植物生理

Genomics has developed a wide range of tools to identify genes that play roles in specific pathways. However, relating individual genes and alleles to agronomic traits is still quite challenging. We describe how association analysis can be used to relate natural variation at candidate gen ...

The transposable element Activator (Ac) has been used in several plant species as a tool for gene isolation and characterization. However, it has not been widely utilized in its native host maize, in part, because of a relatively low germinal transposition rate. The propensity of Ac to move to linked s ...

Quantitative trait locus analysis has been a mainstay approach for obtaining a genetic description of complex agronomic traits for plants. What is sometimes overlooked is the role quantitative trait locus (QTL) analysis can play in identifying genes that underlay complex traits. In th ...

Insertional mutagenesis is a basic genetic tool that allows for a rapid identification of the tagged genes responsible for a particular phenotype. Transposon and Agrobacterium-mediated DNA integration are the most commonly used biological mutagens in plants. The main drawback of t ...

Targeting-induced local lesions in genomes (TILLING) is a general strategy for identifying induced point mutations that can be applied to almost any organism. Here, we describe the basic methodology for high-throughput TILLING. Gene segments are amplified using fluorescently tag ...

Important methods to artificially induce mutations are the use of chemical and physical agents. Most chemical mutagens are alkylating agents and azides. Physical mutagens include electromagnetic radiation, such as γ rays, X rays, and UV light, and particle radiation, such as fast and ther ...

Gene traps and enhancer traps provide a valuable tool for gene discovery. With this system, genes can be identified based solely on the expression pattern of an inserted reporter gene. The use of a reporter gene, such as β-glucuoronidase (GUS), provides a very sensitive assay for the identificati ...

Thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) is a fast and efficient method to amplify unknown sequences adjacent to known insertion sites in Arabidopsis. Nested, insertion-specific primers are used together with arbitrary degenerate primers (AD prim ...

Hairpin (hpRNA)-mediated gene silencing exploits a cellular mechanism that recognizes double-stranded RNA (dsRNA) and subjects it and its corresponding mRNA to a sequence-specific degradation. This phenomenon is known as posttranscriptional gene silencing (PTGS) in plants ...

In the postgenomic era, large-scale functional genomic approaches are necessary for converting sequence information into functional information. A para-genetic approach, called virus-induced gene silencing (VIGS), offers a rapid means of gaining insight into gene function in ...

T-DNA activation tagging is a method to generate dominant mutations in plants or plant cells by random insertion of a T-DNA carrying constitutive enhancer elements, which can cause transcriptional activation of flanking plant genes. The method consists of generating a large number of tra ...

Microarray technology has become increasingly useful in measuring expression levels of a large number of genes and part of a repertoire of functional genomic tools. We describe the methods of cDNA microarray preparation, the use, data collection, and initial data processing. The cDNA fra ...

The recent rapid developments in genomics tools, technologies, and bioinformatics have revolutionized gene expression analysis. It is now routine to measure gene expression modulation at the genomic level. GeneCalling� technology is an open architecture system capable of assa ...

To understand the function of all the genes in an organism, one needs to know not only which genes are expressed, when, and where, but also what the protein end products are and under which conditions they accumulate in certain tissues. Proteomics aims at describing the whole protein output of the genome ...

Recent high-throughput methods for the analysis of biological samples are raising the possibility of data integration between investigators and even across technology platforms. In plant biology, integration of data can be problematic, since heterogeneity of plant growth cond ...

Plants accumulate a very large number of small molecules (phytochemicals) with important functions in the ecology of plants and in the protection against biotic and abiotic stress conditions. Little is known on how phytochemical biosynthetic pathways are regulated, which is a key step to ...

Progress in the understanding of how cells perceive signals and how the perception of specific signals leads to cellular responses has been dramatic over the last decade. One of the many new aspects of cell signaling that has emerged is that several types of lipids play key roles in the transfer of info ...

Substantial evidence implicates important roles for both protein phosphorylation and protein degradation in regulation of plant defense responses. Therefore, interest is growing in applying proteomics techniques to investigate these posttranscriptional changes. We ...

Massively parallel signature sequencing is a sequencing-based method that provides quantitative gene expression data for nearly all transcripts in a particular ribonucleic acid sample. Although the sequencing technology is practiced as a service by a California-based compa ...

Identification of important transcripts from fungal pathogens and host plants is indispensable for full understanding the molecular events occurring during fungal-plant interactions. Recently, we developed an improved LongSAGE method called robust-long serial analys ...