Phytohormone signaling pathway analysis method for comparing hormone responses in plant-pest interactions

Abstract

BackgroundPhytohormones mediate plant defense responses to pests and pathogens. In particular, the hormones jasmonic acid, ethylene, salicylic acid, and abscisic acid have been shown to dictate and fine-tune defense responses, and identification of the phytohormone components of a particular defense response is commonly used to characterize it. Identification of phytohormone regulation is particularly important in transcriptome analyses. Currently there is no computational tool to determine the relative activity of these hormones that can be applied to transcriptome analyses in soybean.FindingsWe 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.ConclusionsThis 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.

Jasmonate-dependent plant defenses mediate soybean thrips and soybean aphid performance on soybean

“…SA signaling pathway was found to mediate an effective defense response with SA-related transcripts induced as early as 6-12 h after aphid infestation in resistant plants compared to susceptible plants (Li et al 2008). Phytohormone analysis (Studham and MacIntosh 2012) to determine the extent of contribution of SA, JA, ET and ABA in plant response to aphids reinforces this finding. Further, a role for ABA as a decoy defense initiated by aphids to suppress activation of SA-mediated defenses was also suggested largely due to the massive induction of ABA-related transcripts in susceptible plants but not in the resistant plants.…”

“…MeJA not SA pretreatment reduces aphid populations Gene expression analysis from previous studies (Li et al 2008;Studham and MacIntosh 2012) and the current study suggests that SA-related genes are induced in response to soybean aphids (Fig. 2a).…”

Fatty acid changes in soybean (Glycine max) under soybean aphid (Aphis glycines) infestation and their implications on plant defense against insects

“…The reduction in PUFA under SBA infestation could partly be responsible for suppression of JA defense responses by limiting precursors of the JA pathway. This hypothesis of JA suppression by SBA is supported by a similar result by [50] who showed that long term exposure of soybean to SBA results in suppression of the JA response. Since there was an increase in expression of JA biosynthesis genes without a corresponding increase in the JA response, we also hypothesize that control of fatty acid metabolism in this system could be posttranscriptional.…”

“…We conducted an analysis of previous microarray data generated in the lab [50] to examine the effect of aphid infestation on expression of JA biosynthesis and response genes in soybean. While the biosynthesis genes were examined together, JAR1 was used to investigate the response to JA.…”

In-depth analysis of jasmonate-mediated indole-3-acetic acid (IAA) biosynthesis and its implication in plant development

“…In this framework, it is known that jasmonic acid (JA) and its metabolites, collectively known as jasmonates (JAs), are plant growth inhibitors, mainly involved in counteract biotic stress, i.e. against herbivore and pathogen attack (Antico et al 2012;Studham & MacIntosh 2012). Earlier observations reported the inhibition of primary root growth in Arabidopsis seedlings grown on media supplemented with 0.1 µM methyl jasmonate (MeJA) (Staswick et al 1992).…”