title: Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms.
abstract: BACKGROUND
  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).
  
  
  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.
authors.affiliation: Systems Biology Research Centre, University of Skövde, 541 28 Skövde, Sweden.
authors.forename: Angelica
authors.initials: A
authors.lastname: Lindlöf
authors.affiliation: CropTailor AB, Department of Pure and Applied Biochemistry, Lund University, Box 124, SE 22100 Lund, Sweden; Department of Immunotechnology, Lund University, SE-22381, Lund, Sweden.
authors.forename: Aakash
authors.initials: A
authors.lastname: Chawade
authors.affiliation: Department of Biological and Environmental Sciences, University of Gothenburg, SE-40530, Gothenburg, Sweden.
authors.forename: Per
authors.initials: P
authors.lastname: Sikora
authors.affiliation: CropTailor AB, Department of Pure and Applied Biochemistry, Lund University, Box 124, SE 22100 Lund, Sweden; Department of Pure and Applied Biochemistry, Lund University, Box 124, SE 22100 Lund, Sweden.
authors.forename: Olof
authors.initials: O
authors.lastname: Olsson
mesh_terms: D002734:Chlorophyll / Q000378:metabolism; D003080:Cold Temperature; D055028:Comparative Genomic Hybridization; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D010766:Phosphorylation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D013312:Stress, Physiological; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors; D002734:Chlorophyll