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Title: Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress

Author
item COTSAFTIS, OLIVIER - University Of Adelaide
item PLETT, DARREN - University Of Adelaide
item JOHNSON, ALEXANDER - University Of Adelaide
item WALIA, HARKAMAL - University Of California
item Wilson, Clyde
item ISMAIL, ABDELBAGI - International Rice Research Institute
item CLOSE, TIMOTHY - University Of California
item TESTER, MARK - University Of Adelaide
item BAUMANN, UTE - University Of Adelaide

Submitted to: Molecular Plant
Publication Type: Review Article
Publication Acceptance Date: 8/27/2010
Publication Date: 1/1/2011
Citation: Cotsaftis, O., Plett, D., Johnson, A.A., Walia, H., Wilson, C., Ismail, A.M., Close, T.J., Tester, M., Baumann, U. 2011. Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress. Molecular Plant. 4(1):25-41.

Interpretive Summary: One of the major stresses limiting crop yields is salinity. Salinity tolerance is a complex trait requiring coordinated processes throughout the life cycle of a plant to enable growth on saline soils. In an earlier study, we documented the expression of rice genes in shoot tissues of a salt-sensitive cultivar (IR29), and the salt-tolerant (FL478) rice brought about by salinity stress. The present paper complements our earlier study on shoots by focusing on salinity-induced changes in gene expression in root tissues of IR29 and FL478, as well as the salt-tolerant rice, Pokkali. We also included the salt-tolerant rice, IR63731, and the salt-tolerant landrace Nona Bokra for comparison of salinity tolerance mechanisms. Currently, Pokkali and Nona Bokra are the two most common source genotypes for salinity-tolerance in rice-breeding programs. We found that in contrast to shoots, the roots of the tolerant FL478 had more transcripts controlled by salt than the sensitive IR29, perhaps indicating that a greater number of adaptive processes related to salinity tolerance occur in the roots than in the shoots. We relate the response of the tissue specific Na+ accumulation of the four genotypes to changes in root transcript profiles. Also documented is the response of several gene families known to be important in plant salinity tolerance? Finally, we identified some novel genes through their response to salt, transcript level and/or chromosomal position. These findings should aid cereal breeder, and other plant breeders, identify salt-tolerant germplasm. It also provides plant breeders with a rational basis by which they may develop salt-tolerant plants.

Technical Abstract: Elevated salinity imposes osmotic and ion toxicity stresses on living cells and requires a multitude of responses in order to enable plant survival. Building on earlier work profiling transcript levels in rice (Oryza sativa) shoots of FL478, a salt-tolerant indica recombinant inbred line, and IR29, a salt-sensitive cultivar, transcript levels were compared in roots of these two accessions as well as in the roots of two additional salt-tolerant indica genotypes, the landrace Pokkali and the recombinant inbred line IR63731. One aim of this study was to compare transcripts in the sensitive and the tolerant lines in order to identify genes likely to be involved in plant salinity tolerance, rather than in responses to salinity, per se. Transcript profiles of several gene families with known links to salinity tolerance are described (e.g. HKTs, NHXs). The putative function of a set of genes identified through their salt responsiveness, transcript levels and/or chromosomal location (i.e. underneath QTLs for salinity tolerance) is also discussed. Finally, the parental origin of the Saltol region in FL478 is further investigated. Overall, the dataset presented appears to be robust and it seems likely that this system could provide a reliable strategy for the discovery of novel genes involved in salinity tolerance.Elevated salinity imposes osmotic and ion toxicity stresses on living cells and requires a multitude of responses in order to enable plant survival. Building on earlier work profiling transcript levels in rice (Oryza sativa) shoots of FL478, a salt-tolerant indica recombinant inbred line, and IR29, a salt-sensitive cultivar, transcript levels were compared in roots of these two accessions as well as in the roots of two additional salt-tolerant indica genotypes, the landrace Pokkali and the recombinant inbred line IR63731. One aim of this study was to compare transcripts in the sensitive and the tolerant lines in order to identify genes likely to be involved in plant salinity tolerance, rather than in responses to salinity, per se. Transcript profiles of several gene families with known links to salinity tolerance are described (e.g. HKTs, NHXs). The putative function of a set of genes identified through their salt responsiveness, transcript levels and/or chromosomal location (i.e. underneath QTLs for salinity tolerance) is also discussed. Finally, the parental origin of the Saltol region in FL478 is further investigated. Overall, the dataset presented appears to be robust and it seems likely that this system could provide a reliable strategy for the discovery of novel genes involved in salinity tolerance.