%0 Journal Article
%T Phytohormone signaling pathway analysis method for comparing hormone responses in plant-pest interactions
%A Matthew E Studham
%A Gustavo C MacIntosh
%J BMC Research Notes
%D 2012
%I BioMed Central
%R 10.1186/1756-0500-5-392
%X We developed a pathway analysis method that provides a broad measure of the activation or suppression of individual phytohormone pathways based on changes in transcript expression of pathway-related genes. The magnitude and significance of these changes are used to determine a pathway score for a phytohormone for a given comparison in a microarray experiment. Scores for individual hormones can then be compared to determine the dominant phytohormone in a given defense response. To validate this method, it was applied to publicly available data from previous microarray experiments that studied the response of soybean plants to Asian soybean rust and soybean cyst nematode. The results of the analyses for these experiments agreed with our current understanding of the role of phytohormones in these defense responses.This method is useful in providing a broad measure of the relative induction and suppression of soybean phytohormones during a defense response. This method could be used as part of microarray studies that include individual transcript analysis, gene set analysis, and other methods for a comprehensive defense response characterization.Plant hormones are involved in many aspects of plant development and responses to biotic and abiotic stresses. The three major phytohormones responsible for mediating defense responses to pests and pathogens are jasmonic acid (JA), ethylene (ET), and salicylic acid (SA) [1-3]. Recently, the participation of other hormones in defense signaling has become evident [3]. Among these, abscisic acid (ABA), a hormone normally associated with responses to abiotic stress, has been recognized as an important fine-tune regulator of defenses [4,5].The production of these defense hormones is induced upon attack and it mediates a series of effective responses that can involve production of antibiotic compounds, production of volatiles emitted to attract predators of the attacker or discourage further attacks, programmed cell death to deprive t
%U http://www.biomedcentral.com/1756-0500/5/392