ARS | Publication request: GENOMIC ANALYSIS OF THE EARLY RESPONSES OF DEVELOPING RICE SEEDLINGS TO COLD STRESS

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 15, 2006
Publication Date: January 15, 2006
Citation: Cheng, C., De Los Reyes, B.G., Zhang, Y., Ressom, H., Jia, Y., Yun, S.J. 2006. Genomic analysis of the early responses of developing rice seedlings to cold stress [abstract]. In: Proceedings of the XIV Annual International Plant & Animal Genome Conference, Janaury 14-18, 2006, San Diego, California. p. 734.

Technical Abstract: Most rice cultivars are highly sensitive to low temperatures particularly during the early stages of seedling establishment and flowering. Seedling cold tolerance, which is exhibited by many japonica cultivars is an important component of seedling vigor and yield potential. Given the biochemical complexity of the adaptive responses, the molecular genetic basis of the differential thermo-sensitivity of indica and japonica subspecies must rely on intricate mechanisms that integrate a plethora of biochemical changes. To address this hypothesis, we developed a collection of Expressed Sequence Tags (EST) enriched with cold stress-upregulated genes. Characterization of few candidates from this library suggests that the early response genes in the genetic circuit are homologous to the genes associated with cold acclimation and salt stress responses in Arabidopsis. We developed a microarray platform consisting of more than 6,000 cDNAs from our cold stress library and another library developed by IRRI from drought stressed rice. We are currently using this microarray to identify in a semi-global scale the early cold stress-responsive genes from the tolerant japonica cultivar CT6748-8-CA-17. Here we present the analysis of the cold stress gene expression highlighting the physiological significance of the early gene expression responses based on the upregulated component of the transcriptome. In summary, the transcriptome of developing rice seedlings (cv. CT6748-8-CA-17) under low temperature stress (13 degrees C) was investigated using a microarray containing more than 6,000 cDNAs from cold and drought stress EST libraries. Analysis of gene expression at five time points during the first 24 hours of stress indicated that the early responses involve a general trend of increasing number of stress-responsive genes from the onset of cold stress. A state of stress was apparent 2 hours after the initiation of cold treatment as indicated by low and high numbers of upregulated and downregulated genes, respectively. The transcriptome profiles at 0.5, 2, 6, 12, 24 hr. also indicated the occurrence of two distinct waves (groups) of gene expression involved in related biochemical processes. Group-I genes (early and rapid) were induced during the first 2 hours and suggestive of a general response to cold shock. This group is composed of proteins involved in the activation of general transcription and translation machineries, fatty acid desaturation, signal transduction, protein chaperoning and degradation and potential defenses against cellular toxicity. Group-II (early but slow) were induced between 6 to 24 hrs. Genes encoding molecular chaperons, signal transduction proteins, stress-related transcription factors, wounding-associated and cellular toxicity defense proteins, energy synthesis, primary metabolic enzymes, and intracellular transport and trafficking proteins showed different magnitudes and patterns of induction are included in this group. Our current results reveal the relative complexity of the initial cellular events that are probably critical in the activation and integration of stress defense mechanisms. These early events are probably crucial for adaptation during more prolonged exposure to cold stress.