Includes supplementary material: sn.pub/extras
Functional genomics is a young discipline whose origin can be traced back to the late 1980s and early 1990s, when molecular tools became available to determine the cellular functions of genes. Today, functional genomics is p- ceived as the analysis, often large-scale, that bridges the structure and organi- tion of genomes and the assessment of gene function. The completion in 2000 of the genome sequence of Arabidopsis thaliana has created a number of new and exciting challenges in plant functional genomics. The immediate task for the plant biology community is to establish the functions of the approximately 25,000 genes present in this model plant. One major issue that will remain even after this formidable task is c- pleted is establishing to what degree our understanding of the genome of one model organism, such as the dicot Arabidopsis, provides insight into the or- nization and function of genes in other plants. The genome sequence of rice, completed in 2002 as a result of the synergistic interaction of the private and public sectors, promises to significantly enrich our knowledge of the general organization of plant genomes. However, the tools available to investigate gene function in rice are lagging behind those offered by other model plant systems. Approaches available to investigate gene function become even more limited for plants other than the model systems of Arabidopsis, rice, and maize.
Part I. Finding Genes in Complex Plant Systems An Improved Method for Plant BAC Library Construction Meizhong Luo and Rod A. Wing Constructing Gene-Enriched Plant Genomic Libraries Using Methylation Filtration Technology Pablo D. Rabinowicz RescueMu Protocols for Maize Functional Genomics Manish N. Raizada Precious Cells Contain Precious Information: Strategies and Pitfalls in Expression Analysis from a Few Cells Isabelle M. Henry and Dina F. Mandoli Combined ESTs from Plant-Microbe Interactions: Using GC Counting to Determine the Species of Origin Edgar Huitema, Trudy A. Torto, Allison Styer, and Sophien Kamoun Part II. In Silico Prediction of Plant Gene Function Computer Software to Find Genes in Plant Genomic DNA Ramana V. Davuluri and Michael Q. Zhang Genomic Colinearity as a Tool for Plant Gene Isolation Wusirika Ramakrishna and Jeffrey L. Bennetzen Using Natural Allelic Diversity to Evaluate Gene Function Sherry R. Whitt and Edward S. Buckler, IV Quantitative Trait Locus Analysis as a Gene Discovery Tool Michael D. McMullen Part III. Forward and Reverse Genetic Strategies Transposon Tagging Using Activator (Ac) in Maize Thomas P. Brutnell and Liza J. Conrad T-DNA Mutagenesis in Arabidopsis Jose M. Alonso and Anna N. Stepanova Physical and Chemical Mutagenesis Andrea Kodym and Rownak Afza High-Throughput TILLING for Functional Genomics Bradley J. Till, Trenton Colbert, Rachel Tompa, Linda C. Enns, Christine A. Codomo, Jessica E. Johnson, Steven H. Reynolds, Jorja G. Henikoff, Elizabeth A. Greene, Michael N. Steine, Luca Comai, and Steven Henikoff Gene and Enhancer Traps for Gene Discovery Marcela Rojas-Pierce and Patricia S. Springer High-Throughput TAIL-PCR as a Tool to Identify DNA Flanking Insertions Tatjana Singer and Ellen Burke Custom Knock-Outs with Hairpin RNA-Mediated Gene Silencing Susan Varsha Wesley, Qing Liu, Anna Wielopolska, Geoff Ellacott, Neil Smith, Surinder Singh, and Chris Helliwell Virus-Induced Gene Silencing S. P. Dinesh-Kumar, Radhamani Anandalakshmi, Rajendra Marathe, Michael Schiff, and Yule Liu Exploring the Potential of Plant RNase P as a Functional Genomics Tool Dileep K. Pulukkunat, M. L. Stephen Raj, Debasis Pattanayak, Lien B. Lai, and Venkat Gopalan Maintaining Collections of Mutants for Plant Functional Genomics Randy Scholl, Martin M. Sachs, and Doreen Ware Part IV. Gain of Function Approaches Vector Construction for Gene Overexpression as a Tool to Elucidate Gene Function Alan Lloyd T-DNA Activation Tagging Johan Memelink Part V. Phenotypic Profiling as a Tool to Determine Gene Function Expression Profiling Using cDNA Microarrays Suling Zhao and Wesley B. Bruce Open Architecture Expression Profiling of Plant Tranillegalscriptomes and Gene Discovery Using GeneCalling® Technology Oswald R. Crasta and Otto Folkerts Proteomics as a Functional Genomics Tool Ulrike Mathesius, Nijat Imin, Siria H. A. Natera, and Barry G. Rolfe Metabolite Profiling as a Functional Genomics Tool Anusha P. Dias, Johnny Brown, Pierluigi Bonello, and Erich Grotewold Growth Stage-Based Phenotypic Profiling of Plants Susanne Kjemtrup, Douglas C. Boyes, Cory Christensen, Amy J. McCaskill, Michelle Hylton, and Keith Davis Index
As more and more plant genomes are sequenced, plant researchers have been inundated with an avalanche of novel methodologies to identify the function of tens of thousands of plant genes. In Plant Functional Genomics, Erich Grotewold has assembled a team of leading plant scientists to describe in detail the most commonly used methods for investigating plant gene function in a wide variety of plants, during plant pathogen interactions, and even in algae. These readily reproducible protocols include computational, molecular, and genetic methodologies designed for both general and specific problems. Here the reader will learn how to identify genes in complex systems that have large genomes, few cells, and mixed cell systems. Readers will also learn the use of powerful computational and statistical tools to help predict gene function, either on the basis of comparative genomics, or from the analysis of complex genome sequences. Because establishing gene function relies on the identification of phenotypes, the authors expand the concept of phenotypes, including the use of multiple outputs as the ultimate phenotypic result of changes in gene activity. Numerous loss-of-function and gain-of-function techniques for discovering gene function are presented in step-by-step detail.
Comprehensive and highly practical, Plant Functional Genomics offers plant biologists readily reproducible computational, molecular, and genetic protocols, powerful tools that will enable them, with little or no experience, successfully to investigate any gene function with the most recent methodologies.
"...provides in a single volume most of the commonly used approaches in plant genomics...worth reading and should interest a large public." - Proteomics
"This well written and illustrated guide reads easily and provides detailed protocols and an up-to-date bibliography for all reviewed strategies, making it the book that everybody in this field would need." - Cell Biochem Funct
Finding Genes in Complex Plant Systems.- An Improved Method for Plant BAC Library Construction.- Constructing Gene-Enriched Plant Genomic Libraries Using Methylation Filtration Technology.- RescueMu Protocols for Maize Functional Genomics.- Precious Cells Contain Precious Information.- Combined ESTs from Plant-Microbe Interactions.- In Silico Prediction of Plant Gene Function.- Computer Software to Find Genes in Plant Genomic DNA.- Genomic Colinearity as a Tool for Plant Gene Isolation.- Using Natural Allelic Diversity to Evaluate Gene Function.- Quantitative Trait Locus Analysis as a Gene Discovery Tool.- Forward and Reverse Genetic Strategies.- Transposon Tagging Using Activator (Ac) in Maize.- T-DNA Mutagenesis in Arabidopsis.- Physical and Chemical Mutagenesis.- High-Throughput TILLING for Functional Genomics.- Gene and Enhancer Traps for Gene Discovery.- High-Throughput TAIL-PCR as a Tool to Identify DNA Flanking Insertions.- Custom Knock-Outs with Hairpin RNA-Mediated Gene Silencing.- Virus-Induced Gene Silencing.- Exploring the Potential of Plant RNase P as a Functional Genomics Tool.- Maintaining Collections of Mutants for Plant Functional Genomics.- Gain of Function Approaches.- Vector Construction for Gene Overexpression as a Tool to Elucidate Gene Function.- T-DNA Activation Tagging.- Phenotypic Profiling as a Tool to Determine Gene Function.- Expression Profiling Using cDNA Microarrays.- Open Architecture Expression Profiling of Plant Tranillegalscriptomes and Gene Discovery Using GeneCalling® Technology.- Proteomics as a Functional Genomics Tool.- Metabolite Profiling as a Functional Genomics Tool.- Growth Stage-Based Phenotypic Profiling of Plants.
"...provides in a single volume most of the commonly used approaches in plant genomics...worth reading and should interest a large public." - Proteomics
"This well written and illustrated guide reads easily and provides detailed protocols and an up-to-date bibliography for all reviewed strategies, making it the book that everybody in this field would need." - Cell Biochem Funct
Dr. Grotewold is an Associate Professor of Plant Biology at The Ohio State University. He recieved his Ph.D from the Instituto de Ingenieria Genetics y Bologia Molecular, University of Buenos Aires, Argentina in 1988. His research focuses on Regulation of Gene Expression; Function and Evolution of Myb Proteins; Plant Metabolic Engineering. Combining molecular, cellular, biochemical and genetic approaches, his laboratory investigates fundamental questions regarding the mechanisms by which plants control gene expression, and how tranillegalscription factors have impacted plant evolution and speciation. He has started to develop regulatory networks in Arabidopsis that should help explain how the 28,000+ Arabidopsis genes are expressed. In addition, he is utilizing his extensive knowledge on tranillegalscription factors for plant metabolic engineering.
Inhaltsverzeichnis
Part I. Finding Genes in Complex Plant Systems
An Improved Method for Plant BAC Library Construction
Meizhong Luo and Rod A. Wing
Constructing Gene-Enriched Plant Genomic Libraries Using Methylation Filtration Technology
Pablo D. Rabinowicz
RescueMu Protocols for Maize Functional Genomics
Manish N. Raizada
Precious Cells Contain Precious Information: Strategies and Pitfalls in Expression Analysis from a Few Cells
Isabelle M. Henry and Dina F. Mandoli
Combined ESTs from Plant-Microbe Interactions: Using GC Counting to Determine the Species of Origin
Edgar Huitema, Trudy A. Torto, Allison Styer, and Sophien Kamoun
Part II. In Silico Prediction of Plant Gene Function
Computer Software to Find Genes in Plant Genomic DNA
Ramana V. Davuluri and Michael Q. Zhang
Genomic Colinearity as a Tool for Plant Gene Isolation
Wusirika Ramakrishna and Jeffrey L. Bennetzen
Using Natural Allelic Diversity to Evaluate Gene Function
Sherry R. Whitt and Edward S. Buckler, IV
Quantitative Trait Locus Analysis as a Gene Discovery Tool
Michael D. McMullen
Part III. Forward and Reverse Genetic Strategies
Transposon Tagging Using Activator (Ac) in Maize
Thomas P. Brutnell and Liza J. Conrad
T-DNA Mutagenesis in Arabidopsis
Jose M. Alonso and Anna N. Stepanova
Physical and Chemical Mutagenesis
Andrea Kodym and Rownak Afza
High-Throughput TILLING for Functional Genomics
Bradley J. Till, Trenton Colbert, Rachel Tompa, Linda C. Enns, Christine A. Codomo, Jessica E. Johnson, Steven H. Reynolds, Jorja G. Henikoff, Elizabeth A. Greene, Michael N. Steine, Luca Comai, and Steven Henikoff
Gene and Enhancer Traps for Gene Discovery
Marcela Rojas-Pierce and Patricia S. Springer
High-Throughput TAIL-PCR as a Tool to Identify DNA Flanking Insertions
Tatjana Singer and Ellen Burke
Custom Knock-Outs with Hairpin RNA-Mediated Gene Silencing
Susan Varsha Wesley, Qing Liu, Anna Wielopolska, Geoff Ellacott, Neil Smith, Surinder Singh, and Chris Helliwell
Virus-Induced Gene Silencing
S. P. Dinesh-Kumar, Radhamani Anandalakshmi, Rajendra Marathe, Michael Schiff, and Yule Liu
Exploring the Potential of Plant RNase P as a Functional Genomics Tool
Dileep K. Pulukkunat, M. L. Stephen Raj, Debasis Pattanayak, Lien B. Lai, and Venkat Gopalan
Maintaining Collections of Mutants for Plant Functional Genomics
Randy Scholl, Martin M. Sachs, and Doreen Ware
Part IV. Gain of Function Approaches
Vector Construction for Gene Overexpression as a Tool to Elucidate Gene Function
Alan Lloyd
T-DNA Activation Tagging
Johan Memelink
Part V. Phenotypic Profiling as a Tool to Determine Gene Function
Expression Profiling Using cDNA Microarrays
Suling Zhao and Wesley B. Bruce
Open Architecture Expression Profiling of Plant Tranillegalscriptomes and Gene Discovery Using GeneCalling® Technology
Oswald R. Crasta and Otto Folkerts
Proteomics as a Functional Genomics Tool
Ulrike Mathesius, Nijat Imin, Siria H. A. Natera, and Barry G. Rolfe
Metabolite Profiling as a Functional Genomics Tool
Anusha P. Dias, Johnny Brown, Pierluigi Bonello, and Erich Grotewold
Growth Stage-Based Phenotypic Profiling of Plants
Susanne Kjemtrup, Douglas C. Boyes, Cory Christensen, Amy J. McCaskill, Michelle Hylton, and Keith Davis
Index
Klappentext
Functional genomics is a young discipline whose origin can be traced back to the late 1980s and early 1990s, when molecular tools became available to determine the cellular functions of genes. Today, functional genomics is p- ceived as the analysis, often large-scale, that bridges the structure and organi- tion of genomes and the assessment of gene function. The completion in 2000 of the genome sequence of Arabidopsis thaliana has created a number of new and exciting challenges in plant functional genomics. The immediate task for the plant biology community is to establish the functions of the approximately 25,000 genes present in this model plant. One major issue that will remain even after this formidable task is c- pleted is establishing to what degree our understanding of the genome of one model organism, such as the dicot Arabidopsis, provides insight into the or- nization and function of genes in other plants. The genome sequence of rice, completed in 2002 as a result of the synergistic interaction of the private and public sectors, promises to significantly enrich our knowledge of the general organization of plant genomes. However, the tools available to investigate gene function in rice are lagging behind those offered by other model plant systems. Approaches available to investigate gene function become even more limited for plants other than the model systems of Arabidopsis, rice, and maize.
Includes supplementary material: sn.pub/extras
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