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Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms
University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. (Bioinformatik, Bioinformatics)ORCID iD: 0000-0003-1837-429X
CropTailor AB, Department of Pure and Applied Biochemistry, Lund University, Lund, Sweden / Department of Immunotechnology, Lund University, Lund, Sweden.
Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
CropTailor AB, Department of Pure and Applied Biochemistry, Lund University, Lund, Sweden / Department of Pure and Applied Biochemistry, Lund University, Lund, Sweden.
2015 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 10, no 5, article id e0125385Article in journal (Refereed) Published
Abstract [en]

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 4x44K. 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.

Place, publisher, year, edition, pages
Public Library of Science , 2015. Vol. 10, no 5, article id e0125385
Keywords [en]
cold stress, rice, Oryza sativa, microarray, data analysis, systems biology, bioinformatics
National Category
Bioinformatics and Systems Biology
Research subject
Bioinformatics
Identifiers
URN: urn:nbn:se:his:diva-10985DOI: 10.1371/journal.pone.0125385ISI: 000354545600015PubMedID: 25973918Scopus ID: 2-s2.0-84929353184OAI: oai:DiVA.org:his-10985DiVA, id: diva2:815939
Note

CC BY 4.0

Available from: 2015-06-02 Created: 2015-06-02 Last updated: 2022-05-06Bibliographically approved

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Lindlöf, Angelica

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