Transcriptome responses to combinations of stresses in Arabidopsis

Abstract

Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity have profound effects on crop performance and yields. Thus, delineation of the regulatory networks and metabolic pathways responding to single and multiple concurrent stresses is required for breeding and engineering crop stress tolerance. Many studies have described transcriptome changes in response to single stresses. However, exposure of plants to a combination of stress factors may require agonistic or antagonistic responses or responses potentially unrelated to responses to the corresponding single stresses. To analyze such responses, we initially compared transcriptome changes in 10 Arabidopsis (Arabidopsis thaliana) ecotypes using cold, heat, high-light, salt, and flagellin treatments as single stress factors as well as their double combinations. This revealed that some 61% of the transcriptome changes in response to double stresses were not predic from the responses to single stress treatments. It also showed that plants prioritized between potentially antagonistic responses for only 5% to 10% of the responding transcripts. This indicates that plants have evolved to cope with combinations of stresses and, therefore, may be bred to endure them. In addition, using a subset of this data from the Columbia and Landsberg erecta ecotypes, we have delineated coexpression network modules responding to single and combined stresses.

Figure 1.

Clustering of transcripts to predefined expression profiles generating the transcriptional response modes. For each stress combination, transcript sets were created by the union of the 500 most significant transcripts for each single stress and for the combination. These transcripts were clustered to 20 predefined expression profiles, each categorizing a potential expression change that may occur when multiple stresses are applied. Each transcript was assigned to the profile with the highest Pearson correlation coefficient. Boxes at left represent the 20 predefined expression profiles described by the transcript expression pattern for stress 1 (S1), stress 2 (S2), and the combination of stress 1 and stress 2 (S1+S2). The dotted line represents transcript expression with no change compared with the control. In the boxes at right, each column represents the union of the two single stresses and the combined stress for a given double stress experiment. In each box, the value and color represents the percentage of transcripts that correlate with the particular predefined expression profile (green is higher). The transcriptional response modes are composed of a given set of the predefined expression profiles as indicated on the right: combinatorial, similar levels in the two individual stresses but a different response to combined stresses; canceled, transcript response to either or both individual stresses returned to control levels; prioritized, opposing responses to the individual stresses and one stress response prioritized in response to combined stresses; independent, response to only one single stress and a similar response to combined stresses; similar, similar responses to both individual stresses and to combined stresses. HL, High light.

Figure 2.

Overview of the mode of responses for the combined stress experiments, showing the percentage of transcript responses that cluster in each response mode (A) and per stress combination (B). Combinatorial, Similar levels in the two individual stresses but a different response to combined stresses; canceled, transcript response to either or both individual stresses returned to control levels; prioritized, opposing responses to the individual stresses and one stress response prioritized in response to combined stresses; independent, response to only one single stress and a similar response to combined stresses; similar, similar responses to both individual stresses and to combined stresses. HL, High light.

Figure 3.

Cumulative log-fold changes of the 500 most significantly responding transcripts in the single stress experiments when the particular stress is combined with another stress in a double stress experiment. The extent of the response of significant transcripts upon combination with the other stress in a double stress experiment (e.g. cold and FLG) is given by the length of the bars from the center, where longer bars represent a greater response of the transcripts. For example, when the plants are exposed to both heat and high light (HL), there is a higher response of the high-light transcripts compared with the heat transcripts.

Figure 4.

Relationships between four modules and the 11 stress treatments. The heat maps show transcript levels across treatments. Magenta is positive expression, black is neutral, and green is negative expression in comparison with the control treatment. Treatments are shown on the bottom as horizontal axis labels. HL, High light. Bar plots are eigengene values (i.e. the first principal component) calculated from the singular value composition for each module.