Suppression of tiller bud activity in tillering dwarf mutants of rice

Arabidopsis Teosinte Branched1-like 1 regulates axillary bud outgrowth and is homologous to monocot Teosinte Branched1

Axillary bud outgrowth is controlled by developmental and environmental signals through the integrated action of hormones and other factors that probably regulate the cell cycle in the buds. While hormonal regulators have been studied extensively, less is known about downstream mechanisms regulating bud outgrowth. The TCP domain protein Teosinte Branched1 (TB1) is a putative transcriptional regulator that represses bud outgrowth in grasses. Phylogenetic analyses have indicated that three hypothetical Arabidopsis (Arabidopsis thaliana) proteins, TCP1, TCP12 and TCP18 [Teosinte Branched1-Like 1 (TBL1)], are closely related to monocot TB1 proteins. A reverse genetics approach was used to identify TBL1 and TCP12 mutants to assess the function of the hypothetical proteins. No obvious phenotype was observed in tcp12 mutants. tbl1 null mutants exhibited a non-pleiotropic hyperbranching phenotype that was due to enhanced outgrowth of primary and secondary buds. The role of TBL1 as a repressor of bud outgrowth was supported by TBL1 mRNA accumulation: abundance was high in unelongated buds, and decreased to low levels in buds that were elongating. Analyses of TBL1 expression in hormone signaling mutants with aberrant branching suggest that TBL1 acts downstream of auxin and the MAX-related hormone to coordinate bud outgrowth. The data are consistent with Arabidopsis TBL1 providing functionality similar to monocot TB1, and highlight the conservation of mechanisms regulating branching across large evolutionary distances.

F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress

F-box proteins constitute a large family in eukaryotes and are characterized by a conserved F-box motif (approximately 40 amino acids). As components of the Skp1p-cullin-F-box complex, F-box proteins are critical for the controlled degradation of cellular proteins. We have identified 687 potential F-box proteins in rice (Oryza sativa), the model monocotyledonous plant, by a reiterative database search. Computational analysis revealed the presence of several other functional domains, including leucine-rich repeats, kelch repeats, F-box associated domain, domain of unknown function, and tubby domain in F-box proteins. Based upon their domain composition, they have been classified into 10 subfamilies. Several putative novel conserved motifs have been identified in F-box proteins, which do not contain any other known functional domain. An analysis of a complete set of F-box proteins in rice is presented, including classification, chromosomal location, conserved motifs, and phylogenetic relationship. It appears that the expansion of F-box family in rice, in large part, might have occurred due to localized gene duplications. Furthermore, comprehensive digital expression analysis of F-box protein-encoding genes has been complemented with microarray analysis. The results reveal specific and/or overlapping expression of rice F-box protein-encoding genes during floral transition as well as panicle and seed development. At least 43 F-box protein-encoding genes have been found to be differentially expressed in rice seedlings subjected to different abiotic stress conditions. The expression of several F-box protein-encoding genes is also influenced by light. The structure and function of F-box proteins in plants is discussed in light of these results and the published information. These data will be useful for prioritization of F-box proteins for functional validation in rice.

Arabidopsis BRANCHED1 acts as an integrator of branching signals within axillary buds

Shoot branching patterns depend on a key developmental decision: whether axillary buds grow out to give a branch or whether they remain dormant in the axils of leaves. This decision is controlled by endogenous and environmental stimuli mediated by hormonal signals. Although genes involved in the long-distance signaling of this process have been identified, the genes responding inside the buds to cause growth arrest remained unknown in Arabidopsis thaliana. Here, we describe an Arabidopsis gene encoding a TCP transcription factor closely related to teosinte branched1 (tb1) from maize (Zea mays), BRANCHED1 (BRC1), which represents a key point at which signals controlling branching are integrated within axillary buds. BRC1 is expressed in developing buds, where it arrests bud development. BRC1 downregulation leads to branch outgrowth. BRC1 responds to developmental and environmental stimuli controlling branching and mediates the response to these stimuli. Mutant and expression analyses suggest that BRC1 is downstream of the MORE AXILLARY GROWTH pathway and that it is required for auxin-induced apical dominance. Therefore, BRC1 acts inside the buds as an integrator of signals controlling bud outgrowth and translates them into a response of cell growth arrest. The conservation of BRC1/tb1 function among distantly related angiosperm species suggests that a single ancestral mechanism of branching control integration evolved before the radiation of flowering plants.

Genetic interaction between 2 tillering genes, reduced culm number 1 (rcn1) and tillering dwarf gene d3, in rice

Mutant genes, reduced culm number 1 (rcn1) and bunketsuwaito tillering dwarf (d3), affect tiller number in rice (Oryza sativa L.) in opposite directions. The d3 mutant was reported to increase tiller number and reduce plant stature. Our objective was to compare the phenotype of the d3rcn1 double mutant with each single mutant and parental rice cultivar "Shiokari" and to clarify whether the Rcn1 gene interacted with the D3 gene. We recovered a new rcn1 mutant from Shiokari and developed d3rcn1 double mutant with Shiokari genetic background. A new rcn1 mutant, designated as "S-97-61" exhibited a reduction in tiller number and plant stature to about the same level as the previously reported original rcn1 mutant. Three near-isogenic lines, rcn1 mutant, d3 mutant, and d3rcn1 double mutant, were grown together with the parental Shiokari. The reduction in tillering by the rcn1 mutation was independent of the d3 genotype, and tillering number of d3rcn1 double mutant was between those of the d3 and rcn1 mutants. These results demonstrated that the Rcn1 gene was not involved in the D3-associated pathway in tillering control.

Rice tillering dwarf mutant dwarf3 has increased leaf longevity during darkness-induced senescence or hydrogen peroxide-induced cell death

Senescence or cell death in plant leaves is known to be inducible by darkness or H(2)O(2). When the Arabidopsis gene MAX2/ORE9 is disrupted, leaf senescence or cell death in response to the above stimuli is delayed. Because the rice (Oryza sativa L.) gene DWARF3 (D3) is orthologous to MAX2/ORE9, we wished to know whether disruption of D3 also results in increased longevity in leaves. We found that darkness-induced senescence or H(2)O(2)-induced cell death in the third leaf [as measured by chlorophyll degradation, membrane ion leakage and expression of senescence-associated genes (SAGs)] in a d3 rice mutant was delayed by 1-3 d compared to that in its reference line Shiokari. Moreover, the mRNA levels of D3, HTD1 and D10, which are orthologs of Arabidopsis MAX2/ORE9, MAX3 and MAX4, respectively, increased during cell death. These results suggest that D3 protein in rice, like MAX2/ORE9 in Arabidopsis, is involved in leaf senescence or cell death.

Overexpression of a NAC-domain protein promotes shoot branching in rice

For a better understanding of shoot branching in rice (Oryza sativa), a rice activation-tagging library was screened for mutations in tiller development. Here, an activation-tagging mutant Ostil1 (Oryza sativa tillering1) was characterized, which showed increased tillers, enlarged tiller angle and semidwarf phenotype. Flanking sequence was obtained by plasmid rescue. RNA-interfering and overexpression transgenic rice plants were produced using Agrobacterium-mediated transformation. The mutant phenotype was cosegregated with the reallocation of Ds element, and the flanking region of the reallocated Ds element was identified as part of the OsNAC2 gene. Northern analysis showed that expression of OsNAC2 was greatly induced in the mutant plants. Transgenic rice overexpressing the OsNAC2 resulted in recapture of the mutant phenotype, while downregulation of OsNAC2 in the Ostil1 mutant through RNA interfering (RNAi) complemented the mutant phenotype, confirming that the Ostil1 was caused by overexpression of OsNAC2. Overexpression of OsNAC2 regulates shoot branching in rice. Overexpression of OsNAC2 contributes tiller bud outgrowth, but does not affect tiller bud initiation. This suggests that OsNAC2 has potential utility for improving plant structure for higher light-use efficiency and higher yield potential in rice.

The rice HIGH-TILLERING DWARF1 encoding an ortholog of Arabidopsis MAX3 is required for negative regulation of the outgrowth of axillary buds

Rice tillering is an important agronomic trait for grain production. The HIGH-TILLERING DWARF1 (HTD1) gene encodes an ortholog of Arabidopsis MAX3. Complementation analyses for HTD1 confirm that the defect in HTD1 is responsible for both high-tillering and dwarf phenotypes in the htd1 mutant. The rescue of the Arabidopsis max3 mutant phenotype by the introduction of Pro(35S):HTD1 indicates HTD1 is a carotenoid cleavage dioxygenase that has the same function as MAX3 in synthesis of a carotenoid-derived signal molecule. The HTD1 gene is expressed in both shoot and root tissues. By evaluating Pro(HTD1):GUS expression, we found that the HTD1 gene is mainly expressed in vascular bundle tissues throughout the plant. Auxin induction of HTD1 expression suggests that auxin may regulate rice tillering partly through upregulation of HTD1 gene transcription. Restoration of dwarf phenotype after the removal of axillary buds indicates that the dwarfism of the htd1 mutant may be a consequence of excessive tiller production. In addition, the expression of HTD1, D3 and OsCCD8a in the htd1 and d3 mutants suggests a feedback mechanism may exist for the synthesis and perception of the carotenoid-derived signal in rice. Characterization of MAX genes in Arabidopsis, and identification of their orthologs in pea, petunia and rice indicates the existence of a conserved mechanism for shoot-branching regulation in both monocots and dicots.

Branching genes are conserved across species. Genes controlling a novel signal in pea are coregulated by other long-distance signals

Physiological and genetic studies with the ramosus (rms) mutants in garden pea (Pisum sativum) and more axillary shoots (max) mutants in Arabidopsis (Arabidopsis thaliana) have shown that shoot branching is regulated by a network of long-distance signals. Orthologous genes RMS1 and MAX4 control the synthesis of a novel graft-transmissible branching signal that may be a carotenoid derivative and acts as a branching inhibitor. In this study, we demonstrate further conservation of the branching control system by showing that MAX2 and MAX3 are orthologous to RMS4 and RMS5, respectively. This is consistent with the long-standing hypothesis that branching in pea is regulated by a novel long-distance signal produced by RMS1 and RMS5 and that RMS4 is implicated in the response to this signal. We examine RMS5 expression and show that it is more highly expressed relative to RMS1, but under similar transcriptional regulation as RMS1. Further expression studies support the hypothesis that RMS4 functions in shoot and rootstock and participates in the feedback regulation of RMS1 and RMS5 expression. This feedback involves a second novel long-distance signal that is lacking in rms2 mutants. RMS1 and RMS5 are also independently regulated by indole-3-acetic acid. RMS1, rather than RMS5, appears to be a key regulator of the branching inhibitor. This study presents new interactions between RMS genes and provides further evidence toward the ongoing elucidation of a model of axillary bud outgrowth in pea.

Formation, maintenance and function of the shoot apical meristem in rice

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 the above-ground and below-ground parts, respectively, of the plant. Because of the importance of SAM function in plant development, the mechanisms of SAM formation during embryogenesis and of SAM maintenance and function in post-embryonic development are priority questions in plant developmental biology. Recent advances in molecular and genetic analysis of morphogenetic mutations in Arabidopsis have revealed several components required for SAM formation, maintenance and function. Although these processes are fundamental to the life cycle of every plant, conservation of the components does not explain the diversity of plant morphologies. Rice is used as a model plant of the grass family and of monocots because of the progress in research infrastructure, especially the collection of unique mutations and genome information. In comparison with the dicot Arabidopsis, rice has many unique organs or processes of development. This review summarizes what is known of the processes of SAM formation, maintenance and function in rice.

Phytochrome B represses Teosinte Branched1 expression and induces sorghum axillary bud outgrowth in response to light signals

Light is one of the environmental signals that regulate the development of shoot architecture. Molecular mechanisms regulating shoot branching by light signals have not been investigated in detail. Analyses of light signaling mutants defective in branching provide insight into the molecular events associated with the phenomenon. It is well documented that phytochrome B (phyB) mutant plants display constitutive shade avoidance responses, including increased plant height and enhanced apical dominance. We investigated the phyB-1 mutant sorghum (Sorghum bicolor) and analyzed the expression of the sorghum Teosinte Branched1 gene (SbTB1), which encodes a putative transcription factor that suppresses bud outgrowth, and the sorghum dormancy-associated gene (SbDRM1), a marker of bud dormancy. Buds are formed in the leaf axils of phyB-1; however, they enter into dormancy soon after their formation. The dormant state of phyB-1 buds is confirmed by the high level of expression of the SbDRM1 gene. The level of SbTB1 mRNA is higher in the buds of phyB-1 compared to wild type, suggesting that phyB mediates the growth of axillary shoots in response to light signals in part by regulating the mRNA abundance of SbTB1. These results are confirmed by growing wild-type seedlings with supplemental far-red light that induces shade avoidance responses. We hypothesize that active phyB (Pfr) suppresses the expression of the SbTB1 gene, thereby inducing bud outgrowth, whereas environmental conditions that inactivate phyB allow increased expression of SbTB1, thereby suppressing bud outgrowth.

Genes controlling plant architecture

Plant architecture, referring here to the aerial part of a higher plant, is mainly determined by factors affecting shoot branching, plant height and inflorescence morphology. Significant progress has been made in isolating and characterizing genes that are directly involved in the formation of plant architecture, especially those controlling the initiation and outgrowth of axillary buds, elongation of stems and architecture of inflorescences. Most of these genes are conserved between dicotyledonous and monocotyledonous plants, indicating that these plants share similar regulatory pathways to establish their shape. The conservation of these genes makes them of great agronomical importance for improving crop yields.

Axillary bud outgrowth: sending a message

Mutants that branch profusely in the presence of a growing shoot tip have highlighted the role of graft-transmissible signals that are produced in roots and stem. Orthologous genes in Arabidopsis, pea and petunia are involved in the transmission of a novel long-distance message. These genes show varying degrees of regulation by auxin and an auxin-independent feedback system, and encode enzymes that might act on carotenoid-like substrates. Axillary bud outgrowth is under homeostatic control, involving developmental stages or checkpoints. Perturbation of the long-range messaging and auxin depletion does not guarantee that bud outgrowth will ensue at a particular node.

The Rice Mutant dwarf bamboo shoot 1: A Leaky Mutant of the NACK-type Kinesin-like Gene Can Initiate Organ Primordia but not Organ Development

That plant dwarfism is caused by hormonal defects related to gibberellin and brassinosteroid has been well documented. Other contributing elements, however, have not been elucidated. Here, we report on one of the most severe dwarf mutants of rice, dwarf bamboo shoot 1 (dbs1). Most mutant plants died within 1 month after sowing, but a few (5.2%) survived and grew. Vacuolation enlarged cells in the leaf primordia and seminal root before abortion, which disrupted the organized cell files in these organs. Relative to the severe defects in shoot and root growth, the overall structure of the dbs1 embryo was almost normal. Similarly, initiation and organogenesis of the leaf primordia at the shoot apical meristem and those of the lateral root primordia at the root elongation zone occurred normally. These observations suggest that DBS1 is involved in the growth and development of organs but not in organ initiation or organogenesis. Positional cloning of DBS1 revealed that it encoded a NACK-type kinesin-like protein (OsNACK), homologous to the essential components of a mitogen-activated protein kinase cascade during plant cytokinesis. A BLAST search indicated that DBS1 was the only gene encoding the OsNACK-type protein in the rice genome, and the dbs1 mutant produced only small amounts of the translatable DBS1 mRNA. Thus, we conclude that the dbs1 mutation causes a severe defect in DBS1 function but does not completely shut it down. We discuss the leaky phenotype of dbs1 under the restricted functioning of OsNACK.

Characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (Oryza sativa L.)

A rice htd-1 mutant, related to tillering and dwarfing, was characterized. We show that the htd-1 mutant increases its tiller number by releasing axillary buds from dormant stage rather than by initiating more axillary buds. The dwarf is caused by averagely reducing each internode and panicle. Based on this dwarfing pattern, the htd-1 mutant could be grouped into dn-type dwarf defined by Takeda (Gamma Field Symp 16:1, 1977). In addition, the dwarfing of the htd-1 mutant was found independent of GA based on the analyses of two GA-mediated processes. Based on the quantitative determination of IAA and ABA and application of the two hormones exogenously to the seedlings, we inferred that the high tillering capacity of the htd-1 mutant should not be attributed to a defect in the synthesis of IAA or ABA. The genetic analysis of the htd-1 mutant indicated that the phenotypes of high tillering and dwarf were controlled by a recessive gene, termed htd1. By map-based cloning, the htd1 gene was fine mapped in a 30-kb DNA region on chromosome 4. Sequencing the target DNA region and comparing the counterpart DNA sequences between the htd-1 mutant and other rice varieties revealed a nucleotide substitution corresponding to an amino acid substitution from prolin to leucine in a predicted rice gene, OsCCD7, the rice orthologous gene of AtMAX3/CCD7. With the evidence of the association between the presence of one amino acid change in OsCCD7 and the abnormal phenotypes of the htd-1 mutant, OsCCD7 was identified as the candidate of the HTD1 gene.

Hormonally controlled expression of the Arabidopsis MAX4 shoot branching regulatory gene

The Arabidopsis MORE AXILLARY BRANCHING 4 (MAX4) gene is required for the production of a long-range, graft-transmissible signal that inhibits shoot branching. Buds of max4 mutant plants are resistant to the inhibitory effects of apically applied auxin, indicating that MAX4 is required for auxin-mediated bud inhibition. The RAMOSUS 1 (RMS1) and DECREASED APICAL DOMINANCE 1 (DAD1) genes of pea and petunia, respectively, are orthologous to MAX4 and function in a similar way. Here we show that, despite the similarities between these three genes, there are significant differences in the regulation of their expression. RMS1 is known to be upregulated by auxin in the shoot, suggesting a straightforward link between the RMS1-dependent branch-inhibiting signal and auxin, whereas we find that MAX4 is only upregulated by auxin in the root and hypocotyl, and this is not required for the inhibition of shoot branching. Furthermore, both RMS1 and DAD1 are subject to feedback regulation, for which there is no evidence for MAX4. Instead, overexpression studies and reciprocal grafting experiments demonstrate that the most functionally significant point of interaction between auxin and MAX4 is post-transcriptional and indeed post-synthesis of the MAX4-dependent graft-transmissible signal.

Shoot and inflorescence branching

A major aspect of postembryonic plant development is the formation of secondary axes of growth: vegetative branches, inflorescence branches, or flowers. The first step in side-shoot development is the establishment of lateral meristems in the axils of leaves. GRAS-, MYB-, and bHLH-type transcription factors act as key regulators of early steps in this process. The REVOLUTA subfamily of HD-ZIP transcription factors controls the organization of lateral meristems. Whereas the development of lateral meristems into lateral buds is only poorly understood, recent studies have provided new insights into the regulation of lateral bud outgrowth. The MORE AXILLARY GROWTH (MAX) genes of Arabidopsis and the RAMOSUS (RMS) genes of pea are involved in the production, perception, and transduction of a signal that inhibits lateral bud outgrowth. Synthesis of this not-yet-identified hormone is positively regulated by the main shoot tip through auxin signalling.

Analysis of the rice mutant dwarf and gladius leaf 1. Aberrant katanin-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling

Molecular genetic studies of plant dwarf mutants have indicated that gibberellin (GA) and brassinosteroid (BR) are two major factors that determine plant height; dwarf mutants that are caused by other defects are relatively rare, especially in monocot species. Here, we report a rice (Oryza sativa) dwarf mutant, dwarf and gladius leaf 1 (dgl1), which exhibits only minimal response to GA and BR. In addition to the dwarf phenotype, dgl1 produces leaves with abnormally rounded tip regions. Positional cloning of DGL1 revealed that it encodes a 60-kD microtubule-severing katanin-like protein. The protein was found to be important in cell elongation and division, based on the observed cell phenotypes. GA biosynthetic genes are up-regulated in dgl1, but the expression of BR biosynthetic genes is not enhanced. The enhanced expression of GA biosynthetic genes in dgl1 is not caused by inappropriate GA signaling because the expression of these genes was repressed by GA3 treatment, and degradation of the rice DELLA protein SLR1 was triggered by GA3 in this mutant. Instead, aberrant microtubule organization caused by the loss of the microtubule-severing function of DGL1 may result in enhanced expression of GA biosynthetic genes in that enhanced expression was also observed in a BR-deficient mutant with aberrant microtubule organization. These results suggest that the function of DGL1 is important for cell and organ elongation in rice, and aberrant DGL1-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling.