Differential gene expression of rice two-component signaling elements during reproductive development and regulation by abiotic stress

The two-component signaling elements have been implicated in diverse cellular processes in plants. Earlier, we reported the identification, characterization and expression analysis of type-A response regulators in rice. In this study, we have comprehensively analyzed the expression profile of all the two-component signaling elements identified in rice at various stages of vegetative and reproductive development by employing microarray analysis. Most of the components are expressed in all the developmental stages analyzed. A few of these were found to be specifically expressed during certain stages of seed development, suggesting their role in embryo and endosperm development. In addition, some of these components express differentially under various abiotic stress conditions, indicating their involvement at various levels of hierarchy in abiotic stress signaling. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Differential regulation of waxy gene expression in rice endosperm

Summary In order to examine the effects of different alleles on the gene expression at the waxy locus, the Wx gene product which controls the synthesis of amylose was isolated from endosperm starch of rice plants and analysed by electrophoretic techniques. The major protein bound to starch granules was absent in most of waxy strains and increased with the number of Wx alleles in triploid endosperms, suggesting that the major protein is the Wx gene product. In addition to wx alleles which result in the absence or drastic reduction of the Wx gene product and amylose, differentiation of Wx alleles seemed to have occurred among nonwaxy rice strains. At least two Wx alleles with different efficiencies in the production of the major protein as well as amylose were detected. These alleles are discussed in relation to regulation of the gene expression.     

Organization and expression of two Arabidopsis DREB2 genes encoding DRE-binding proteins involved in dehydration- and high-salinity-responsive gene expression

In plants, a cis-acting element, DRE/CRT, is involved in ABA-independent gene expression in response to dehydration and low-temperature stress. To understand signal transduction pathways from perception of the dehydration stress signal to gene expression, we characterized a gene family for DRE/CRT-binding proteins DREB2A and DREB2B in Arabidopsis thaliana. Northern analysis showed that both genes are induced by dehydration and high-salt stress. Organ-specific northern analysis with gene-specific probes showed that these genes are strongly induced in roots by high-salt stress and in stems and roots by dehydration stress. The DREB2A gene is located on chromosome 5, and DREB2B on chromosome 3. We screened an Arabidopsis genomic DNA library with cDNA fragments of DREB2A and DREB2B as probes, and isolated DNA fragments that contained 5-flanking regions of these genes. Sequence analysis showed that both genes are interrupted by a single intron at identical positions in their leader sequence. Several conserved sequences were found in the promoter regions of both genes. The -glucuronidase (GUS) reporter gene driven by the DREB2 promoters was induced by dehydration and high-salt stress in transgenic Arabidopsis plants.     

Retrograde regulation of nuclear gene expression in CW-CMS of rice

The CW-cytoplasmic male sterility (CMS) line has the cytoplasm of Oryza rufipogon Griff, and mature pollen is morphologically normal under an optical microscope but lacks the ability to germinate; restorer gene Rf17 has been identified as restoring this ability. The difference between nuclear gene expression in mature anthers was compared for the CW-CMS line, [cms-CW] rf17rf17, and a maintainer line with normal cytoplasm of Oryza sativa L., [normal] rf17rf17. Using a 22-k rice oligoarray we detected 58 genes that were up-regulated more than threefold in the CW-CMS line. Expression in other organs was further investigated for 20 genes using RT-PCR. Five genes, including genes for alternative oxidase, were found to be preferentially expressed in [cms-CW] rf17rf17 but not in [normal] rf17rf17 or [cms-CW] Rf17Rf17. Such [cms-CW] rf17rf17-specific gene expression was only observed in mature anthers but not in leaves, stems, or roots, indicating the presence of anther-specific mitochondrial retrograde regulation of nuclear gene expression, and that Rf17 has a role in restoring the ectopic gene expression. We also used a proteomic approach to discover the retrograde regulated proteins and identified six proteins that were accumulated differently. These results reveal organ-specific induced mitochondrial retrograde pathways affecting nuclear gene expression possibly related to CMS. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Comprehensive expression analysis of rice phospholipase D gene family during abiotic stresses and development

Phospholipase D is one of the crucial enzymes involved in lipid mediated signaling, triggered during various developmental and physiological processes. Different members of PLD gene family have been known to be induced under different abiotic stresses and during developmental processes in various plant species. In this report, we are presenting a detailed microarray based expression analysis and expression profiles of entire set of PLD genes in rice genome, under three abiotic stresses (salt, cold and drought) and different developmental stages (3-vegetative stages and 11-reproductive stages). Seven and nine PLD genes were identified, which were expressed differentially under abiotic stresses and during reproductive developmental stages, respectively. PLD genes, which were expressed significantly under abiotic stresses exhibited an overlapping expression pattern and were also differentially expressed during developmental stages. Moreover, expression pattern for a set of stress induced genes was validated by real time PCR and it supported the microarray expression data. These findings emphasize the role of PLDs in abiotic stress signaling and development in rice. In addition, expression profiling for duplicated PLD genes revealed a functional divergence between the duplicated genes and signify the role of gene duplication in the evolution of this gene family in rice. This expressional study will provide an important platform in future for the functional characterization of PLDs in crop plants.     

Functional characterization of transposon-tagged abiotic stress-responsive rice genes and their molecular polymorphisms among various stress-tolerant genotypes

Dissociation (Ds) insertional mutagenesis has been regarded as an efficient tool to generate insertion mutants for functional genomics and molecular breeding. However, little is known about the application of the tool on exploring biological functions of abiotic stress-related genes and their molecular breeding experience. In this study, a total of 833 Ds insertion lines have been obtained, which showed significantly higher tolerance or sensitivity to high salinity, drought or cold stress, by screening around 20,000 Ds lines. Analysis of Ds flanking sequence tags revealed that 165 rice genes were tagged by Ds insertion. Gene Ontology (GO) and gene set enrichment analysis showed that over-represented Ds-tagged genes might function in the response to exogenous stimuli. These Ds-tagged genes showed expression divergence among five high salinity and five drought tolerant rice lines under either high salinity or drought stress. Higher percentages of Ds-tagged genes were down- or up-regulated by these abiotic stresses. These Ds-tagged genes were also frequently reduced or suppressed by various phytohormones including abscisic acid and jasmonate. On the other hand, we have also detected single nucleotide polymorphisms (SNPs) and 1–10 base pairs of insertion and deletions (indels) of these Ds-tagged genes among ten high salinity/drought tolerant rice lines by comparing with the reference genome Nipponbare. Our data showed that SNPs were detected among 102 out of 165 genes and indels were identified in 39 out of 165 genes. All the data provided additional information to further explore the biological functions of these genes or to carry out molecular breeding.     

MADS box genes expressed in developing inflorescences of rice and sorghum

With the aim of elucidating the complex genetic system controlling flower morphogenesis in cereals, we have characterized two rice and two sorghum MADS box genes isolated from cDNA libraries made from developing inflorescences. The rice clones OsMADS24 and OsMADS45, which share high homology with the Arabidopsis AGL2 and AGL4 MADS box genes, are expressed in the floral meristem, in all the primordia, and in mature floral organs. High expression levels have also been found in developing kernels. The sorghum clone SbMADS1 is also homologous to AGL2 and AGL4: expression analysis and mapping data suggest that it is the ortholog of OsMADS24. The pattern of expression of SbMADS2, the other sorghum MADS box gene, suggests that it may play a role as a meristem identity gene, as does AP1 in Arabidopsis, to which it shows considerable homology. The four genes have been mapped on a rice RFLP genetic map: the results are discussed in terms of synteny among cereals. Received: 25 April 1996 / Accepted: 29 August 1996