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Publications (77)
Fertilization controls various aspects of cereal growth such as tiller number, leaf size, and panicle size. However, despite such benefits, global chemical fertilizer use must be reduced to achieve sustainable agriculture. Here, based on field transcriptome data from leaf samples collected during rice cultivation, we identify fertilizer responsive...
Barley (Hordeum vulgare) is the fourth most highly produced cereal in the world after wheat, rice and maize and is mainly utilized as malts and for animal feed. Barley, a model crop of the tribe Triticeae, is important in comparative analyses of Poaceae. However, molecular understanding about the developmental processes is limited in barley. Our pr...
The molecular basis for leaf development, a major focus in developmental biology, remains unclear in the monocotyledonous grass, rice (Oryza sativa). Here, we performed a mutant screen in rice and identified an AP2-type transcription factor family protein, NARROW AND DWARF LEAF1 (NDL1). NDL1 is the orthologue of Arabidopsis thaliana (subsequently c...
The plastochron, the time interval between the formation of two successive leaves, is an important determinant of plant architecture. We genetically and phenotypically investigated many-noded dwarf ( mnd ) mutants in barley. The mnd mutants exhibited a shortened plastochron and a decreased leaf blade length, and resembled previously reported plasto...
Background
Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover gene...
Background: Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover gen...
Asymmetric cell division is a key step in cellular differentiation in multicellular organisms. In plants, asymmetric zygotic division produces the apical and basal cells. The mitogen-activated protein kinase (MPK) cascade in Arabidopsis acts in asymmetric divisions such as zygotic division and stomatal development, but whether the effect on cellula...
Axis formation is a fundamental issue in developmental biology. Axis formation and patterning in plant leaves is crucial for morphology and crop productivity. Here, we reveal the basis of proximal-distal patterning in rice leaves, which consist of a proximal sheath, a distal blade, and boundary organs formed between these two regions. Analysis of t...
Regulation of cell proliferation is critical for establishing the shape of plant leaves. We identifiedMAKIBA3(MKB3), a loss-of-function mutant of which in rice exhibited a narrowed- and rolled-leaf phenotype.MKB3was found to be an ortholog of ArabidopsisANGUSTIFOLIA3(AN3), which positively regulates cell proliferation. The reduced leaf size ofmkb3p...
Floods impede gas (O 2 and CO 2 ) exchange between plants and the environment. A mechanism to enhance plant gas exchange under water comprises gas films on hydrophobic leaves, but the genetic regulation of this mechanism is unknown.
We used a rice mutant ( dripping wet leaf 7 , drp7 ) which does not retain gas films on leaves, and its wild‐type (Ki...
Root system is essential for absorbing water and nutrients as well as anchoring shoots to the ground. Understanding the genetic mechanisms related to the formation of root system architecture is necessary for improving rice productivity. Here, we first describe the potential of genetic improvement using quantitative trait locus (QTL) for root syste...
In several eudicot species, one copy of each member of the WUSCHEL-RELATED HOMEOBOX (WOX) gene family, WOX1 and WOX3, are redundantly or differentially involved in lateral leaf outgrowth, whereas only WOX3 gene regulating the lateral domain of leaf development has been reported in grass. In this study, we show that a WOX3 gene, LEAF LATERAL SYMMETR...
Juvenile-adult phase transition is an important shift for the acquisition of adult vegetative character and subsequent reproductive competence. We identified a recessive precocious (pre) mutant exhibiting long leaf phenotype in rice. The long leaf phenotype is conspicuous in 2nd through 4th leaves that are juvenile and juvenile-adult transition lea...
Barley (Hordeum vulgare L.) is the fourth most-produced cereal in the world and is mainly utilized as animal feed and malts. Recently barley attracts considerable attentions as healthy food rich in dietary fiber. However, limited knowledge is available about developmental aspects of barley leaves. In the present study, we investigated barley narrow...
Embryogenesis in rice is unique from most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, the formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled...
Leaf cells undergo two main developmental events; i.e., cell proliferation and cell differentiation, before maturation. These events occur sequentially at specific positions and with specific timing during leaf development. To understand the transition from cell proliferation to cell differentiation of rice leaves, we analyzed rice leaves from both...
Background
The rice PLASTOCHRON (PLA) genes PLA1 and PLA2 regulate leaf maturation and the temporal pattern of leaf initiation. Although the function of PLA genes in the leaf initiation process has been analyzed, little is known about how they affect leaf growth. Previously, we suggested that PLA1 and PLA2 function downstream of the gibberellin (GA...
Auxin is a fundamental plant hormone and its localization within organs plays pivotal roles in plant growth and development. Analysis of many Arabidopsis mutants defective in auxin biosynthesis revealed that the indole-3-pyruvic acid (IPA) pathway, catalyzed by the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) families, is the ma...
Maintenance of organ separation is one of the essential phenomena for normal plant development. We have identified and analyzed
ONION3 (ONI3), which is required for avoiding organ fusions in rice. Loss-of-function mutations of ONI3, which were identified as mutants with ectopic expression of KNOX genes in leaves and morphologically resembling KNOX...
Juvenile-to-adult phase change is an indispensable event which guarantees a successful life cycle. Phase change has been studied in maize, Arabidopsis and rice, but is mostly unknown in other species. Soybean/Fabaceae plants undergo drastic changes of shoot architecture at the early vegetative stage including phyllotactic change and leaf type alter...
Cellulose synthase-like (CSL) genes are predicted to catalyse the biosynthesis of non-cellulosic polysaccharides such as the β-d-glycan backbone of hemicelluloses and are classified into nine subfamilies (CSLA–CSLH and CSLJ). The CSLD subfamily is conserved in all land plants, and among the nine CSL subfamilies, it shows the highest sequence simila...
We analyzed the abnormal shoot in youth (asy) mutant to understand the phase-specific regulation of shoot development. asy showed various shoot abnormalities, including small leaves due to the
precocious termination of cell division, defects in leaf blade-sheath boundary
formation, and abnormal shoot apical meristem maintenance at the early vegetat...
Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction o...
Primers used in this study.
(DOCX)
Multiple sequence alignment of the five copies of pre-miR820 and a part of the OsDRM2 sequence in the Nipponbare genome. Sequence alignment was made using ClustalX at default settings. The blue line, black lines, and red box indicate the regions corresponding to the OsDRM2 second exon, third intron, and miR820*, respectively, in the pre-miR820 sequ...
Decreased expression of OsDRM2 by RNAi is associated with increased TE expression. (A–C) Relative expression levels of OsDRM2 (A), RIRE7 (B), and the pre-miR820 region of CACTA (C) in independent transgenic lines transformed with an OsDRM2 RNAi construct (n = 6) or an empty vector (n = 3). Relative expression levels were measured by qRT-PCR and nor...
Sequence alignments of miR820 and its target site in DRM2 among Oryza species. (A) Alignment of sequences of miR820 among various Oryza species. (B) Alignment of sequences of the miR820 target site in DRM2 among various Oryza species. Dots indicate nucleotides identical to those in Nipponbare miR820a/b/c (A) or DRM2 (B).
(TIF)
Sequencing analysis of miR820 and its target site in DRM2 among various Oryza species.
(DOCX)
Structures and sequences of the five copies of miR820 in Nipponbare rice. (A) Schematic representations of the structures of the five copies of CACTA transposons carrying miR820. (B) Stem-loop structures of the five copies of pre-miR820 in Nipponbare, predicted by the mfold program. The miR820 sequences are designated by red rectangles. (C) Sequenc...
Multiple sequence alignment of the five copies of pre-miR820 in the Nipponbare genome. Sequence alignment was made using ClustalX at default settings. The blue lines, red box, and black box indicate the regions corresponding to the stem-loop structure, miR820, and miR820*, respectively.
(TIF)
The target of miR820 is OsDRM2. (A) Phylogenetic tree of de novo DNA methyltransferases. Amino acid sequences in the Cyt-C5 DNA methylase domain were used for this analysis. The bootstrap values from 1000 replicates are indicated at each node. Os, rice; Z and Zm, maize; At, Arabidopsis; Nt, tobacco; Mt, Medicago; Hv, barley; Hs, human. (B) Analysis...
Overexpression of pre-miR820 decreases OsDRM2 expression. (A) Relative expression levels of pre-miR820 measured by qRT-PCR in pre-miR820 overexpression lines (n = 5) and empty-vector lines (n = 6). The expression level of pre-miR820 was normalized to OsGAPDH and the expression level of the empty-vector lines was set as 1. (B) Northern blot analysis...
RNA silencing is a defense system against "genomic parasites" such as transposable elements (TE), which are potentially harmful to host genomes. In plants, transcripts from TEs induce production of double-stranded RNAs (dsRNAs) and are processed into small RNAs (small interfering RNAs, siRNAs) that suppress TEs by RNA-directed DNA methylation. Thus...
Phyllotaxy is defined as a spatial arrangement of leaves on the stem. The mechanism responsible for this extremely regular pattern is one of the most fascinating enigmas in plant biology. In this study, we identified a gene regulating the phyllotactic pattern in rice. Loss-of-function mutants of the DECUSSATE (DEC) gene displayed a phyllotactic con...
Rice PLASTOCHRON 1 (PLA1) and PLA2 genes regulate leaf maturation and plastochron, and their loss-of-function mutants exhibit small organs and rapid leaf emergence. They encode a cytochrome P450 protein CYP78A11 and an RNA-binding protein, respectively. Their homologs in Arabidopsis and maize are also associated with plant development/organ size. D...
The rice peter pan syndrome-1 (pps-1) mutant shows a prolonged juvenile phase and early flowering. Although the early vegetative phase and flowering time of pps-1 have been closely examined, the phenotypes in the late vegetative and reproductive phases are not yet well understood. In the ninth leaf blade of pps-1, the relative length of the midrib...
The temporal and spatial control of meristem identity is a key element in plant development. To better understand the molecular mechanisms that regulate inflorescence and flower architecture, we characterized the rice aberrant panicle organization 2 (apo2) mutant which exhibits small panicles with reduced number of primary branches due to the preco...
Because plant reproductive development occurs only in adult plants, the juvenile-to-adult phase change is an indispensable part of the plant life cycle. We identified two allelic mutants, peter pan syndrome-1 (pps-1) and pps-2, that prolong the juvenile phase in rice (Oryza sativa) and showed that rice PPS is an ortholog of Arabidopsis thaliana CON...
In rice (Oryza sativa), trans-acting small interfering RNA (ta-siRNA) is essential for shoot development, including shoot apical meristem (SAM) formation and leaf morphogenesis. The rice wavy leaf1 (waf1) mutant has been identified as an embryonic mutant resembling shoot organization1 (sho1) and sho2, homologs of a loss-of-function mutant of DICER-...
Summary Leaf veins have a complex network pattern. Formation of this vein pattern has been widely studied as a model of tissue pattern formation in plants. To understand the molecular mechanism governing the vascular patterning process, we isolated the rice mutant, commissural vein excessive1 (coe1). The coe1 mutants had short commissural vein (CV)...
The adaxial-abaxial axis in leaf primordia is thought to be established first and is necessary for the expansion of the leaf lamina along the mediolateral axis. To understand axis information in leaf development, we isolated the adaxialized leaf1 (adl1) mutant in rice, which forms abaxially rolled leaves. adl1 leaves are covered with bulliform-like...
Numerous genes are involved in the regulation of plant development, including those that regulate floral homeotic genes, We identified two recessive allelic rice mutants, open beak-1 (opb-1) and opb-2, which exhibited pleiotropic defects in leaf morphogenesis, inflorescence architecture, and floral organ identity. Abnormal cell proliferation was ob...
Most aerial parts of the plant body are products of the continuous activity of the shoot apical meristem (SAM). Leaves are the major component of the aerial plant body, and their temporal and spatial distribution mainly determines shoot architecture. Here we report the identification of the rice gene PLASTOCHRON3 (PLA3)/GOLIATH (GO) that regulates...
We describe how rice leaves are regionalized and regulated along the central-marginal axis. The shoot organization2 (sho2) mutant, a weak allele of SHOOTLESS4 that is a ZIPPY/ARGONAUTE7 homolog in rice, shows a variety of leaf abnormalities; filamentous leaves, bi- or trifurcated leaves, separation of the filamentous structure from the leaf blade o...
We isolated flattened shoot meristem (fsm) mutants in rice that showed defective seedling growth and died in the vegetative phase. Since most fsm plants had flat and small shoot apical meristems (SAMs), we suggest that FSM is required for proper SAM maintenance. FSM encodes a putative ortholog of Arabidopsis FASCIATA1 (FAS1) that corresponds to the...
Members of the Class III homeodomain leucine zipper (Class III HD-Zip) gene family are central regulators of crucial aspects of plant development. To better understand the roles of five Class III HD-Zip genes in rice (Oryza sativa) development, we investigated their expression patterns, ectopic expression phenotypes, and auxin responsiveness. Four...
Cleistogamy is an efficient strategy for preventing gene flow from genetically modified (GM) crops. We identified a cleistogamous mutant of rice harbouring a missense mutation (the 45th residue isoleucine to threonine; I45T) in the class-B MADS-box gene SUPERWOMAN1 (SPW1), which specifies the identities of lodicules (equivalent to petals) and stame...
The shoot apical meristem (SAM) is a group of stem cells that are responsible for plant development. Mutations in rice SHOOTLESS2 (SHL2), SHL4/SHOOT ORGANIZATION2 (SHO2), and SHO1 cause complete deletion or abnormal formation of the SAM. In this study we showed that defects in SAM formation in shl mutants are associated with the loss of expression...
In order to facilitate the functional analysis of rice genes, we produced about 50,000 insertion lines with the endogenous retrotransposon Tos17. Phenotypes of these lines in the M2 generation were observed in the field and characterized based on 53 phenotype descriptors. Nearly half of the lines showed more than one mutant phenotype. The most freq...
In higher plants, the process of embryogenesis establishes the plant body plan (body axes). On the basis of positional information specified by the body axes, the shoot apical meristem (SAM) and root apical meristem (RAM) differentiate at fixed positions early in embryogenesis. After germination, SAM and RAM are responsible for the development of t...
In higher plants, leaves initiate in constant spatial and temporal patterns. Although the pattern of leaf initiation is a key element of plant shoot architecture, little is known about how the time interval between initiation events, termed plastochron, is regulated. Here, we present a detailed analysis of plastochron2 (pla2), a rice (Oryza sativa)...
Rice is becoming a model plant in monocotyledons and a model cereal crop. For better understanding of the rice plant, it is essential to elucidate the developmental programs of the life cycle. To date, several attempts have been made in rice to categorize the developmental processes of some organs into substages. These studies are based exclusively...
A novel mutation affecting the lateral symmetry of rice leaves, leaf lateral symmetry 1 (lsy1), was identified. The lsy1 mutant showed two major phenotypes of leaves; a narrow leaf due to the deletion of a part or whole of one lateral half, and a bifurcated leaf in which an additional midrib is formed in one lateral halt Developmental analysis reve...
During postembryonic development of higher plants, the shoot apical meristem produces lateral organs in a regular spacing (phyllotaxy) and a regular timing (plastochron). Molecular analysis of mutants associated with phyllotaxy and plastochron would greatly increase understanding of the developmental mechanism of plant architecture because phyllota...
Asymmetric cell division is one of the most important mechanisms in the diversification of cell function and fate. In Arabidopsis, SCARECROW (SCR) is essential for the asymmetric division of the cortex/endodermis progenitor cell in the root. To learn more about how SCR is involved in asymmetric division, we analyzed the rice SCR (OsSCR) expression....
To characterize the SHL2 and SHL1 genes in detail, we analyzed three strains carrying weak alleles of SHL2, shl2-6, shl2-7, and shl2-8, and one weak allele of SHL1, shl1-3. In contrast to strong alleles, which result in lack of shoot meristem, strains bearing these weak alleles formed shoot meristem frequently during embryogenesis. In shl2-6 and sh...
The rice heterochronic gene plastochron1, pla1, shows shorter plastochron and ectopic expression of the vegetative program during the rice reproductive phase resulting in aberrant panicle formation. A genetic and physical map was constructed to isolate the causal gene for the pla1 syndrome. Small-scale mapping was carried out to determine the appro...
The mechanism regulating the pattern of leaf initiation was analyzed by using shoot organization (sho) mutants derived from three loci (SHO1, SHO2, and SHO3). In the early vegetative phase, sho mutants show an increased rate of leaf production with random phyllotaxy. The resulting leaves are malformed, threadlike, or short and narrow. Their shoot a...
The mechanism regulating the pattern of leaf initiation was analyzed by using shoot organization (sho) mutants derived from three loci (SHO1, SHO2, and SHO3). In the early vegetative phase, sho mutants show an increased rate of leaf production with random phyllotaxy. The resulting leaves are malformed, threadlike, or short and narrow. Their shoot a...
The morphology of the ligular region and the leaf epidermis of four regions, adaxial and abaxial surfaces of blade and sheath was investigated in 22 species representing 17 genera and 8 tribes of Poaceae. Leaf epidermal features varied widely among the species. The adaxial surface features of sheath were common to all the species; it lacked any typ...
