One of the major objectives of Italian rice (Oryza sativa L.) breeding programs is the development of less water-demanding varieties, for the adaptation of rice to suboptimal climate and soil conditions. Polyethylene glycol (PEG)-mediated osmotic stress is an experimental systems which decreases the water potential of the nutrient solution and therefore it has been often used to study drought response in plants. Previously, we performed a physiological characterization of 17 Italian rice cultivars for their response to PEG-mediated osmotic treatment. Differential responses among the genotypes were highlighted and two cultivars showing opposite phenotypes were selected for transcriptome analysis: the high sensitive cultivar Loto and the high tolerant Eurosis. A RNA-Seq analysis (Illumina technology) was performed on leaf and root samples of these cultivars, after 3h and 24h of osmotic stress treatment. The analysis of transcriptomic data revealed that a 3h-treatment led to a substantial modulation of genes in the roots of Eurosis, whereas fewer DEGs were called in the roots of the sensitive cultivar Loto. After 24h of treatment, a similar number of DEGs was found in Eurosis and Loto. In leaves, the highest number of DEGs was observed in Loto after 24h of stress treatment. GO enrichment analysis of DEGs in the various contrasts highlighted some differences between the cultivars, with several genotype-specific GO terms (i.e. enriched GO terms from one genotype/tissue/treatment missing in the alternative genotype in the same tissue/treatment). Some enriched GO terms specific to the tolerant genotype Eurosis were related to chromatin and cytoskeleton. Many genes associated with these GO terms were down-regulated in 3h-treated Eurosis roots, whereas in Loto they were down-regulated only after 24h, suggesting a delay in the Loto response. These data indicated a different modulation of gene sets between the tolerant and the sensitive cultivars. In particular, Eurosis showed an earlier regulation of gene expression in response to osmotic stress which is not paralleled, at least at early stages, in Loto. The analysis of the expression data is in progress to reveal genes putatively responsible for the contrasting phenotypes of the analyzed genotypes. Many genes showed a contrasting regulation between the two cultivars, especially in roots at 3h of stress treatment; among them, several transcription factors and two helicases encoding genes. Helicases are involved in RNA metabolism and may be important for increasing transcriptional and translational activity under stress conditions. Interestingly, some myb and WRKY genes seemed to be involved in the different response to the osmotic stress, since they showed a different regulation in the two genotypes. For instance in roots, at 3h of treatment, OsMYB55, known to be involved in the heat stress response, and the myb-related NIGT1 gene, known to be involved in salt stress and nitrate response, were up-regulated only in Eurosis; WRKY30 was up-regulated in Loto and down-regulated in Eurosis, whereas WRKY106 and WRKY117 were down-regulated only in Eurosis. This work was supported by Progetto AGER, grant n° 2010-2369 (RISINNOVA - Integrated genetic and genomic approaches for new Italian rice breeding strategies).
Dissection of the response to osmotic stress in Italian rice (Oryza sativa L.) cultivars
Baldoni E;Locatelli F;Mattana M;Genga A
2014
Abstract
One of the major objectives of Italian rice (Oryza sativa L.) breeding programs is the development of less water-demanding varieties, for the adaptation of rice to suboptimal climate and soil conditions. Polyethylene glycol (PEG)-mediated osmotic stress is an experimental systems which decreases the water potential of the nutrient solution and therefore it has been often used to study drought response in plants. Previously, we performed a physiological characterization of 17 Italian rice cultivars for their response to PEG-mediated osmotic treatment. Differential responses among the genotypes were highlighted and two cultivars showing opposite phenotypes were selected for transcriptome analysis: the high sensitive cultivar Loto and the high tolerant Eurosis. A RNA-Seq analysis (Illumina technology) was performed on leaf and root samples of these cultivars, after 3h and 24h of osmotic stress treatment. The analysis of transcriptomic data revealed that a 3h-treatment led to a substantial modulation of genes in the roots of Eurosis, whereas fewer DEGs were called in the roots of the sensitive cultivar Loto. After 24h of treatment, a similar number of DEGs was found in Eurosis and Loto. In leaves, the highest number of DEGs was observed in Loto after 24h of stress treatment. GO enrichment analysis of DEGs in the various contrasts highlighted some differences between the cultivars, with several genotype-specific GO terms (i.e. enriched GO terms from one genotype/tissue/treatment missing in the alternative genotype in the same tissue/treatment). Some enriched GO terms specific to the tolerant genotype Eurosis were related to chromatin and cytoskeleton. Many genes associated with these GO terms were down-regulated in 3h-treated Eurosis roots, whereas in Loto they were down-regulated only after 24h, suggesting a delay in the Loto response. These data indicated a different modulation of gene sets between the tolerant and the sensitive cultivars. In particular, Eurosis showed an earlier regulation of gene expression in response to osmotic stress which is not paralleled, at least at early stages, in Loto. The analysis of the expression data is in progress to reveal genes putatively responsible for the contrasting phenotypes of the analyzed genotypes. Many genes showed a contrasting regulation between the two cultivars, especially in roots at 3h of stress treatment; among them, several transcription factors and two helicases encoding genes. Helicases are involved in RNA metabolism and may be important for increasing transcriptional and translational activity under stress conditions. Interestingly, some myb and WRKY genes seemed to be involved in the different response to the osmotic stress, since they showed a different regulation in the two genotypes. For instance in roots, at 3h of treatment, OsMYB55, known to be involved in the heat stress response, and the myb-related NIGT1 gene, known to be involved in salt stress and nitrate response, were up-regulated only in Eurosis; WRKY30 was up-regulated in Loto and down-regulated in Eurosis, whereas WRKY106 and WRKY117 were down-regulated only in Eurosis. This work was supported by Progetto AGER, grant n° 2010-2369 (RISINNOVA - Integrated genetic and genomic approaches for new Italian rice breeding strategies).I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
