Identification of genes induced upon water-deficit stress in a drought-tolerant rice cultivar (original) (raw)
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Identification of functional candidate genes for drought tolerance in rice
Molecular Genetics and Genomics, 2007
Drought tolerance (DT) in rice is known to be controlled by many quantitative trait loci (QTLs) and involved diVerential expression of large numbers of genes, but linking QTLs with their underlying genes remains the most challenging issue in plant molecular biology. To shed some light on this issue, diVerential gene expression in response to PEG simulated drought in 3 unique genetic materials (a lowland rice, IR64 and its derived line, PD86 which has 11 introgressed DT QTLs, and a upland rice IRAT109) was investigated using a PCR-based subtractive hybridization strategy. More than 300 unique subtracted cDNA sequences, covering genes of diverse cellular activities and functions, were identiWed and conWrmed by semiquantitative and quantitative RT-PCR. Detailed bioinformatics analyses of the data revealed two interesting results. First, the levels and mechanisms of DT of the three rice lines were associated with the number and types of diVerentially expressed genes, suggesting diVerent DT mechanisms in rice are controlled by diVerent sets of genes and diVerent metabolic pathways, and most diVerentially expressed genes under drought were able to contribute to DT. Second, there appeared a high correspondence in genomic location between DT QTLs and clusters of diVerentially expressed genes in rice, suggesting some DT QTLs may represent clusters of co-regulated and functionally related genes. Thus, diVerential gene expression analyses using genetically characterized materials can provide additional insights into the molecular basis of QTLs and convergent evidence to shortlist the candidate genes for target QTLs.
Investigation of the effect of drought stress on the rice transcriptome
2008
Abiotic stresses such as drought are very important factors that endanger the crop production and stability. Plant root is the most important organ for uptake of water, therefore it plays important role in tolerance to osmotic and drought stresses. Plants developing stronger and deeper roots suffer less from water deficit. The aim of our work was to understand and improve the drought stress-tolerance in cereals by analyzing the transcriptional changes in the root system of different rice cultivars under drought stress conditions. According to the results of the DNA chip hybridizations the response of the genes to the drought stress is altered in roots during the day. Further experiments showed that the expression patterns of genes in cultivars with distinct levels of stress tolerance are different, and that may correlate to their stress tolerance.
Plant Biotechnology Journal, 2010
Genetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stress-responsive transcriptome between drought-tolerant (DT) landraces/genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechanisms involved in stress tolerance. Here, we report transcriptome analysis in a highly DT rice landrace, Nagina 22 (N22), versus a high-yielding but drought-susceptible rice variety IR64. Both genotypes exhibited a diverse global transcriptional response under normal and drought conditions. Gene ontology (GO) analysis suggested that drought tolerance of N22 was attributable to the enhanced expression of several enzyme-encoding genes. Drought susceptibility of IR64 was attributable to significant down-regulation of regulatory components that confer drought tolerance. Pathway analysis unravelled significant up-regulation of several components of carbon fixation, glycolysis/gluconeogenesis and flavonoid biosynthesis and down-regulation of starch and sucrose metabolism in both the cultivars under drought. However, significant up-regulation of α-linolenic acid metabolic pathway observed in N22 under drought appears to be in good agreement with high drought tolerance of this genotype. Consensus cis-motif profiling of drought-induced co-expressed genes led to the identification of novel cis-motifs. Taken together, the results of the comparative transcriptome analysis led to the identification of specific genotype-dependent genes responsible for drought tolerance in the rice landrace N22.
Plant biotechnology journal, 2011
Genetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stress-responsive transcriptome between drought-tolerant (DT) landraces/genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechanisms involved in stress tolerance. Here, we report transcriptome analysis in a highly DT rice landrace, Nagina 22 (N22), versus a high-yielding but drought-susceptible rice variety IR64. Both genotypes exhibited a diverse global transcriptional response under normal and drought conditions. Gene ontology (GO) analysis suggested that drought tolerance of N22 was attributable to the enhanced expression of several enzyme-encoding genes. Drought susceptibility of IR64 was attributable to significant down-regulation of regulatory components that confer drought tolerance. Pathway analysis unravelled significant up-regulation of several components of carbon fixation, glycolysis/gluconeogenesis and flavonoid biosynthesis and down-regulation of starch and sucrose metabolism in both the cultivars under drought. However, significant up-regulation of α-linolenic acid metabolic pathway observed in N22 under drought appears to be in good agreement with high drought tolerance of this genotype. Consensus cis-motif profiling of drought-induced co-expressed genes led to the identification of novel cis-motifs. Taken together, the results of the comparative transcriptome analysis led to the identification of specific genotype-dependent genes responsible for drought tolerance in the rice landrace N22.
Expression profiling of rice cultivars differing in their tolerance to long-term drought stress
Plant Molecular Biology, 2009
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 droughtsensitive (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 9 environment (G 9 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 9 E interaction colocalized 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 9 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.
Journal of Experimental Botany, 2006
The impacts of drought on plant growth and development limit cereal crop production worldwide. Rice (Oryza sativa) productivity and production is severely affected due to recurrent droughts in almost all agroecological zones. With the advent of molecular and genomic technologies, emphasis is now placed on understanding the mechanisms of genetic control of the droughtstress response. In order to identify genes associated with water-stress response in rice, ESTs generated from a normalized cDNA library, constructed from droughtstressed leaf tissue of an indica cultivar, Nagina 22 were used. Analysis of 7794 cDNA sequences led to the identification of 5815 rice ESTs. Of these, 334 exhibited no significant sequence homology with any rice ESTs or full-length cDNAs in public databases, indicating that these transcripts are enriched during drought stress. Analysis of these 5815 ESTs led to the identification of 1677 unique sequences. To characterize this drought transcriptome further and to identify candidate genes associated with the drought-stress response, the rice data were compared with those for abiotic stressinduced sequences obtained from expression profiling studies in Arabidopsis, barley, maize, and rice. This comparative analysis identified 589 putative stressresponsive genes (SRGs) that are shared by these diverse plant species. Further, the identified leaf SRGs were compared to expression profiles for a drought-stressed rice panicle library to identify common sequences. Significantly, 125 genes were found to be expressed under drought stress in both tissues. The functional classification of these 125 genes showed that a majority of them are associated with cellular metabolism, signal transduction, and transcriptional regulation.
Differential Expressions of Two-Component Element Genes in Rice Under Drought Stress
Acta Agronomica Sinica, 2009
The objectives of this study were to gain insight into the temporal and spatial expression patterns of two-component system (TCS) genes in rice (Oryza sativa L.) under drought stress and to understand the relationship between TCS gene expression and drought resistance. Using a whole rice genome microarray, the expression profiles of TCS genes of rice lines with different drought resistance were analyzed at various growth stages. The TCS genes showed greatly difference of expression pattern in various organs but in similar patterns in the same tissues at different stages. Genes for type-A response regulator (RR), a negative regulator of cytokinin (CK) signaling, were mostly repressed by drought stress, whereas, genes for type-B RR with an opposite role to type-A RR were mostly induced by drought stress. These changes were supposed to be related to the enhancement of CK signaling under drought stress. This supposition was confirmed by the down regulation of ethylene receptor genes and the cross-talk of hormones under drought condition. The His kinase genes (HK5 and HK3) that are homologous to CK receptor genes (AHK2, AHK3, and CRE1) in Arabidopsis were induced by drought stress. However, HK6 homologous to AHK5 (CK-independent 2, CKI2) was repressed when exposed to drought stress. These results provided further confirmations of the above supposition. In drought resistant introgression lines and IR64, no significant differences of TCS gene expression profiles were observed under drought stress. This result indicates that the TCS genes are probably in relation to drought responsiveness.
Aob Plants, 2021
Drought is one of the most critical abiotic stresses that threaten crop production worldwide. This stress affects the rice crop in all stages of rice development; however, the occurrence during reproductive and grain-filling stages has the most impact on grain yield. Although many global transcriptomic studies have been performed during the reproductive stage in rice, very limited information is available for the grain-filling stage. Hence, we intend to investigate how the rice plant responds to drought stress during the grain-filling stage and how the responses change over time under field conditions. Two rice genotypes were selected for RNA-seq analysis: '4610', previously reported as a moderately tolerant breeding line, and Rondo, an elite indica rice cultivar susceptible to drought conditions. Additionally, 10 agronomic traits were evaluated under normal irrigated and drought conditions. Leaf tissues were collected during grain-filling stages at two time points, 14 and 21 days after the drought treatment, from both the drought field and normal irrigated field conditions. Based on agronomic performances, '4610' was less negatively affected than Rondo under mild drought conditions, and expression profiling largely aligned with the phenotypic data. The transcriptomic data indicated that, in general, '4610' had much earlier responses than its counterpart in mitigating the impact of drought stress. Several key genes and gene families related to drought stress or stress-related conditions were found differentially expressed in this study, including transcription factors, drought tolerance genes and reactive oxygen species scavengers. Furthermore, this study identified novel differentially expressed genes (DEGs) without function annotations that may play roles in drought tolerance-related functions. Some of the important DEGs detected in this study can be targeted for future research.
Identification of Novel Stress-responsive Transcription Factor Genes in Rice by cDNA Array Analysis
Journal of Integrative Plant Biology, 2006
Numerous studies have shown that array of transcription factors has a role in regulating plant responses to environmental stresses. Only a small portion of them however, have been identified or characterized. More than 2 300 putative transcription factors were predicted in the rice genome and more than half of them were supported by expressed sequences. With an attempt to identify novel transcription factors involved in the stress responses, a cDNA array containing 753 putative rice transcription factors was generated to analyze the transcript profiles of these genes under drought and salinity stresses and abscisic acid treatment at seedling stage of rice. About 80% of these transcription factors showed detectable levels of transcript in seedling leaves. A total of 18 up-regulated transcription factors and 29 down-regulated transcription factors were detected with the folds of changes from 2.0 to 20.5 in at least one stress treatment. Most of these stress-responsive genes have not been reported and the expression patterns for five genes under stress conditions were further analyzed by RNA gel blot analysis. These novel stress-responsive transcription factors provide new opportunities to study the regulation of gene expression in plants under stress conditions.(Managing editor: Li-Hui Zhao)
TRANSCRIPTOMIC ANALYSIS FOR TWO EGYPTIAN RICE CULTIVARS (Oryza sativa) UNDER DROUGHT STRESS
Egyptian Journal of Genetics and Cytology, 2020
Rice (Oryza sativa L.) is a semiaquatic plant, grow well in tropical, subtropical and temperate regions and it is highly affected by water shortage. Differential display reverse transcription (DDRT) technique was used to investigate differential gene expression between two Egyptian Oryza sativa cultivars under drought treatment, in an attempt to identify stress genes whose expression is regulated by drought and define their function. Fifty-six and fourty-seven fragments were differentially expressed under drought in G179 and Sk101, respectively. These differentially display (DD-PCR) fragments were categorized into up- and down- regulated fragments. DNA sequences of 17 fragments out of the total DD-PCR fragments was subjected to a nucleotide and amino acid sequence homology search through BLAST analysis programs from the National Center for Biotechnology and Information (NCBI). Four of the DD-PCR fragments were found to have the same base sequences showed homology with chaperone prot...