Weedy and Invasive Plant Genomics

Contributors xi

Preface xv

Chapter 1 Why Should Weed Scientists Care About Genomics? 3
WILLIAM K. VENCILL

Genomics To A Weed Scientist 3

Resistance 4

Better Use Of Existing Herbicides 8

Chapter 2 An Introduction To Molecular Genetic And Genomic Techniques 11
CHHANDAK BASU AND SAM R. ZWENGER

Weeds As A Source Of Genes For Crop Improvement 11

Tools And Approaches For Understanding Weediness At

The Molecular Level 12

Chapter 3 Arabidopsis Is Not A Weed, And Mostly Not A Good Model For Weed Genomics; There Is No Good Model For Weed Genomics 25
JONATHAN GRESSEL

Introduction: Arabidopsis And Weediness 25

Questions About Weeds—Can Arabidopsis Genomics Answer Them? 27

The Misdirected Approach In Using Arabidopsis To Elucidate New Herbicide Targets 28

Arabidopsis Genomics Can Help In Dealing With Transgene Flow—In A Limited Manner 29

Lessons To Be Learned 30

Chapter 4 Model Weeds For Genomics Research 33
WUN S. CHAO AND DAVID P. HORVATH

What Makes A Good Model Species? 34

Leveraging From Other Models 36

Genomics Tools For Weeds That Are Under Development 44

Chapter 5 21st-Century Weed Science: A Call For Amaranthus Genomics 53
PATRICK J. TRANEL AND FEDERICO TRUCCO

The Amaranthus Genus 53

Hybridization And Adaptive Evolution 61

Herbicide Resistance 64

Currently Available Genomic Resources 71

Needs And Opportunities 75

Chapter 6 Evolutionary Genomics Of Weedy Rice 83
BRIANA L. GROSS AND KENNETH M. OLSEN

Phenotypic Diversity Of Weedy Rice 84

Genomic Diversity Of Weedy Rice 85

The Origin(s) And Evolution Of Weedy Rice 89

The Genetic Basis Of Weediness And Use Of Weedy Rice In Crop Breeding 94

Chapter 7 Rhizomatousness: Genes Important For A Weediness Syndrome 99
ANDREW H. PATERSON

Developmental Context 100

An Exemplary Case: Johnsongrass 101

Dissecting The Genetic Control Of Rhizomatousness 103

Early Insights Into The Sorghum Rhizo-Transcriptome 105

Future Work And Potential Applications 107

Synthesis 109

Chapter 8 Leafy Spurge: An Emerging Model To Study Traits Of Perennial Weeds 113
DAVID P. HORVATH AND JAMES V. ANDERSON

Regulation Of Shoot Development And Growth 113

Regulation Of Bud Dormancy 116

Case Study: Leafy Spurge 117

Future Work 122

Chapter 9 Herbicide Resistance: Target Site Mutations 127
CHRISTOPHER PRESTON

Resistance To Photosystem II-Inhibiting Herbicides 128

Resistance To Acetohydroxyacid Synthase-Inhibiting Herbicides 131

Resistance To Acetyl Coenzyme A Carboxylase-Inhibiting Herbicides 136

Resistance To Glyphosate 138

Resistance To Microtubule Assembly Inhibitors 140

Resistance To Phytoene Desaturase Inhibitors 141

Chapter 10 Molecular and Genomic Mechanisms Of Non-Target-Site Herbicide Resistance 149
JUN HU, PATRICK J. TRANEL, C. NEAL STEWART JR., AND JOSHUA S. YUAN

Herbicide Application And Resistance 149

Herbicide Classification And Resistance 150

Non-Target Herbicide Resistance 150

Signal Transduction 150

Detoxification and Modification 151

Chapter 11 A Herbicide Defense Trait That Is Distinct From Resistance: The Evolutionary Ecology And Genomics Of Herbicide Tolerance 163
REGINA S. BAUCOM

Resistance Versus Tolerance In Weed Science 163

Tolerance In Evolutionary Ecology 166

Tolerance Traits And The Genomics Of Tolerance 171

Why Again Should We Focus On Tolerance, Tolerance Traits, And The Genomics Of Tolerance? 172

Chapter 12 The Genomics of Plant Invasion: A Case Study In Spotted Knapweed 177
AMANDA K. BROZ AND JORGE M. VIVANCO

Why Study Invasive Plant Genomics? 177

Spotted Knapweed Life History 178

Allelopathy And The Novel Weapons Hypothesis 180

Genomics Resources And Approaches For Studying Spotted Knapweed 185

Chapter 13 Molecular Ecology Of Plant Competition 197
DOMINIK D. SCHMIDT, MERIJN R. KANT, AND IAN T. BALDWIN

Competition Signals And Their Perception By Plants 198

Molecular Basis Of Competitively Important Traits 207

Transcriptomic Insights Into Competitive Interactions Of Weedy Plants 211

Chapter 14 Genomics And Weeds: A Synthesis 221
STEPHEN O. DUKE, SCOTT R. BAERSON, AND JONATHAN GRESSEL

From Fundamental Information To Practical Solutions 222

Where Do We Go From Here? 241

Index 249