Abstract
BackgroundRice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements.ResultsThere were 5,284 genes detected to be differentially expressed under drought stress. Most of these genes were tissue- or stage-specific regulated by drought. The tissue-specific down-regulated genes showed distinct function categories as photosynthesis-related genes prevalent in leaf, and the genes involved in cell membrane biogenesis and cell wall modification over-presented in root and young panicle. In a drought environment, several genes, such as GA2ox, SAP15, and Chitinase III, were regulated in a reciprocal way in two tissues at the same development stage. A total of 261 transcription factor genes were detected to be differentially regulated by drought stress. Most of them were also regulated in a tissue- or stage-specific manner. A cis-element containing special CGCG box was identified to over-present in the upstream of 55 common induced genes, and it may be very important for rice plants responding to drought environment.ConclusionsGenome-wide gene expression profiling revealed that most of the drought differentially expressed genes (DEGs) were under temporal and spatial regulation, suggesting a crosstalk between various development cues and environmental stimuli. The identification of the differentially regulated DEGs, including TF genes and unique candidate cis-element for drought responsiveness, is a very useful resource for the functional dissection of the molecular mechanism in rice responding to environment stress.
Highlights
Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages
Rice plants are less affected by water deficit at the seedling stage, drought stress at the vegetative stage does result in reduced height, fewer tillers, and smaller leaf
Rice plants at the four-leaf stage were transplanted in PVC tubes with Turface (Applied Industrial Materials, Corp., Buffalo Grove, introgression lines (ILs), USA) and watered with alternate applications of half-strength nutrient solution [17] and distilled water
Summary
Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. The effect of drought on rice plants considerably varies with genotypes, different developmental stages, and degree and duration of drought stress. Genome-wide genetic analysis of DT has identified many genomic regions associated with drought tolerance or responsiveness [4]. Some secondary traits, such as root architecture and osmotic adjustment, have been identified to be related to drought response [5,6,7]. DT QTL mapping results can be most usefully applied to the identification of promising chromosome regions for the confirmation of functional candidate genes of drought tolerance
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