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. 2009 Jan;69(1-2):133-53.
doi: 10.1007/s11103-008-9412-7. Epub 2008 Oct 19.

Expression profiling of rice cultivars differing in their tolerance to long-term drought stress

Thomas Degenkolbe  1 , Phuc Thi Do, Ellen Zuther, Dirk Repsilber, Dirk Walther, Dirk K Hincha, Karin I Köhl
Affiliations

Expression profiling of rice cultivars differing in their tolerance to long-term drought stress

Thomas Degenkolbe et al. Plant Mol Biol. 2009 Jan.

Abstract

Understanding the molecular basis of plant performance under water-limiting conditions will help to breed crop plants with a lower water demand. We investigated the physiological and gene expression response of drought-tolerant (IR57311 and LC-93-4) and drought-sensitive (Nipponbare and Taipei 309) rice (Oryza sativa L.) cultivars to 18 days of drought stress in climate chamber experiments. Drought stressed plants grew significantly slower than the controls. Gene expression profiles were measured in leaf samples with the 20 K NSF oligonucleotide microarray. A linear model was fitted to the data to identify genes that were significantly regulated under drought stress. In all drought stressed cultivars, 245 genes were significantly repressed and 413 genes induced. Genes differing in their expression pattern under drought stress between tolerant and sensitive cultivars were identified by the genotype x environment (G x E) interaction term. More genes were significantly drought regulated in the sensitive than in the tolerant cultivars. Localizing all expressed genes on the rice genome map, we checked which genes with a significant G x E interaction co-localized with published quantitative trait loci regions for drought tolerance. These genes are more likely to be important for drought tolerance in an agricultural environment. To identify the metabolic processes with a significant G x E effect, we adapted the analysis software MapMan for rice. We found a drought stress induced shift toward senescence related degradation processes that was more pronounced in the sensitive than in the tolerant cultivars. In spite of higher growth rates and water use, more photosynthesis related genes were down-regulated in the tolerant than in the sensitive cultivars.

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Figures

Fig. 1
Fig. 1
Total dry weight of the rice cultivars Nipponbare (NB), Taipei (TP), LC-93-4 (LC) or IR57311 (IR) after 18 days of growth under control or drought treatment. Mean values from three experiments with five plants per cultivar, experiment and treatment condition. Biomass of cultivars was compared within a condition, different letters indicate that log-transformed means differ significantly (α = 0.05). F for condition = 357, p < 0.001; F for condition × cultivar = 0.46, p = 0.708
Fig. 2
Fig. 2
Gel picture of PCR amplicons for subspecies-specific STS markers S01022, S03020, S03136, S04128, S07011, S070103 with expected fragment sizes for japonica (J) and indica (I) cultivars. Cultivars Nipponbare (NB), Taipei (TP), LC-93-4 (LC) and IR57311 (IR)
Fig. 3
Fig. 3
Venn diagrams for groups of genes with significantly different expression levels. Numbers indicate the number of genes in a given group. Numbers in the circle overlap indicate the number of genes common to both compared groups, numbers outside the overlap indicate the number of genes exclusive to the group defined by the criteria given above the circle. a Comparison of significantly differently expressed genes between tolerant (T) and sensitive (S) cultivars under control condition (cT − cS) and under drought stress conditions (dT − dS). b Comparison of significantly drought-repressed genes in the tolerant group (dT − cT) and the sensitive group (dS − cS). c. Comparison of significantly drought-induced genes, abbreviations as in a. d Comparison of genes that were significantly drought induced or repressed in all cultivars taken together (d − c) with genes that showed a significant condition x tolerance group interaction effect
Fig. 4
Fig. 4
Induction or repression (log-scale) of genes under drought treatment in all four cultivars encoding enzymes involved in metabolism grouped in functional bins according to MapMan. Red indicates down-regulated, blue up-regulated genes
Fig. 5
Fig. 5
Published QTL related to drought tolerance in rice with a size below 5 Mb and location of genes with a significant E effect (circles) or a significant G × E effect (squares). Red symbols indicate repression of gene expression or interaction factor <−1.5, blue symbol induction of gene expression or interaction factor >1.5
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