To investigate the effect of soluble silicate zeolite dressing of the rice against bakanae disease, field trial in reclaimed land and in vitro were carried out. The coated rice seeds (SCS) which were dressed with the mixture of 25% silicic acids (binder), and the zeolite (coating powder). In wet direct seeding, uniform scattering of rice seeds on the soil surface and the better seedling establishment were shown in SCS treatment plots. The incidence of bakanae disease began from the mid tillering stage toward the heading stage. Around heading stage, the ratio of infected tillers reached its highest point by 9.9% in non-SCS treatment plots. While, in SCS treatment plots, the ratio of infected tillers was no more than 0.01%. The vitality of the pathogenic fungi of bakanae disease in the SCS and non-SCS samples were assessed. Samples were incubated for one week keeping proper humidity at 30°C after inoculated with panicles of infected rice plants from experimental field plots. In non-SCS treatment, pinkish colonies were formed on the grain surface of panicle of infected plants, and mycelium, macro-conidia and micro-conidia were developed actively inside part of infected grain inoculated. While in SCS treatment, micro-conidia and mycelium were not survived and the growth of macro-conidia, mycelia were greatly inhibited and withered. Based on the results, it is concluded that the environmental friendly control of bakanae disease by use of SCS is possible and soluble silicate can be applied as agents for replacement of seed disinfection.

MLO is a unique gene family which is identified in plant and carries out abiotic and biotic stress responses in various plants. The understanding on the roles and functional diversity of this family is quite limited in rice, a model crop plant. Rice genome has 12 potential MLO family members. To do systematic functional assignment of MLO family in rice, we performed phylogenomic analysis of integrating meta-expression data based on public sources of microarray data or RT-PCR data into the phylogenic tree. As a result, we identified 12 MLO genes carrying various tissue-preferred expression patterns such as leaf, root, pollen, and ubiquitous expression, suggesting functional diversity in terms of anatomy or development. RT-PCR analysis confirmed, integrated transcriptome data were used to estimate the functional redundancy or specificity among MLO family: MLO12 showed mature pollen preferred expression; MLO4, root tip; MLO10, overall root except root tip; MLO8, leaf; MLO2 and MLO9 showed redundant expression in overall tissues except root. Also, abiotic stress meta-expression data and RT-PCR performance suggested the functional association of 5 MLO and 6 MLO genes with heat and cold stress, respectively. Our analysis will provide basic information to study diverse developmental or physiological phenomena mediated by MLO family in rice, a major model crop plant.

We recently reported rice promoters that are active in late stages of pollen development. However, rice promoters that allow manipulation of gene expression at earlier stages of pollen development are still very limited to date. In this study, we have chosen 10 putative microspore promoters, OsMSP1 through OsMSP10, based on publicly available transcriptomic datasets in rice (Oryza sativa L.). Sequence analysis of these promoter regions revealed some cis regulatory elements involved in pollen-specific expression. We also examined promoter activities using the promoter-GUS reporter constructs in both transgenic rice and Arabidopsis. In rice, all of the 10 promoters directed GUS signals from the microspore stage throughout the all stages of pollen development. In addition, while GUS signals from 4 promoters, OsMSP2, OsMSP7, OsMSP9 and OsMSP10, seem to be expressed preferentially during pollen development, those from other six promoters were observed in vegetative tissues such as leaves, stems, and roots of seedlings. Similarly, in Arabidopsis, all of the 10 promoters directed GUS signals during pollen development. In detail, 8 promoters, OsMSP1 ~ OsMSP8 directed GUS signals from the microspore stage, whereas 2 promoters, OsMSP9 and OsMSP10, exhibited GUS signals from tricellular stage. Furthermore, seven promoters, except for OsMSP1, OsMSP2 and OsMSP10, showed GUS signals in shoot apical region or root tissues of seedlings. Furthermore, we verified microspore activity of four promoters, OsMSP1, OsMSP2, OsMSP3 and OsMSP6, by complementation analysis of the sidecar pollen (scp) mutant which displays microspore-specific defects. Currently, further analyses are underway for GUS expression of T2 generation in transgenic rice and scp complementation with remaining promoters.

The detrimental effect of high salinity on crop production is a serious problem. However, the number of genes with known functions relating to salinity tolerance is very limited in rice. To effectively address this limitation, selection of useful candidate genes and identification of major regulatory factors through global approaches are necessary. To this end, we used three data series of affymetrix array data produced with salt-treated samples from NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) and identified 653 rice genes commonly differentially expressed under three salt-stress conditions. While evaluating the quality of selected candidate genes for salt-stress responses, Gene ontology enrichment analysis revealed that responses to salt and water stresses of biological process category are highly overrepresented in salt-stress conditions. In addition, the major salt stress-responsive metabolism process and regulatory gene modules are classified through MapMan analysis, and detailed elements for further studies are suggested. Based on this, we proposed a salt stress-responsive signaling pathway in rice. The functional analysis of the main signal transduction and transcription regulation factors identified in this pathway will shed light on a novel regulatory metabolism process that can be manipulated to develop crops with enhanced salinity tolerance.

Rice gene functional annotation is greatly hindered due to functional redundancy. Based on OGRO database information, function of only 1022 genes were characterized previously where estimated expressed genes is approximately 50000. TFs protein class consist of 80 families and function of only 211 were reported. To address this issue, we developed web resource using MySQL, PHP and related frame work. Database integrates expression pattern and diverse data in phylogenomic contest. Since TFs plays diverse role in plants, meta-expression analysis would provide putative function of remaining genes. Using this approach and in-house database, we have identified featured expression groups: 228 belongs to anatomy, 224 to abiotic stress, 202 to biotic stress and hormone responsive group includes 267 genes. Out of 315 known genes through loss of functional studies, 294 genes have no closely related family members. Among 12 pairs with probes in database, 6 genes have PCC value with more than 0.5 among closely related genes. These data suggest that TFs showing more than 0.5 PCC value among closely relating family members more likely have functional dominancy. This study will provide useful functional information for whole rice TFs and suggest promising functional genomic studies.

Water-deficiency is one of the most serious challenges which restrict crop production. Root is the primary tissues exposed to water limitation in soil. Although a number of transcriptome data under water limitation have been produced in rice, but most of them have analyzed the effect of leaf or shoot. Thus, understanding of relating molecular mechanism is still limited. To get global view of the effect on water deficiency in rice root, we carried out RNA-Seq experiment. To do this, we compared the RNA-Seq transcriptome data of 3 day samples under water deficiency with those of unstressed rice roots with unstressed control. As a result, we identified 1,098 genes upregulated in water stress condition for 3 days. Gene ontology (GO) enrichment analysis revealed that 18 GO terms are overrepresented. Of them, valyl-tRNA aminoacylation, transcription from RNA polymerase II promoter, glycine catabolic process, and L-phenylalanine catabolic process are more significant, indicating that transcription of new transcripts, control of translation fidelity, and reuse of primary and secondary metabolites can be activated during water stress.

Functional identification of rice on a whole genome scale is required to significantly improve the quality of rice, rice yield, and stress tolerance in response to changing climate. In addition to conventional approaches, new methodologies are required for identification of key genes associated with new agronomical traits. Systems biology is an upcoming trend in the field of functional genomics. Recently, there has been a significant improvement in the resources for systems biology in Oryza sativa (rice), a model crop. These resources include whole genome sequencing/re-sequencing data, transcriptomes, protein-protein interactomes, reactomes, functional gene network tools, and gene indexed mutant populations. The integration of diverse omics data can lead to greater understanding of the functional genomics of rice. Here, we address the development and current progress of the resources available for systems biology in rice: Genome browsers and databases for the orthology identification, transcriptome analysis, protein-protein interaction network and functional gene network analyses, co-expression network, metabolic pathway analysis for promoter analysis, and gene indexed mutants.

E3 ubiquitin ligase plays a central role in determining specificity of the ubiquitination system by selecting appropriate candidate proteins. Compared with other eukaryotic species there are significantly more U-box protein-encoding genes in plant genome. The rice genome contain 77 U-box-type E3 encoding genes. The 77 members of the rice plant U-box (PUB) E3 family can be placed into 8 major groups based on their domain organizations. In this study, we generate and analyze phylogenomic data integrating anatomical expression patterns consisting of anatomical and stress responsive expression patterns base on 1150 affymetrix arrays to the phylogenic tree of rice plant U-box E3 family. We further developed functional gene network meditated by E3 ligases and refined the components in network by integrating gene expression patterns in response to drought stresses. We expect that our analysis will be a useful platform to facilitate the functional identification for each of U-box E3 family.

A male gametophyte, or pollen develops in the anther, and its development plays an important male reproductive process in flowering plants. A properly designed transgene construct can help to tailor transgene expression in plants by altering the expression strength, timing, and location. In this process, the promoter plays a pivotal role in controlling transgene expression. In this research, the promoter regions of rice anther/pollen-specific genes, named as OsMSP1 to OsMSP11,were selected from the microarray data sets covering 4 developmental stage of male gametophyte and then used for the construction of vector by Gateway cloning method and transformed into rice and Arabidopsis. All 11 promoters in rice and 9 in Arabidopsis were displayed as anther/pollen-specific/preferential genes by GUS assay and RT-PCR analysis. Three out of 11 promoters showed consistent results with published data. In this study, we demonstrated on eight new anther/pollen-specific or -preferential promoters (OsMSP1, OsMSP2, OsMSP3, OsMSP4, OsMSP5, OsMSP6, OsMSP8, and OsMSP9, which have not been reported before. Although the expression pattern of different genes active in pollen grains is diverse and complex, these experimental results would be helpful to understand the molecular mechanism of regulatory elements in rice microspore/pollen-specific genes.

Drought and salinity are two major environmental factors determining plant productivity that due to their high magnitude of impact and wide distribution. The regulatory circuits include stress sensors, signaling pathways comprising a network of protein-protein reactions, transcription factors and promoters, and finally the output proteins or metabolites. Plant receptor-like kinases (RLKs) are transmembrane proteins family, are predicted to be major components of the signaling pathways that allow plants to respond to diverse environmental and development condition. Subfamily of Catharanthus roseus RLK1-like kinases (CrRLK1Ls) is a novel type of RLK, was identified in Arabidopsis with 17 members carrying a putative extracellular carbonhydrate-binding malectin-like domain. To study the function of CrRLK1Ls subfamily in rice which is a most widely consumed staple food, we produced the phylogenomic data with the integration of microarray-based anatomical and stress expression profiling data to the context of rice CrRLK1Ls family phylogenic tree. The expression profiling data are based on a large number of public microarray data such as 1150 Affymetrix arrays and 209 Agilent 44K arrays. Chromosomal localization of CrRLK1Ls reveals that three of 16 genes were tandem duplicated. Subsequently, we identified 7 genes that showed circadian regulation pattern and three genes of them simultaneously response to drought stress: two were down-regulated and one was up-regulated. Functional gene network development mediated by these stress responsible genes might be an useful foundation to explain the molecular mechanism of stress response mediated by this gene family.

Drought and salinity are two major environmental factors determining plant productivity that due to their high magnitude of impact and wide distribution. The regulatory circuits include stress sensors, signaling pathways comprising a network of protein-protein reactions, transcription factors and promoters, and finally the output proteins or metabolites. Plant receptor-like kinases (RLKs) are transmembrane proteins family, are predicted to be major components of the signaling pathways that allow plants to respond to diverse environmental and development condition. Subfamily of Catharanthus roseus RLK1-like kinases (CrRLK1Ls) is a novel type of RLK, was identified in Arabidopsis with 17 members carrying a putative extracellular carbonhydrate-binding malectin-like domain. To study the function of CrRLK1Ls subfamily in rice which is a most widely consumed staple food, we produced the phylogenomic data with the integration of microarray-based anatomical and stress expression profiling data to the context of rice CrRLK1Ls family phylogenic tree. The expression profiling data are based on a large number of public microarray data such as 1150 Affymetrix arrays and 209 Agilent 44K arrays. Chromosomal localization of CrRLK1Ls reveals that three of 16 genes were tandem duplicated. Subsequently, we identified 7 genes that showed circadian regulation pattern and three genes of them simultaneously response to drought stress: two were downregulated and one was up-regulated. Functional gene network development mediated by these stress responsible genes might be an useful foundation to explain the molecular mechanism of stress response mediated by this gene family.

Pollen development in flowering plants is regulated by a comprehensive pattern of genes. One way to produce hybrid rice based on nuclear male sterility is to find out firstly the potential promoters that function specifically in anthers since it is a specific site for transcription initiation and play key roles for the spatial and temporal expression of the genes. To implement this objective, we were selected promoter region of 16 genes based on the expression pattern of microarray and then those were introduced into the promoterless final destination vector which containing the GFP and GUS reporters genes. The resulting twelve vectors were transformed into monocotyledonous rice (Oryza sativa L) and a dicotyledonous Arabidopsis as heterologous system. Minimum 20 plants for each vector were analyzed by histochemical GUS assay at the flowering stage in Arabidopsis. 9 vectors out of 12 vectors constructed were expressed exclusively at the anther, especially in pollen, however one vector exhibited expression in stigma. For rice, T-DNA insertion were confirmed with specific primers in each promoter and GFP region. All T0 transgenic plants contained T-DNA insertion in their genome. This study would provide valuable information for biotechnological application for the induction of male sterility in plants.

The rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most serious diseases of cultivated rice (Oryza sativa L.) in most rice-growing regions of the world. In order to investigate early responsible genes in rice in response to M. oryzae, we analyzed transcriptomics analysis using 300 K tilling microarray chip. The quality of RNA samples was initially validated by 4 defense related genes and phytoalexins measurement using RT-PCR and HPLC, respectively, which are well known defense markers. We determined that accumulation of 608 genes showed statistically significant changes in the level of transcription (>2 fold change, P<0.05). Among them, 261 genes were more up-regulated in incompatible interaction than that of compatible one. We further analyzed GO enrichment analysis of the 41 and 231 which were 2 fold up-regulated genes at 12h and 48h in incompatible interaction, respectively, using Rice Oligo nucleotide Array Database (http://ricearray.org). Furthermore, MapMan analysis (http://mapman.gabipd.org/) revealed that 21 and 85 genes including 18 receptor-like genes which were more induced in incompatible interaction compared to compatible interaction were found to be involved in biotic stress. Thus, this study suggests that early inducible genes including receptor-like protein kinases in incompatible interaction may play a key role in disease resistance against M. oryzae attacks.

E3 ubiquitin ligase plays a central role in determining specificity of the ubiquitination system by selecting appropriate candidate proteins. Compared with other eukaryotic species there are significantly more U-box protein-encoding genes in plant genome. The rice genome contain 77 U-box-type E3 encoding genes. The 77 members of the rice plant U-box (PUB) E3 family can be placed into 8 major groups based on their domain organizations. In this study, we generate and analyze phylogenomic data integrating anatomical expression patterns consisting of anatomical and stress responsive expression patterns base on 1150 affymetrix arrays to the phylogenic tree of rice plant U-box E3 family. Then, we highlighted 8 genes in subfamilies II (5) and VII (3) of E3 ligases showing significant upregulation in water stress conditions such as drought and high concentration of salt stress. We further developed functional gene network meditated by E3 ligases and refined the components in network by integrating gene expression patterns in response to drought and salt stresses. We expect that our analysis will be a useful platform to facilitate the functional identification for each of U-box E3 family.

ATP-binding cassette (ABC) proteins comprise a large superfamily and play as key in the physiology and development of plants but it is highly likely that more functions for members of this interesting family are still in dark. Thus systematic analysis for this family will be helpful to design effective experimental plans for functional analysis of each of ABC family in rice. To do this, we performed phylogenomic analysis of integrating anatomy and stress meta-profiling data based on a large collection of rice affymetrix array data which provide useful clues to study functions of ABC transporter family in rice in term of anatomy and stress response. Then, we processed Significance analysis for Microarray to identify ABC transporters involved in water stress such as drought and salt. Subsequently, we identified 23 genes showing significant upregulation or downregulation by both drought and salt. Finally, we developed the interaction network mediated by six of them and then integrated diverse data such as co-expression patterns, putative functions and sub-cellular localization to the network and the network was further refined based on coexpression patterns in response to drought and salt stresses. Our analysis will provide molecular basis to study diverse biological phenomena mediated by ABC family in rice, a major model crop plant.

Global warming and climate changing nowadays are known as one of the most harmful factors concerning the yield of worldwide crop plants. To adapt with new challenges, a well-known strategy of plants is water-balance control. Aquaporins are a gene family of integral membrane proteins which play a central role in water transport regulation. By searching diverse databases, we expanded the number of rice aquaporin family from 33 to 37 genes. After that, the phylogenomic data integrating anatomical expression patterns consisting of 1150 affymetrix arrays and 209 Agilent 44K arrays, and stress responsible expression patterns were constructed and analyzed. The systemic overview of gene expression for rice aquaporin family is used to evaluate functional redundancy within this family and identify suitable target genes in response to water stress. Functional gene network mediated by water stress relating aquaporin genes also suggested a useful platform for further researches.

Pollen development in flowering plants is regulated by a comprehensive pattern of genes. One way to produce hybrid rice based on nuclear male sterility is to find out firstly the potential promoters that function specifically in anthers since it is a specific site for transcription initiation and play key roles for the spatial and temporal expression of the genes. To implement this objective, we were selected promoter region of 16 genes based on the expression pattern of microarray and then those were introduced into the promoterless final destination vector which containing the GFP and GUS reporters genes. The resulting twelve vectors were transformed into monocotyledonous rice (Oryza sativa L) and a dicotyledonous Arabidopsis as heterologous system. Minimum 20 plants for each vector were analyzed by histochemical GUS assay at the flowering stage in Arabidopsis. 9 vectors out of 12 vectors constructed were expressed exclusively at the anther, especially in pollen, however one vector exhibited expression in stigma. For rice, T-DNA insertion were confirmed with specific primers in each promoter and GFP region. All T0 transgenic plants contained T-DNA insertion in their genome. This study would provide valuable information for biotechnological application for the induction of male sterility in plants.

Global warming and climate changing nowadays are known as one of the most harmful factors concerning the yield of worldwide crop plants. To adapt with new challenges, a well-known strategy of plants is water-balance control. Aquaporins are a gene family of integral membrane proteins which play a central role in water transport regulation. By searching diverse databases, we expanded the number of rice aquaporin family from 33 to 37 genes. After that, the phylogenomic data integrating anatomical expression patterns consisting of 1150 affymetrix arrays and 209 Agilent 44K arrays, and stress responsible expression patterns were constructed and analyzed. The systemic overview of gene expression for rice aquaporin family is used to evaluate functional redundancy within this family and identify suitable target genes in response to water stress. Functional gene network mediated by water stress relating aquaporin genes also suggested a useful platform for further researches.