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Title: Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage

Author
item WALIA, HARKAMAL - UC RIVERSIDE, CA
item Wilson, Clyde
item Zeng, Linghe
item ISMAIL, ABDELBAGI - INT'L RICE RESEARCH INST
item CONDAMINE, PASCAL - UC RIVERSIDE, CA
item CLOSE, TIMOTHY - UC RIVERSIDE, CA

Submitted to: Plant Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/2006
Publication Date: 12/12/2006
Citation: Walia, H., Wilson, C., Zeng, L., Ismail, A.M., Condamine, P., Close, T. 2006. Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage. Plant Molecular Biology. Vol 63:609-623

Interpretive Summary: There is significant genetic variation both within and between cereal crops in their ability to maintain significant growth and yield under saline conditions. Recent work on genetic mapping of cereals with common DNA probes indicates a highly conserved gene content and gene order within Poaceae. This finding coupled with the completion of the rice genome sequence (2004) has generated considerable interest in elucidating the physiological and genetic mechanisms that confer salt tolerance. An understanding of these mechanisms would provide a rationale basis to help develop more salt tolerant crops. Rice yield is most sensitive to salinity imposed during panicle initiation. We examined the response of salt-sensitive and salt tolerant cultivars. The physiological response indicated that tolerant genotypes maintained much lower shoot Na+ levels relative to salt-sensitive genotypes under salt stress. Gene expression studies showed that in salt-sensitive cultivars, a large number of genes were induced by salinity compared to tolerant lines. We specifically focused on the expression of SKC1, a cation transporter reported by others as a major source of variation in salt tolerance in rice. The transcript level of SKC1 did not change in response to salinity stress at panicle initiation stage in the shoot tissue of all four genotypes. However, we found the transcript level of SKC1 to be higher in tolerant japonica Agami relative to sensitive japonica M103 under control and stressed conditions during panicle initiation stage. Additionally, the transcript level of SKC1 was found to increase in the roots of salt-tolerant indicas (IR63731, Pokkali and FL478) during the early vegetative stage but not in the sensitive indica, IR29. This will be the focus of future investigations

Technical Abstract: Rice yield is most sensitive to salinity imposed during panicle initiation stage. In this study, we have focused on physiological and transcriptional responses of four rice genotypes exposed to salinity stress during panicle initiation. The genotypes selected included a pair of indicas (IR63731 and IR29) and a pair of japonica (Agami and M103) rice subspecies with contrasting salt tolerance. Physiological characterization showed that tolerant genotypes maintained a much lower shoot Na+ concentration relative to sensitive genotypes under salinity stress. Global gene expression analysis revealed a strikingly large number of genes which are induced by salinity stress in sensitive genotypes, IR29 and M103 relative to tolerant lines. We found 19 probe sets to be commonly induced in all four genotypes. We found several salinity modulated, ion homeostasis related genes from our analysis. We specifically focused on the expression of SKC1, a cation transporter reported by others as a major source of variation in salt tolerance in rice. The transcript abundance of SKC1 did not change in response to salinity stress at panicle initiation stage in the shoot tissue of all four genotypes. However, we found the transcript abundance of SKC1 to be significantly higher in tolerant japonica Agami relative to sensitive japonica M103 under control and stressed conditions during panicle initiation stage. Additionally, the transcript level of SKC1 was found to increase in the roots of salt-tolerant indicas (IR63731, Pokkali and FL478) during the early vegetative stage but not in the sensitive indica, IR29.