Weedy and Invasive Plant Genomics

C. Neal Stewart is Racheff Chair of Excellence in Plant Molecular Genetics and Professor, Department of Plant Sciences, University of Tennessee.

• Contributors xiPreface xvChapter 1 Why Should Weed Scientists Care About Genomics? 3WILLIAM K. VENCILLGenomics To A Weed Scientist 3Resistance 4Better Use Of Existing Herbicides 8Chapter 2 An Introduction To Molecular Genetic And Genomic Techniques 11CHHANDAK BASU AND SAM R. ZWENGERWeeds As A Source Of Genes For Crop Improvement 11Tools And Approaches For Understanding Weediness AtThe Molecular Level 12Chapter 3 Arabidopsis Is Not A Weed, And Mostly Not A Good Model For Weed Genomics; There Is No Good Model For Weed Genomics 25JONATHAN GRESSELIntroduction: Arabidopsis And Weediness 25Questions About Weeds—Can Arabidopsis Genomics Answer Them? 27The Misdirected Approach In Using Arabidopsis To Elucidate New Herbicide Targets 28Arabidopsis Genomics Can Help In Dealing With Transgene Flow—In A Limited Manner 29Lessons To Be Learned 30Chapter 4 Model Weeds For Genomics Research 33WUN S. CHAO AND DAVID P. HORVATHWhat Makes A Good Model Species? 34Leveraging From Other Models 36Genomics Tools For Weeds That Are Under Development 44Chapter 5 21st-Century Weed Science: A Call For Amaranthus Genomics 53PATRICK J. TRANEL AND FEDERICO TRUCCOThe Amaranthus Genus 53Hybridization And Adaptive Evolution 61Herbicide Resistance 64Currently Available Genomic Resources 71Needs And Opportunities 75Chapter 6 Evolutionary Genomics Of Weedy Rice 83BRIANA L. GROSS AND KENNETH M. OLSENPhenotypic Diversity Of Weedy Rice 84Genomic Diversity Of Weedy Rice 85The Origin(s) And Evolution Of Weedy Rice 89The Genetic Basis Of Weediness And Use Of Weedy Rice In Crop Breeding 94Chapter 7 Rhizomatousness: Genes Important For A Weediness Syndrome 99ANDREW H. PATERSONDevelopmental Context 100An Exemplary Case: Johnsongrass 101Dissecting The Genetic Control Of Rhizomatousness 103Early Insights Into The Sorghum Rhizo-Transcriptome 105Future Work And Potential Applications 107Synthesis 109Chapter 8 Leafy Spurge: An Emerging Model To Study Traits Of Perennial Weeds 113DAVID P. HORVATH AND JAMES V. ANDERSONRegulation Of Shoot Development And Growth 113Regulation Of Bud Dormancy 116Case Study: Leafy Spurge 117Future Work 122Chapter 9 Herbicide Resistance: Target Site Mutations 127CHRISTOPHER PRESTONResistance To Photosystem II-Inhibiting Herbicides 128Resistance To Acetohydroxyacid Synthase-Inhibiting Herbicides 131Resistance To Acetyl Coenzyme A Carboxylase-Inhibiting Herbicides 136Resistance To Glyphosate 138Resistance To Microtubule Assembly Inhibitors 140Resistance To Phytoene Desaturase Inhibitors 141Chapter 10 Molecular and Genomic Mechanisms Of Non-Target-Site Herbicide Resistance 149JUN HU, PATRICK J. TRANEL, C. NEAL STEWART JR., AND JOSHUA S. YUANHerbicide Application And Resistance 149Herbicide Classification And Resistance 150Non-Target Herbicide Resistance 150Signal Transduction 150Detoxification and Modification 151Chapter 11 A Herbicide Defense Trait That Is Distinct From Resistance: The Evolutionary Ecology And Genomics Of Herbicide Tolerance 163REGINA S. BAUCOMResistance Versus Tolerance In Weed Science 163Tolerance In Evolutionary Ecology 166Tolerance Traits And The Genomics Of Tolerance 171Why Again Should We Focus On Tolerance, Tolerance Traits, And The Genomics Of Tolerance? 172Chapter 12 The Genomics of Plant Invasion: A Case Study In Spotted Knapweed 177AMANDA K. BROZ AND JORGE M. VIVANCOWhy Study Invasive Plant Genomics? 177Spotted Knapweed Life History 178Allelopathy And The Novel Weapons Hypothesis 180Genomics Resources And Approaches For Studying Spotted Knapweed 185Chapter 13 Molecular Ecology Of Plant Competition 197DOMINIK D. SCHMIDT, MERIJN R. KANT, AND IAN T. BALDWINCompetition Signals And Their Perception By Plants 198Molecular Basis Of Competitively Important Traits 207Transcriptomic Insights Into Competitive Interactions Of Weedy Plants 211Chapter 14 Genomics And Weeds: A Synthesis 221STEPHEN O. DUKE, SCOTT R. BAERSON, AND JONATHAN GRESSELFrom Fundamental Information To Practical Solutions 222Where Do We Go From Here? 241Index 249