Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit

Different genes involved in ABA and calcium signaling in leaf tissue of rice NILs and the parent IR64 under different water-deficit treatments. 1: up-regulated; -1: down-regulated; blank: no change in expression; 10: IR77298-14-1-2-B tolerant NIL, i.e., IR77298-14-1-2-B-10; 13: IR77298-14-1-2-B susceptible NIL, i.e., IR77298-14-1-2-B-13; 18: IR77298-5-6-B tolerant NIL, i.e., IR77298-5-6-B-18; 11: IR77298-5-6-B susceptible NIL, i.e., IR77298-5-6-B-11; 0.2 and 0.5 FTSW are severe and mild water-deficit treatments (XLSX 46 kb

Development of a novel data mining tool to find cis-elements in rice gene promoter regions

<p>Abstract</p> <p>Background</p> <p>Information on more than 35 000 full-length <it>Oryza sativa </it>cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as <it>cis</it>-regulatory elements with key roles under the various conditions.</p> <p>Results</p> <p>We have developed a novel tool that searches for <it>cis</it>-element candidates in the upstream, downstream, or coding regions of differentially regulated genes. The tool first lists <it>cis-</it>element candidates by motif searching based on the supposition that if there are <it>cis-</it>elements playing important roles in the regulation of a given set of genes, they will be statistically overrepresented and will be conserved. Then it evaluates the likelihood scores of the listed candidate motifs by association rule analysis. This strategy depends on the idea that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes. The tool is designed so that any biological researchers can use it easily at the publicly accessible Internet site <url>http://hpc.irri.cgiar.org/tool/nias/ces</url>. We evaluated the accuracy and utility of the tool by using a dataset of auxin-inducible genes that have well-studied <it>cis-</it>elements. The test showed the effectiveness of the tool in identifying significant relationships between <it>cis-</it>element candidates and related sets of genes.</p> <p>Conclusion</p> <p>The tool lists possible <it>cis-</it>element motifs corresponding to genes of interest, and it will contribute to the deeper understanding of gene regulatory mechanisms in plants.</p

Comprehensive gene expression analysis of the NAC gene family under normal growth conditions, hormone treatment, and drought stress conditions in rice using near-isogenic lines (NILs) generated from crossing Aday Selection (drought tolerant) and IR64

The NAC (NAM, ATAF1/2 and CUC2) genes are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. We describe the rice (Oryza sativa) OsNAC genes expression profiles (GEPs) under normal and water-deficit treatments (WDTs). The GEPs of the OsNAC genes were analyzed in 25 tissues covering the entire life cycle of Minghui 63. High expression levels of 17 genes were demonstrated in certain tissues under normal conditions suggesting that these genes may play important roles in specific organs. We determined that 16 genes were differentially expressed under at least 1 phytohormone (NAA, GA3, KT, SA, ABA, and JA) treatment. To investigate the GEPs in the root, leaf, and panicle of three rice genotypes [e.g., 2 near-isogenic lines (NILs) and IR64], we used two NILs from a common genetic combination backcross developed by Aday Selection and IR64. WDTs were applied using the fraction of transpirable soil water at severe, mild, and control conditions. Transcriptomic analysis using a 44K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from the two NILs under both WDTs, and the majority of the OsNAC genes that were activated were in the drought-tolerant IR77298-14-1-2-B-10 line compared with the drought-susceptible IR77298-14-1-2-B-13 or IR64. In IR77298-14-1-2-B-10, seventeen genes were very specific in their expression levels. Approximately 70 % of the genes from subgroups SNAC and NAM/CUC3 were activated in the leaf, but 37 % genes from subgroup SND were inactivated in the root compared with the control under severe stress conditions. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00438-012-0686-8) contains supplementary material, which is available to authorized users

Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme

Abscisic acid (ABA) regulates abiotic stress and developmental responses including regulation of seed dormancy to prevent seeds from germinating under unfavorable environmental conditions. ABA HYPERSENSITIVE GERMINATION1 (AHG1) encoding a type 2C protein phosphatase (PP2C) is a central negative regulator of ABA response in germination; however, the molecular function and regulation of AHG1 remain elusive. Here we report that AHG1 interacts with DELAY OF GERMINATION1 (DOG1), which is a pivotal positive regulator in seed dormancy. DOG1 acts upstream of AHG1 and impairs the PP2C activity of AHG1 in vitro. Furthermore, DOG1 has the ability to bind heme. Binding of DOG1 to AHG1 and heme are independent processes, but both are essential for DOG1 function in vivo. Our study demonstrates that AHG1 and DOG1 constitute an important regulatory system for seed dormancy and germination by integrating multiple environmental signals, in parallel with the PYL/RCAR ABA receptor-mediated regulatory system