Plant Functional Genomics

Plant Functional Genomics : Methods and Protocols

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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.
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Product details

  • Hardback | 452 pages
  • 128 x 262.6 x 29.7mm | 866.38g
  • Totowa, NJ, United States
  • English
  • 2003 ed.
  • XVI, 452 p.
  • 1588291456
  • 9781588291455

Back cover copy

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.
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Table of contents

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 Transcriptomes and Gene Discovery Using GeneCalling (R) 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

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Review quote

"...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
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