Shoshi Kikuchi

National Institute of Agrobiological Sciences

A blast-resistance rice mutant, GR978, generated by gamma-irradiation of indica cultivar IR64 was used to characterize the disease resistance transcriptome of rice to gain a better understanding of genes or chromosomal regions contributing to broad-spectrum disease resistance. GR978 was selected from the IR64 mutant collection at IRRI. To facilitat...

Next to their essential roles in plant growth and development, phytohormones play a central role in plant immunity against pathogens. In this study we studied the previously reported antagonism between the plant-pathogenic oomycete Pythium arrhenomanes and the root-knot nematode Meloidogyne graminicola, two root pathogens that co-occur in aerobic r...

Drought tolerance (DT) is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. The study of DT and related mechanisms in rice as a staple food crop in the world has a long history starting with testing the performance of rice genotypes in field conditions to employing omics technologi...

Background Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we carried out gene-expression profiling of the leaves of near-isogenic lines (NILs) with similar genetic backgrounds and different...

Rice GRH2 confers enhanced resistance to green rice leafhoppers (GRH), Nephotettix cincticeps Uhler. A pyramided line carrying GRH2 and GRH4 (TGRH29) showed strong resistance to GRH insects compared with a GRH2 near-isogenic line (TGRH11), although GRH4 alone did not confer any resistance to GRH. To explore the effects of GRH2 and GRH4 on GRH resis...

Expression levels of the NAC gene family were studied in rice infected with Rice dwarf virus (RDV), Rice black-streaked dwarf virus (RBSDV), Rice grassy stunt virus (RGSV), Rice ragged stunt virus (RRSV), and Rice transitory yellowing virus (RTYV). Microarray analysis showed that 75 (68%) OsNAC genes were differentially regulated during infection w...

Over the past decades, a multitude of studies have shown the ability of silicon (Si) to protect various plants against a range of microbial pathogens exhibiting different lifestyles and infection strategies. Despite this relative wealth of knowledge, understanding of the action mechanism of Si is still in its infancy, which hinders its widespread a...

In the summer of 2012, 1 year after the nuclear accident in March 2011 at the Fukushima Daiichi nuclear power plant, we examined the effects of gamma radiation on rice at a highly contaminated field of Iitate village in Fukushima, Japan. We investigated the morphological and molecular changes on healthy rice seedlings exposed to continuous low-dose...

Background Throughout Asia, including Japan, rice plants are cultivated in a wide range of areas from lowlands to highlands and are frequently exposed to fog, including acid fog. Some physiological studies have shown that acid fog can be a stress factor for plants. We analyzed the gene expression profiles of rice plants treated with artificially pr...

Rice proteomics has progressed with tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of pre...

Rice tungro disease is a complex disease caused by the interaction between Rice tungro bacilliform virus and Rice tungro spherical virus (RTSV). RTSV alone does not cause recognizable symptoms in most Asian rice (Oryza sativa) plants, whereas some African rice (O. glaberrima) plants were found to become stunted by RTSV. Stunting of rice plants by v...

A suspension culture of bromegrass (Bromus inermis Leyss cv. Manchar) provides a unique system for studying cold hardiness mechanism, where freezing tolerance can be independently induced by two different stimuli, cold and exogenous abscisic acid (ABA). Freezing tolerance was induced in bromegrass cells by exposure to low temperatures for 7 days (L...

The OsWRKY genes play various roles in developmental processes and in stress-related responses in plants. We describe the rice OsWRKY gene expression profiles (GEPs) under control, hormone-treated, and water-deficit treatment (WDT) conditions. The preferential expression of 3 genes was observed in specific tissues, suggesting that these genes may p...

Rice grassy stunt virus (RGSV) is a serious threat to rice production in Southeast Asia. RGSV is a member of the genus Tenuivirus, and it induces leaf yellowing, stunting, and excess tillering on rice plants. Here we examined gene responses of rice to RGSV infection to gain insight into the gene responses which might be associated with the disease...

High ozone (O 3) concentrations not only damage plant life but also cause considerable losses in plant productivity. To screen for molecular factors usable as potential biomarkers to identify for O 3-sensitive and -tolerant lines and design O 3 tolerant crops, our project examines the effects of O 3 on rice, using high-throughput omics approaches....

NAC transcription factors are one of the largest families of transcriptional regulators in plants, and members of the NAC gene family have been suggested to play important roles in the regulation of the transcriptional reprogramming associated with plant stress responses. A phylogenetic analysis of NAC genes, with a focus on rice and Arabidopsis, w...

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is...

Background: Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield u...

Performance of 84 IR64-NILs under non –stress (NS) and drought stress (S) conditions. (DOCX)

List of candidate genes associated with yield-under-drought QTLs. (DOCX)

QTLs identified for grain yield under drought stress. (DOCX)

Soil water potential measured by tensiometers in each field study season. (DOCX)

QTLs for yield related traits under drought stress and non-stress in IR64×Aday Sel derived populations. (DOCX)

Regions of aggregation of differentially expressed genes from the re-analyzed transcriptome dataset. (DOCX)

Enriched Gramene QTL categories of the subset candidate genes in IR77298-14-1-2-B-10 (+QTL) and IR77298-14-1-2-B-13 (−QTL). (DOCX)

Candidate genes/gene families and their biological functions under stress conditions. (DOCX)

Major effect QTL DTY2.2 and DTY9.1 identified in multiple populations. (DOCX)

Mean for yield and related traits under drought stress and non-stress conditions during 2007DS to 2010DS. (DOCX)

QTLs for grain yield under drought identified by multi-population joint analyses. (DOCX)

Supplementary References. (DOCX)

The pentatricopeptide repeat (PPR) family has been reported to be involved in many post-transcriptional processes, including RNA editing and RNA splicing in both chloroplasts and mitochondria. There are a large number of PPR proteins in plant genome, however, the biological functions of most PPR proteins have not yet been determined. We describe th...

Unlabelled: The 'ozone (O3)-responsive transcriptome' behavior in the panicles and grains of rice plant was studied individually through high-throughput oligo-DNA microarray technique. O3 differentially and separately regulated 620 and 130 genes in the panicles and grains. Among the O3-responsive genes, 176 and 444 genes were up- and down-regulate...

Calcium-dependent protein kinases (CDPKs) constitute a large multigene family in various plant species. CDPKs have been shown to have important roles in various physiological processes, including plant growth and development and abiotic and biotic stress responses in plants. Functional analysis using gain-of-function and loss-of-function mutants ha...

Thioredoxin (TRX) is a multi-functional redox protein. Genome-wide survey and expression profiles of different stresses were observed. Conserved amino acid residues and phylogeny construction using the OsTRX conserved domain sequence suggest that the TRX gene family can be classified broadly into six subfamilies in rice. We compared potential gene...

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 entir...

Brassinosteroids (BRs) are a unique class of plant steroid hormones that orchestrate myriad growth and developmental processes. Although BRs have long been known to protect plants from a suite of biotic and abiotic stresses, our understanding of the underlying molecular mechanisms is still rudimentary. Aiming to further decipher the molecular logic...

Plant roots are important organs to uptake soil water and nutrients, perceiving and transducing of soil water deficit signals to shoot. The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) wi...

The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesti...

Calcium-dependent protein kinases (CDPKs) regulate the downstream components in calcium signaling pathways. We investigated the effects of overexpression and disruption of an Oryza sativa (rice) CDPK (OsCPK12) on the plant's response to abiotic and biotic stresses. OsCPK12-overexpressing (OsCPK12-OX) plants exhibited increased tolerance to salt str...

Therefore, 3,895 candidate genes related to anthocyanin biosynthesis in Chinese cabbage were identified using a 300K Brassica rapa microarray analysis. Gene expression during six stages of leaf developmental stages were examined in FC (green leaf) and FA(red leaf) Chinese cabbage cultivars. The 317 transcription factor genes found to be associated...

Given the essential role of proteomics in understanding the biology of plants, we are establishing a global plant proteomics organization to properly organize, preserve and disseminate collected information on plant proteomics. We call this organization 'International Plant Proteomics Organization (INPPO; http://www.inppo.com).' Ten initiatives of...

Response in abiotic stress responsive gene families to RDV infection. See Figure 4 for details. (TIF)

Response of genes for transcription factors involved in development and morphogenesis processes to RDV infection. See Figure 4 for details. (TIF)

Response of genes whose products localized in cell wall to RDV infection. See Figure 4 for details. (TIF)

Disease symptoms in plants infected with three RDV strains. A): Rice plants stunted by infection with RDV strains at 30 dpi. Bar: 10 cm. B) Chlorotic stripes on leaf of an RDV-S-infected plant. Bar: 1 cm. C) (TIF)

Response of genes associated with photosynthesis-, and carbon fixation-related processes to RDV infection. See Figure 4 for details. (TIF)

Characterization of three RDV strains. A: raw data of plant height, B: nucleotide sequences of 12 segments, C: amino acid sequences of 12 proteins (XLS)

DEGs evaluated by RT-PCR. The numbers are the normalized signal intensity and log2-based differential expression ratios by microarray analysis. ns: log2-based differential expression ratio of the gene not significantly differentially expressed. (TIF)

The list of DEGs. (XLS)

Rice dwarf virus (RDV) is the causal agent of rice dwarf disease, which often results in severe yield losses of rice in East Asian countries. The disease symptoms are stunted growth, chlorotic specks on leaves, and delayed and incomplete panicle exsertion. Three RDV strains, O, D84, and S, were reported. RDV-S causes the most severe symptoms, where...

We identified 163 AP2/EREBP (APETALA2/ethylene-responsive element-binding protein) genes in rice. We analyzed gene structures, phylogenies, domain duplication, genome localizations and expression profiles. Conserved amino acid residues and phylogeny construction using the AP2/ERF conserved domain sequence suggest that in rice the OsAP2/EREBP gene f...

We applied the full-length cDNA overexpressor (FOX) gene-hunting system for systematic and genome-wide functional analysis of rice genes. In this study, we constructed a novel binary vector carrying the Gateway site-specific recombination cassette and then constructed rice FOX libraries containing a maximum of 13,823 independent, full-length cDNAs...

This study identifies 2,617 candidate genes related to anthocyanin biosynthesis in rice using microarray analysis and a newly developed maximum boundary range algorithm. Three seed developmental stages were examined in white cultivar and two black Dissociation insertion mutants. The resultant 235 transcription factor genes found to be associated wi...

The rice CHLH gene encodes the Mg2+-chelatase H subunit, which is involved in chlorophyll biosynthesis. Growth of the chlorophyll-deficient oschlh mutant is supported by mitochondrial activity. In this study, we investigated the activity of mitochondrial respiration in the illuminated leaves during oschlh seedling development. Growth of mutant plan...

We investigated 151 non-redundant NAC genes in rice and 117 in Arabidopsis. A complete overview of this gene family in rice is presented, including gene structures, phylogenies, genome localizations, and expression profiles. We also performed a comparative analysis of these genes in rice and Arabidopsis. Conserved amino acid residues and phylogeny...

Rice (Oryza sativa) endosperm accumulates a massive amount of storage starch and storage proteins during seed development. However, little is known about the regulatory system involved in the production of storage substances. The rice flo2 mutation resulted in reduced grain size and starch quality. Map-based cloning identified FLOURY ENDOSPERM2 (FL...

To better understand the functional characterization of anthocyanin gene expression in black rice, we performed a detailed computational examination. The experiment was performed using the newly designed 135K Oryza sativa microarray to assess gene expression at three time points after the heading stage in Ds insertion lines. Transcription factors r...

Anthocyanins are a major class of flavonoids that are produced in the tissues of many plant species in response to environmental signals. The pigmentation of Chinese cabbage (Brassica rapa) was analyzed using newly developed 300K Brassica rapa microarrays. The significantly expressed genes were analyzed by clusters of orthologous groups (COGs) and...

Chimeric full-length cDNAs. Accession number of FL-cDNA (Acc. no.), position of chimeric junction (Junction), number of chimeric junctions (No. of junctions), and library or origin (Library) are described. Where the sequences of the original loci at the junction were identical, the exact position of the junction was not determined to the single nuc...

Primers used in this study.

Rice tungro disease (RTD) is a serious constraint to rice production in South and Southeast Asia. RTD is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Rice cv. Utri Merah is resistant to RTSV. To identify the gene or genes involved in RTSV resistance, the association of genotypic and phenotypic variations for RTSV...

Rice tungro disease (RTD) is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV) transmitted by green leafhoppers. Rice cv. Utri Merah is highly resistant to RTD. To define the RTD resistance of Utri Merah, near-isogenic lines (NIL, BC(5) or BC(6)) developed from Utri Merah and susceptible cv. Taichung Native 1 (TN...

P-log co-regulatory networks of Arabidopsis MADS-BOX genes. Co-regulatory networks of Arabidopsis MADS-BOX genes obtained using log-transformed Pearson Correlation Coefficient analysis (P-log analysis). A: PCC threshold value of 0.6 B: PCC threshold value of 0.7. Unbroken lines indicate experimentally validated edges reported in literature; broken...

OsWRKY primer sequences used for quantitative RT-PCR analysis. The sequences of primers used to analyse the expression levels of 14 OsWRKY genes by quantitative RT-PCR analysis are listed.

Co-regulatory networks of Arabidopsis WRKY genes. Co-regulatory networks of Arabidopsis WRKY genes obtained with the PCC threshold value of 0.7 in the untransformed (P-lin) (panel A) and log transformed (P-log) Pearson Correlation Coefficient analysis (panel B). The thickness of the edges is proportional to the value of the Pearson Correlation Coef...