 160
IV. Ethylene, Nitric Oxide, Gibberellic Acid, and Abscisic Acid Contribute to the Regulation of the Emergence and the Development of CR......Page 161
V. Similarities between Initiation Mechanisms and Tissue Origin of Root-Derived Roots and Stem-Derived Roots May Give Information about the Common Telomic Origin of Plant Axes......Page 162
VI. Conclusions: Adventitious Roots and Plant Improvement......Page 163
References......Page 164
A. Root Types and Their Formation during Development......Page 167
B. Root Initiation Mutants......Page 169
D. Root Maturation Mutants......Page 171
V. Conclusions and Outlook......Page 172
References......Page 173
II. Process of AR Formation......Page 175
B. Molecular Mechanism Underlying the Juvenile to Mature Phase Change in Woody Plants......Page 177
C. Molecular Mechanism of the Juvenile to Mature Phase Change in Herbaceous Plants......Page 178
A. Woody Plants......Page 179
A. Auxin/Cytokinins......Page 180
A. NO Metabolism and Role in Plants......Page 181
B. NO Donors as AR Enhancers......Page 182
References......Page 183
III. Regulation of Root Growth......Page 189
II. Auxin Distribution in the Primary Root......Page 190
A. ABP1 Auxin Receptor......Page 191
B. T IR1/AFBs and Aux/IAA Nuclear Coreceptors......Page 192
C. Other Putative Receptor......Page 194
1. ABP1 Receptor and Meristem Maintenance......Page 195
B. Auxin Control of Cell Elongation......Page 196
References......Page 197
A. Biosynthesis of Active GAs and Their Inactivation......Page 201
B. Site of GA Synthesis and Transport......Page 203
A. GA-Mediated Growth Regulation of Roots......Page 204
B. GA-Mediated Control of Root Thickness......Page 205
C. GA-Mediated Growth and Cell Wall Extension......Page 206
A. Early GA-Signaling Events......Page 207
3. GA and Root Meristem Size......Page 208
5. GA Sensitivity in the Root......Page 209
V. Concluding Remarks......Page 210
References......Page 211
I. Introduction......Page 215
A. Cytokinin Homeostasis......Page 216
A. Cytokinins Control Cell Differentiation Rate of Meristematic Cells......Page 217
C. Rate of Cell Differentiation Controls Root Meristem Growth......Page 218
D. Cytokinins and Root Embryo Development......Page 220
E. Cytokinins and Root Vascular Development......Page 221
IV. Cytokinins and Root Nodule Organogenesis......Page 222
References......Page 223
II. Ethylene Signaling Pathway......Page 227
III. Ethylene Alters Root Growth and Development......Page 228
IV. Examination of Cross Talk between Auxin and Ethylene Signaling Pathways......Page 230
V. Ethylene Modulates Auxin Transport......Page 232
References......Page 234
II. ABA Biosynthesis and Signaling......Page 238
A. ABA Content and Distribution in Roots......Page 239
3. ABA Transport between Roots and Shoots......Page 240
A. ABA and Inhibition or Promotion of Root Growth......Page 241
V. ABA and Lateral Roots......Page 242
A. ABA-Mediated Control on Root System Architecture in Changing Environment......Page 243
VII. Model for ABA Function in Plant Growth and Development: A Tale Emerging from Studies in Roots......Page 244
References......Page 245
II. Brassinosteroid Signaling Pathway......Page 251
III. Brassinosteroids Contribute to Important Aspects of Plant Postembryonic Development......Page 253
IV. Brassinosteroid Contribution to Root Growth and Development......Page 255
B. Root Analysis for the Study of BRs in Cell-Cycle Progression and Differentiation......Page 256
References......Page 258
II. Strigolactones: Biosynthesis and Composition......Page 261
III. Effects of Strigolactones on Shoot Development......Page 262
A. Primary Root Formation......Page 263
B. Strigolactone-Ethylene Cross Talk......Page 264
VIII. Strigolactones Are Signaling Molecules of Beneficial Plant Communication......Page 265
X. Strigolactones’ Primary Biological Role......Page 267
References......Page 269
I. Introduction......Page 273
A. Columella Represents the Site of Gravity Perception in the Arabidopsis Root......Page 274
C. Translating Statolith Sedimentation into a Physiological Signals......Page 275
A. Auxin Represents the Primary Gravitropic Signal......Page 276
C. AUX1/PIN2: Channeling the Auxin Gradient via the Lateral Root Cap to Elongation Zone......Page 278
F. AUX1: Facilitating Efficient Auxin Uptake......Page 279
1. Early Events in Graviresponse Are Likely to Be Nongenomic......Page 280
V. Conclusion and Perspectives......Page 281
References......Page 282
I. Calcium as a Macronutrient......Page 287
II. Calcium and Signaling Networks......Page 288
A. Root Calcium Signaling and the Mechanical Environment of the Soil......Page 289
IV. Obstacle Avoidance and Root System Architecture......Page 293
V. Parallels between Mechanical Signaling and Root Hair Growth......Page 294
References......Page 295
IV. Soil Resource Acquisition......Page 300
II. Water......Page 302
III. Root Traits to Increase Yield Potential......Page 305
A. Nitrogen......Page 307
B. Phosphorus......Page 308
A. Roots Adapted to Marginal, Hostile Soils......Page 309
B. Roots Adapted to Farming Practices That Conserve Soil Properties......Page 310
VI. Challenge for the Future: Linking Laboratory to the Field......Page 311
References......Page 312
I. Introduction......Page 319
A. Genotypic Variation in WheatSeminal Root Characteristics......Page 320
B. Quantitative Description of Root Architecture......Page 322
IV. Implications of Root Architectural Traits for Resource Acquisition......Page 323
1. Phosphorus......Page 324
2. Nitrogen......Page 325
B. Water Accessibility and Drought Tolerance......Page 326
1. Adaptation to Contrasting Drought Environments......Page 327
V. Selecting for Desirable Root Traits......Page 329
VI. Summary and Conclusions......Page 330
References......Page 331
A. Microelectrodes......Page 337
C. NMR Spectroscopy......Page 338
A. pH Changes during Normal Growth and Development......Page 339
B. pH Changes under Adverse Conditions......Page 340
A. Contribution of Membrane Transport to pH Regulation......Page 341
B. Contribution of Metabolism to pH Regulation......Page 344
IV. Physiological Consequences of pH Changes......Page 348
References......Page 349
I. Introduction......Page 355
II. Water Moves in a Complex System......Page 356
A. Soil Hydraulic Properties That Affect Water Flow to the Roots......Page 357
D. Soil, Constitutive Part of the Soil?Plant?Atmosphere Continuum......Page 358
C. Regulation by Water Channels......Page 359
D. Interplay between Root Anatomy and Aquaporin Activity......Page 360
C. Cavitation Recovery......Page 361
B. Root Placement and the Availability of Water......Page 363
A. Novel Techniques Supporting Integration......Page 364
C. Integration Helps in Understanding Water Uptake Patterns......Page 365
E. Future Outlooks......Page 366
References......Page 367
I. Introduction......Page 373
B. High- and Low-Affinity Transport Systems......Page 374
D. NO3? HATS......Page 375
F. NO3? Efflux Out of the Roots......Page 376
III. Regulation of Root NO3? and NH4+ Uptake Systems......Page 377
A. Regulation by NO3?......Page 378
B. Feedback Repression by the N Status of the Whole Plant......Page 379
V. Nitrogen Regulation of the Root System Architecture......Page 382
B. Systemic Repression of Lateral Root Growth by High N Status of the Plant......Page 383
C. Local Stimulation of Lateral Root Growth by NO3? and NH4+......Page 384
References......Page 386
A. One-Dimensional Models......Page 391
C. Radial-Flow or Single-Root Models......Page 393
D. Demand by Plants......Page 394
III. Processes at the Root?Soil Interface......Page 395
V. Modeling Root System Structure and Function......Page 396
VI. Root System Modeling: The Next Generation......Page 399
References......Page 400
B. Ephemeral Portion of the Root System......Page 405
A. Sources of Variation......Page 406
C. Difficulties and Definitions......Page 407
A. Elevated Atmospheric CO2......Page 408
B. Altered Precipitation......Page 409
C. Temperature......Page 411
D. Soil Nitrogen......Page 413
References......Page 414
II. Desert Environmental Conditions......Page 418
C. Perennial Grasses......Page 419
E. Phreatophytes......Page 420
F. Succulents......Page 421
A. Root Tissue Differentiation and Resistance to Water Loss......Page 422
B. Root Determinacy and Its Ecological Significance......Page 423
D. Root Dormancy and Developmental Timing as Adaptation......Page 425
G. Changes in the Root Apical Meristem Depend on the Temperature......Page 427
I. Developmental Adaptations Dependent on Inter-Root Communication......Page 428
J. Specialized Root Types: Succulent, Tuberous Storage, and Contractile Roots......Page 429
References......Page 430
I. Introduction......Page 435
III. Measurement Methods......Page 436
A. Functions of Fine Roots......Page 437
C. Plasticity and Resources......Page 438
D. Soil Properties, Horizontal and Vertical Spread......Page 439
A. Coarse-Root Measurements......Page 441
VI. Architecture of Root Systems......Page 442
VIII. Anchorage Mechanics......Page 447
A. Mechanisms That Increase Anchorage Strength......Page 449
IX. Conclusions......Page 451
References......Page 452
II. Are “Root Crops? Really Roots?......Page 461
c. Production......Page 464
c. Production......Page 465
b. Origin and Domestication......Page 466
b. Origin and Domestication......Page 467
c. Production......Page 468
2. Origin and Domestication......Page 469
2. Origin and Domestication......Page 470
2. Origin and Domestication......Page 471
1. Classification and Relatives......Page 472
V. Future of Root Crops......Page 473
Acknowledgments......Page 474
References......Page 475
V. Root Response to Stress......Page 486
II. Dynamics of Soil Temperature......Page 487
B. Alteration of Soil Temperature in the Greenhouse and under Laboratory Conditions......Page 488
A. Response to Low Temperature......Page 489
B. Response to High Temperature......Page 490
C. Response to Temperature Gradient versus Homogenous Soil Temperatures......Page 491
V. Noninvasive Methods for Studying Temperature Effects on Root Growth......Page 492
References......Page 494
II. Starting Point: Basic Anatomy of the Root......Page 498
B. Aerenchyma Formation and Programmed Cell Death Signaling......Page 499
C. Development of the Radial Oxygen Loss Barrier......Page 503
D. Root and Rhizome Ventilation during Waterlogging Enables Fast Exchange of Gases......Page 504
A. Aquaporins......Page 505
B. Mineral Uptake and Ion Transport under Oxygen Shortage......Page 506
IV. Physiological Adaptations to Low O2......Page 507
1. Carbohydrate Metabolism Is Strongly Affected by Low O2......Page 508
2. Starch Metabolism under Low O2......Page 509
3. Sucrose Metabolism under Low O2......Page 511
2. ROS and NO Formation in Plant Mitochondria......Page 512
A. ROS Formation under Oxygen Deprivation......Page 515
1. Interaction of Class I Hemoglobins and NO......Page 516
VI. Antioxidant Protection of Root Tissues with Special Emphasis on Low-Oxygen Conditions......Page 517
B. Enzymatic Antioxidants......Page 518
References......Page 519
II. Occurrence and Chemistry of Al......Page 530
B. Hormone and Al Toxicity......Page 531
A. Cell Wall......Page 532
C. Aluminum Toxicity Recovery......Page 533
VI. Callose......Page 535
C. Genetic Evidence Supporting a Link between Al Stress and Oxidative Stress......Page 536
VIII. Signal Transduction and Al Signal......Page 537
A. Exudation of Organic Acids......Page 538
B. Organic Anion Transporter......Page 539
A. ALMT1 Family......Page 540
C. MATE Family......Page 542
XV. Internal Al-Tolerance Mechanism......Page 543
XVII. pH Regulation in the Rhizosphere......Page 544
References......Page 545
II. Classifications of Trace Metallic Elements......Page 554
A. Occurrence of Trace Metallic Elements in Soils and Strategies to Address Human Health and Environmental Issues......Page 556
C. Uptake Systems of Trace Metallic Elements in Plants......Page 557
4. Manganese......Page 558
D. Transport and Circulation of Trace Metallic Elements in Plants......Page 559
IV. Response of Roots to Trace Metallic Elements......Page 560
A. Inventory of Root Morphological Responses to Critical Trace Metallic Element Concentrations......Page 561
e. Nickel......Page 563
1. Perception of Trace Metallic Element Concentration......Page 564
b. Nitric Oxide......Page 565
4. Role of MicroRNAs in Signaling Trace Metallic Element Stress......Page 566
a. Auxin......Page 567
e. Salicylic Acid......Page 568
1. Foraging Capacity of Hyperaccumulators......Page 569
1. Uptake of Trace Metallic Elements by Roots......Page 570
2. Metal Mobility through the Roots......Page 571
References......Page 573
I. Introduction......Page 584
A. Experimental Approaches Highlight Focal Points of Control......Page 585
B. Hormonal Regulation of Root Growth......Page 586
D. Modulation of Cell Production, Cell Wall Extensibility, and Root Growth by Reactive Oxygen Species......Page 587
E. Other Effects on Cell Wall Properties at Low ψw......Page 588
III. Root Growth in Drying Soil in the Field......Page 589
References......Page 590
II. Root Growth under Salt Stress......Page 595
A. Osmotic Effects......Page 598
a. Na+ and Cl? Uptake......Page 599
b. Reduced K+ Supply......Page 600
C. Oxidative Stress......Page 601
B. Membrane Composition......Page 602
VI. Root Hydraulic Conductivity......Page 603
B. Cell-Wall Composition and Ultrastructure......Page 604
References......Page 605
II. Measuring Soil Strength......Page 613
A. Soil Strength due to Soil Drying......Page 614
B. Soil Strength due to Compaction......Page 615
C. Effects of Soil Type on Soil Strength......Page 616
IV. Growth Pressure Generated by Roots......Page 617
V. Root Penetration and Bending Stiffness......Page 618
VI. Experimental Approaches to Investigate the Effects of Strong Soil......Page 619
VII. Effect of Soil Strength on Root Morphology: Elongation and Cell Expansion......Page 620
VIII. Root System Growth and Function in Heterogeneous Soil......Page 623
X. Conclusions......Page 624
References......Page 625
VI. Root?Rhizosphere Interactions......Page 628
I. Introduction......Page 629
A. Dark Septate Endophytes......Page 630
1. Phialocephala fortinii s.l.?Acephala applanata Species Complex......Page 631
III. Methods of Detection......Page 632
1. Anatomy......Page 633
B. Orchid Endophytes......Page 639
1. Anatomy......Page 643
2. Endophyte?Pathogen, Endophyte?Nematode, and Endophyte?Insect Interactions......Page 647
4. Endophyte?Environment Interactions......Page 649
A. Root Endophytes of Woody Ericales......Page 650
B. Root Endophytes of Pinales......Page 654
1. Anatomy......Page 658
3. Endophyte?Plant Interactions......Page 659
4. Endophyte?Environment Interactions......Page 660
C. Root Endophytes in Other Woody Plant Species......Page 661
4. Endophyte?Environment Interactions......Page 665
References......Page 666
I. Introduction......Page 678
A. Transcriptional, Physiological, and Morphological Changes in Roots during Mycorrhizal Formation......Page 680
B. Transcriptional, Physiological, and Morphological Changes in EM-Forming Fungi during Mycorrhizal Establishment and Functioning......Page 681
A. Secreted Ectomycorrhizal Enzymes Involved in Exploitation of Phosphorus......Page 688
C. Ectomycorrhizal Enzymes Involved in Degradation of Complex C-Bearing Compounds......Page 690
References......Page 693
I. Introduction......Page 699
II. Tree Species Richness of Neotropical Rain Forests as Supported by Common Mycorrhizal Fungi......Page 700
III. From Individual ECM Trees to Monodominant ECM Stands in the Wet Tropics......Page 701
IV. Impact of Mycobionts on Establishment of Orchids in Open Habitats, Tropical AM Forests, and ECM Forests......Page 704
V. Conclusions......Page 707
References......Page 708
I. Introduction......Page 712
II. Carbohydrate Synthesis and Metabolism at the Nematode Feeding Site......Page 715
IV. Cell Walls......Page 717
A. Hypersensitive Response......Page 719
B. Jasmonic Acid and Salicylic Acid......Page 720
VI. Changes of Protein Expression in Plants Upon Infection by Nematodes......Page 721
References......Page 722
VII. Modern Research Techniques......Page 727
I. Introduction......Page 728
B. Angle of Installation......Page 729
D. Time Lag before First Measurement......Page 730
E. Material and Types of Minirhizotron Observation Tubes......Page 731
A. Image Capturing Devices......Page 732
C. Image Analysis......Page 733
A. Minirhizotrons and Measurements of Standing Stock and Root Depth Distribution......Page 734
B. Minirhizotrons for Estimation of Root Production and Demography......Page 735
D. Minirhizotrons for Studying Belowground Interactions......Page 736
C. Measurement of Environmental Parameters......Page 737
References......Page 738
I. Introduction......Page 744
B. Use of Microassays in Root Studies......Page 745
III. Self-Referencing Physiological Sensors......Page 746
A. SR Ion-Selective Microelectrodes......Page 747
C. SR Fiber-Optic Microsensors......Page 749
A. Oxygen Flux in Developing Roots......Page 750
C. Proton Flux in Developing Typha latifolia Roots......Page 751
D. Nitrogen Flux in Maize Roots......Page 752
A. Ultradian Oscillatory Transport in Roots......Page 753
B. Pharmacological Studies in Roots......Page 755
VII. Future Directions......Page 757
References......Page 758
Genes and Mutants Index......Page 762
Organism Index......Page 769
Terms Index......Page 778
Color Insert......Page 784