Dataset Information

Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms.

ABSTRACT:

Introduction

Low temperature is one of the major environmental factors that adversely affect plant growth and yield. Many cereal crops from tropical regions, such as rice, are chilling sensitive and, therefore, are affected already at <10 °C. Interestingly, it has been demonstrated that chilling susceptibility varies greatly among rice varieties, which indicates differences in the underlying molecular responses. Understanding these differences is vital for continued development of rational breeding and transgenic strategies for more tolerant varieties. Thus, in this study, we conducted a comparative global gene expression profiling analysis of the chilling tolerant varieties Sijung and Jumli Marshi (spp. Japonica) during early chilling stress (<24 h, 10 °C).

Methods and results

Global gene expression experiments were conducted with Agilent Rice Gene Expression Microarray 4 x 44 K. The analysed results showed that there was a relatively low (percentage or number) overlap in differentially expressed genes in the two varieties and that substantially more genes were up-regulated in Jumli Marshi than in Sijung but the number of down-regulated genes were higher in Sijung. In broad GO annotation terms, the activated response pathways in Sijung and Jumli Marshi were coherent, as a majority of the genes belonged to the catalytic, transcription regulator or transporter activity categories. However, a more detailed analysis revealed essential differences. For example, in Sijung, activation of calcium and phosphorylation signaling pathways, as well as of lipid transporters and exocytosis-related proteins take place very early in the stress response. Such responses can be coupled to processes aimed at strengthening the cell wall and plasma membrane against disruption. On the contrary, in Jumli Marshi, sugar production, detoxification, ROS scavenging, protection of chloroplast translation, and plausibly the activation of the jasmonic acid pathway were the very first response activities. These can instead be coupled to detoxification processes.

Conclusions

Based on the results inferred from this study, we conclude that different, but overlapping, strategies are undertaken by the two varieties to cope with the chilling stress; in Sijung the initial molecular responses seem to be mainly targeted at strengthening the cell wall and plasma membrane, whereas in Jumli Marshi the protection of chloroplast translation and detoxification is prioritized.

SUBMITTER: Lindlof A

PROVIDER: S-EPMC4431715 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Publications

Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms.

Lindlöf Angelica A Chawade Aakash A Sikora Per P Olsson Olof O

PloS one 20150514 5

<h4>Introduction</h4>Low temperature is one of the major environmental factors that adversely affect plant growth and yield. Many cereal crops from tropical regions, such as rice, are chilling sensitive and, therefore, are affected already at <10 °C. Interestingly, it has been demonstrated that chilling susceptibility varies greatly among rice varieties, which indicates differences in the underlying molecular responses. Understanding these differences is vital for continued development of ration ...[more]

PMID: 25973918

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Project description:Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in LTH, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in LTH and strong repression in IR29. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. In present study, comprehensive gene expression using an Affymetrix rice genome array revealed a diverse global transcription reprogramming between two rice genotypes under chilling stress and subsequent recovery conditions. The dominant change in gene expression at low temperature was up-regulation in the chilling-tolerant genotype and down-regulation in the chilling-sensitive genotype. Early responses to chilling stress common to both genotypes featured up-regulated genes related to transcription regulation and signal transduction, while functional categories of LR-chilling regulated genes were clearly diverse with a wide range of functional adaptations. At the end of the chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovery capacity at the transcriptional level. Finally, analysis of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, are involved in chilling stress tolerance.

Project description:The central role of transcriptional regulation in integrating various low temperature response mechanisms has been established in Arabidopsis, where the CBF/DREB regulon plays a prominent role during acclimation. Rice is sensitive to chilling but many japonica cultivars can survive continuous exposure to as low as 10oC for up to 7 days during the most critical stage of seedling establishment better than most indica cultivars. The transcriptional regulatory networks that define this variation have not been studied in detail as cold acclimation has been scrutinized in Arabidopsis. Towards the comparison of the compositional complexity of low temperature response regulons of rice and Arabidopsis, we used the cultivar Nipponbare for genome-wide survey of regulatory clusters by integrative analysis of promoter architectures and temporal expression profiles during exposure to 10oC at narrow time intervals. Temporal profiles revealed major clusters of genes that were induced within the initial 24 hours. These clusters were further defined by common features of having either CRT/DRE-like elements, as1/ocs-like elements or both in their promoters. Genes containing as1/ocs-like elements with or without CRT/DRE, but not those containing only CRT/DRE-like elements were induced by exogenous H2O2 but not by ABA at ambient temperature, suggesting that they belong to a potential regulon (ROS-bZIP – as1/ocs module) that responds to elevated levels of reactive oxygen species (ROS) during the initial stages of stress. Parallel analysis of transcription factors during the initial 12 hours revealed candidate regulator(s) of this putative early response regulon. Cultivar-specific expression signatures of selected members of this regulatory cluster were also positively correlated with genotypic variation in chilling tolerance. We hypothesized that the ROS-bZIP – as1/ocs cluster has important roles in configuring the transcriptome of rice seedlings during the early stages of chilling stress and it appears to be independent of ABA and functions in parallel to the CBF/DREB regulon. Keywords: time course (response to low temperature)

Dataset Information

Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms.

Introduction

Methods and results

Conclusions

Publications

Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms.

Similar Datasets

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