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.

Includes supplementary material: sn.pub/extras

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 Transcriptomes 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.