A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus

Abstract

In this study, genome-wide expression profiling based on Affymetrix ATH1 arrays was used to identify discriminating responses of Arabidopsis thaliana to five herbicides, which contain active ingredients targeting two different branches of amino acid biosynthesis. One herbicide contained glyphosate, which targets 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), while the other four herbicides contain different acetolactate synthase (ALS) inhibiting compounds. In contrast to the herbicide containing glyphosate, which affected only a few transcripts, many effects of the ALS inhibiting herbicides were revealed based on transcriptional changes related to ribosome biogenesis and translation, secondary metabolism, cell wall modification and growth. The expression pattern of a set of 101 genes provided a specific, composite signature that was distinct from other major stress responses and differentiated among herbicides targeting the same enzyme (ALS) or containing the same chemical class of active ingredient (sulfonylurea). A set of homologous genes could be identified in Brassica napus that exhibited a similar expression pattern and correctly distinguished exposure to the five herbicides. Our results show the ability of a limited number of genes to classify and differentiate responses to closely related herbicides in A. thaliana and B. napus and the transferability of a complex transcriptional signature across species.

Fig. 1

Composite signature of transcriptional responses of 101 marker genes to herbicide treatments and selected stresses. a Clustering of the responses to five herbicide treatments (Table S4). Group 1 marker differentiates all ALS-inhibitors from EPSPS-inhibitor and group 2 marker differentiates among four ALS inhibitors and towards EPSPS-inhibitor. The TIGR/TAIR 6 genome annotation code was used as the gene identifier. b The two top correlated stress response patterns with each herbicide (Table S8) were assorted to the gene matrix of panel A showing a signature clearly distinct from all herbicides in all seven cases. Red color indicates up-regulation of transcripts in treatment group compared to control; blue indicates down-regulation and black indicates no change. Abbreviations: ARS [Arsenal™, imazapyr active ingredient (a.i.)], BEA (Beacon™, primisulfuron a.i.), FIR (FirstRate™, cloransulam a.i.), OUS (Oust™, sulfometuron a.i.), ROU (Roundup Original™, glyphosate a.i.), Nor norflurazon, UV-B ultraviolet B, P infest: Phytophthora infestans; P syrin p: Pseudomonas syringae pv. phaseolicola; P syrin t: Pseudomonas syringae pv. tomato avr Rpm1; Met jas: methyl jasmonate

Fig. 2

Classification of independent Arabidopsis experiments based on leave-one-out cross-validation and association of B. napus signatures with reduced Arabidopsis data set. a Canonical coefficients of a diagonal discriminant analysis based on leave-one-out cross-validation with the transcriptional responses of 101 Arabidopsis marker genes. All 15 experiments were perfectly classified to the correct herbicide signature (“Materials and methods”). b Canonical coefficients of a diagonal discriminant analysis with the reduced data set of 23 Arabidopsis genes and orthologous B. napus data. Even with this reduced data set the Arabidopsis signatures are correctly classified with the respective herbicide treatments (symbols). Furthermore, the signatures of the orthologous B. napus genes (numbers) are correctly associated to the Arabidopsis herbicide treatments (symbols). With only two components displayed, both the B. napus BEA and FIR expression patterns seem to be related to the A. thaliana BEA data; however, with all four components they are correctly differentiated (not shown). Abbreviations: ARS [triangle 1, Arsenal™, imazapyr active ingredient (a.i.)], BEA (square, 2, Beacon™, primisulfuron a.i.); FIR (star, 3, FirstRate™, cloransulam a.i.); OUS (rhombus, 4: Oust™, sulfometuron a.i.); ROU (sphere, 5, Roundup Original™, glyphosate a.i.)