Emerging Use of Gene Expression Microarrays in Plant Physiology

Abstract

Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

New approaches to Prunus transcriptome analysis

“…Currently, most microarray profiling systems employ glass slides containing thousands of anchored sequences of interest (Aharoni and Vorst 2001;Wullschleger and Difazio 2003). The development of custom microarrays with probe sets designed to detect individual exons, or using combinations of probes specific to exon and splice junction sequences, has overcome many of the obstacles encountered when analyzing EST/cDNA data and thus offers a rapid means of profiling RNA expression and processing in different biological contexts (Clark et al 2002).…”

“…For this reason and thanks to the availability of full genome sequence for some species, new tilling microarray platforms have been developed using different spaced oligonucleotides that span the entire genome of an organism (Yazaki et al 2007). However, further contributing to the limited sensitivity and specificity of this technology is the fact that detection is indirect, measured by fluorescent signal, and is thus subjected to a variety of confounding noise variables (Bellin et al 2009;Aharoni and Vorst 2001;Wullschleger and Difazio 2003).…”

Dissecting Out the Crosstalk Between Salinity and Hormones in Roots of Arabidopsis

“…Our study demonstrates that phytohormone-responsive genes from ABA, auxin ethylene, and cytokinin are involved in response to salt stress in Arabidopsis roots. We used the expression data available from microarrays, which is becoming a routine tool for the global analysis of gene expression in several organisms (Wullschleger and Difazio, 2003). It is often irresistable to correlate the expression data with biological functions of genes that show differential expression patterns.…”

Coordinated Genetic Regulation of Growth and Lignin Revealed by Quantitative Trait Locus Analysis of cDNA Microarray Data in an Interspecific Backcross of Eucalyptus

“…Microarrays have identified clusters of coexpressed genes (Eisen et al, 1998) and allowed inferences about biological processes implicated in plant development and environmental responses (Wullschleger and Difazio, 2003). Recently, the value of microarrays to elucidate the genetic control of gene expression variation was demonstrated in mice and Drosophila melanogaster (Karp et al, 2000;Eaves et al, 2002;Wayne and McIntyre, 2002).…”