The LAX1 and FRIZZY PANICLE 2 genes determine the inflorescence architecture of rice by controlling rachis-branch and spikelet development

Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.)

Architecture of the rice inflorescence, which is determined mainly by the morphology, number and length of primary and secondary inflorescence branches, is an important agronomical trait. In the current study, we characterized a novel dense and erect panicle (EP) mutant, dep3, derived from the Oryza sativa ssp. japonica cultivar Hwacheong treated with N-methyl-N-nitrosourea. The panicle of the dep3 mutant remained erect from flowering to full maturation, whereas the panicle of the wild type plant began to droop after flowering. The dep3 mutation also regulated other panicle characteristics, including panicle length, grain shape and grain number per panicle. Anatomical observations revealed that the dep3 mutant had more small vascular bundles and a thicker culm than wild type plants, explaining the EP phenotype. Genetic analysis indicated that the phenotype with the dense and EP was controlled by a single recessive gene, termed dep3. The DEP3 gene was identified as the candidate via a map-based cloning approach and was predicted to encode a patatin-like phospholipase A2 (PLA2) superfamily domain-containing protein. The mutant allele gene carried a 408 bp genomic deletion within LOC_Os06g46350, which included the last 47 bp coding region of the third exon and the first 361 bp of the 3'-untranslated region. Taken together, our results indicated that the patatin-like PLA2 might play a significant role in the formation of vascular bundles, and that the dep3 mutant may provide another EP resource for rice breeding programs.

Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice

BACKGROUND

Plant growth depends on synergistic interactions between internal and external signals, and yield potential of crops is a manifestation of how these complex factors interact, particularly at critical stages of development. As an initial step towards developing a systems-level understanding of the biological processes underlying the expression of overall agronomic potential in cereal crops, a high-resolution transcriptome analysis of rice was conducted throughout life cycle of rice grown under natural field conditions.

RESULTS

A wide range of gene expression profiles based on 48 organs and tissues at various developmental stages identified 731 organ/tissue specific genes as well as 215 growth stage-specific expressed genes universally in leaf blade, leaf sheath, and root. Continuous transcriptome profiling of leaf from transplanting until harvesting further elucidated the growth-stage specificity of gene expression and uncovered two major drastic changes in the leaf transcriptional program. The first major change occurred before the panicle differentiation, accompanied by the expression of RFT1, a putative florigen gene in long day conditions, and the downregulation of the precursors of two microRNAs. This transcriptome change was also associated with physiological alterations including phosphate-homeostasis state as evident from the behavior of several key regulators such as miR399. The second major transcriptome change occurred just after flowering, and based on analysis of sterile mutant lines, we further revealed that the formation of strong sink, i.e., a developing grain, is not the major cause but is rather a promoter of this change.

CONCLUSIONS

Our study provides not only the genetic basis for functional genomics in rice but also new insight into understanding the critical physiological processes involved in flowering and seed development, that could lead to novel strategies for optimizing crop productivity.

Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae

Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.

A rapid, direct observation method to isolate mutants with defects in starch grain morphology in rice

Starch forms transparent grains, referred to as starch grains (SGs), in amyloplasts. Despite the simple glucose polymer composition of starch, SGs exhibit different morphologies depending on plant species, especially in the endosperm of the Poaceae family. This study reports a novel method for preparing thin sections of endosperm without chemical fixation or resin embedding that allowed us to visualize subcellular SGs clearly. Using this method, we observed the SG morphologies of >5,000 mutagenized rice seeds and were able to isolate mutants in which SGs were morphologically altered. In five mutants, named ssg (substandard starch grain), increased numbers of small SGs (ssg1-ssg3), enlarged SGs (ssg4) and abnormal interior structures of SGs (ssg5) were observed. Amylopectin chain length distribution analysis and identification of the mutated gene suggested a possible allelic relationship between ssg1, ssg2, ssg3 and the previously isolated amylose-extender (ae) mutants, while ssg4 and ssg5 seemed to be novel mutants. Compared with conventional observation methods, the methods developed here are more effective for obtaining fine images of subcellular SGs and are suitable for the observation of a large number of samples.

A conserved mechanism of bract suppression in the grass family

Suppression of inflorescence leaf, or bract, growth has evolved multiple times in diverse angiosperm lineages, including the Poaceae and Brassicaceae. Studies of Arabidopsis thaliana mutants have revealed several genes involved in bract suppression, but it is not known if these genes play a similar role in other plants with suppressed bracts. We identified maize (Zea mays) tassel sheath (tsh) mutants, characterized by the loss of bract suppression, that comprise five loci (tsh1-tsh5). We used map-based cloning to identify Tsh1 and found that it encodes a GATA zinc-finger protein, a close homolog of HANABA TARANU (HAN) of Arabidopsis. The bract suppression function of Tsh1 is conserved throughout the grass family, as we demonstrate that the rice (Oryza sativa) NECK LEAF1 (NL1) and barley (Hordeum vulgare) THIRD OUTER GLUME (TRD) genes are orthologous with Tsh1. Interestingly, NL1/Tsh1/TRD expression and function are not conserved with HAN. The existence of paralogous NL1/Tsh1/TRD-like genes in the grasses indicates that the NL1/Tsh1/TRD lineage was created by recent duplications that may have facilitated its neofunctionalization. A comparison with the Arabidopsis genes regulating bract suppression further supports the hypothesis that the convergent evolution of bract suppression in the Poaceae involved recruitment of a distinct genetic pathway.

Genetic and molecular bases of rice yield

Grain yield in rice is a complex trait multiplicatively determined by its three component traits: number of panicles, number of grains per panicle, and grain weight; all of which are typical quantitative traits. The developments in genome mapping, sequencing, and functional genomic research have provided powerful tools for investigating the genetic and molecular bases of these quantitative traits. Dissection of the genetic bases of the yield traits based on molecular marker linkage maps resolved hundreds of quantitative trait loci (QTLs) for these traits. Mutant analyses and map-based cloning of QTLs have identified a large number of genes required for the basic processes underlying the initiation and development of tillers and panicles, as well as genes controlling numbers and sizes of grains and panicles. Molecular characterization of these genes has greatly advanced the mechanistic understanding of the regulation of these rice yield traits. These findings have significant implications in crop genetic improvement.

Erect panicle2 encodes a novel protein that regulates panicle erectness in indica rice

Rice (Oryza sativa L.) inflorescence (panicle) architecture is an important agronomic trait for rice breeding. A number of high-yielding japonica rice strains, characterized by an erect panicle (EP) of their architecture, have been released as commercial varieties in China. But no EP-type indica varieties are released so far. Here, we identified two allelic erect-panicle mutants in indica rice, erect panicle2-1 (ep2-1) and erect panicle2-2 (ep2-2), exhibiting the characteristic erect panicle phenotype. Both mutants were derived from spontaneous mutation. We cloned the EP2 gene by way of a map-based cloning strategy, and a transgenic complementation test rescued the phenotype of ep2-1. Anatomical investigations revealed that the ep2 mutants have more vascular bundles and a thicker stem than that of wild-type plants, explaining the panicle erectness phenotype in ep2 mutants. It was shown that EP2 was specifically expressed in the vascular bundles of internodes by GUS staining and RT-PCR. EP2 encodes a novel plant-specific protein, which localizes to the endoplasmic reticulum with unknown biochemical function. In addition, EP2 also regulates other panicle characteristics, such as panicle length and grain size, but grain number per panicle shows little change, indicating that the mutation of the ep2 gene could be applied in EP-type indica rice breeding.

Fine mapping and candidate gene analysis of spd6, responsible for small panicle and dwarfness in wild rice (Oryza rufipogon Griff.)

Identification of genes in rice that affect production and quality is necessary for improving the critical global food source. CSSL58, a chromosome segment substitution line (CSSL) containing a chromosome segment of Oryza rufipogon in the genetic background of the indica cultivar Teqing showed significantly smaller panicles, fewer grains per panicle, smaller grains and dwarfness compared with the recurrent parent Teqing. Genetic analysis of the BC(4)F(1) and BC(4)F(2) generations, derived from a cross between CSSL58 and Teqing, showed that these traits are controlled by the recessive gene spd6, which mapped to the short arm of chromosome 6. Fine mapping and high-resolution linkage analysis using 24,120 BC(4)F(3) plants and markers flanking spd6 were carried out, and the gene was localized to a 22.4 kb region that contains four annotated genes according to the genome sequence of japonica Nipponbare. Phenotypic evaluation of the nearly isogenic line NIL(spd6) revealed that spd6 from wild rice has pleiotropic effects on panicle number per plant, grain size, grain weight, grain number per panicle and plant height, suggesting that this gene might play an important role in the domestication of rice. The discovery of spd6 may ultimately be useful for the design and breeding of crops with high grain yield and quality.

Heterochronic development of the floret meristem determines grain number per spikelet in diploid, tetraploid and hexaploid wheats

BACKGROUND AND AIMS

The inflorescence of grass species such as wheat, rice and maize consists of a unique reproductive structure called the spikelet, which is comprised of one, a few, or several florets (individual flowers). When reproductive growth is initiated, the inflorescence meristem differentiates a spikelet meristem as a lateral branch; the spikelet meristem then produces a floret meristem as a lateral branch. Interestingly, in wheat, the number of fertile florets per spikelet is associated with ploidy level: one or two florets in diploid, two or three in tetraploid, and more than three in hexaploid wheats. The objective of this study was to identify the mechanisms that regulate the architecture of the inflorescence in wheat and its relationship to ploidy level.

METHODS

The floral anatomy of diploid (Triticum monococcum), tetraploid (T. turgidum ssp. durum) and hexaploid (T. aestivum) wheat species were investigated by light and scanning electron microscopy to describe floret development and to clarify the timing of the initiation of the floret primordia. In situ hybridization analysis using Wknox1, a wheat knotted1 orthologue, was performed to determine the patterning of meristem formation in the inflorescence.

KEY RESULTS

The recessive natural mutation of tetraploid (T. turgidum ssp. turgidum) wheat, branching head (bh), which produces branched inflorescences, was used to demonstrate the utility of Wknox1 as a molecular marker for meristematic tissue. Then an analysis of Wknox1 expression was performed in diploid, tetraploid and hexaploid wheats and heterochronic development of the floret meristems was found among these wheat species.

CONCLUSIONS

It is shown that the difference in the number of floret primordia in diploid, tetraploid and hexaploid wheats is caused by the heterochronic initiation of floret meristem development from the spikelet meristem.

Short panicle1 encodes a putative PTR family transporter and determines rice panicle size

The architecture of the rice inflorescence, which is determined mainly by the number and length of primary and secondary inflorescence branches, is of importance in both agronomy and developmental biology. The position and number of primary branches are established during the phase transition from vegetative to reproductive growth, and several of the genes identified as participating in this process do so by regulating the meristemic activities of inflorescence. However, little is known about the molecular mechanism that controls inflorescence branch elongation. Here, we report on a novel rice mutant, short panicle1 (sp1), which is defective in rice panicle elongation, and thus leads to the short-panicle phenotype. Gene cloning and characterization indicate that SP1 encodes a putative transporter that belongs to the peptide transporter (PTR) family. This conclusion is based on the findings that SP1 contains a conserved PTR2 domain consisting of 12 transmembrane domains, and that the SP1-GFP fusion protein is localized in the plasma membrane. The SP1 gene is highly expressed in the phloem of the branches of young panicles, which is consistent with the predicted function of SP1 and the sp1 phenotype. Phylogenetic analysis implies that SP1 might be a nitrate transporter. However, neither nitrate transporter activity nor any other compounds transported by known PTR proteins could be detected in either a Xenopus oocyte or yeast system, in our study, suggesting that SP1 may need other component(s) to be able to function as a transporter, or that it transports unknown substrates in the monocotyledonous rice plant.

Two-Step Regulation of LAX PANICLE1 Protein Accumulation in Axillary Meristem Formation in Rice

Axillary meristem (AM) formation is an important determinant of plant architecture. In rice (Oryza sativa), LAX PANICLE1 (LAX1) function is required for the generation of AM throughout the plant's lifespan. Here, we show a close relationship between AM initiation and leaf development; specifically, the plastochron 4 (P4) stage of leaf development is crucial for the proliferation of meristematic cells. Coincident with this, LAX1 expression starts in the axils of leaves at P4 stage. LAX1 mRNA accumulates in two to three layers of cells in the boundary region between the initiating AM and the shoot apical meristem. In lax1 mutants, the proliferation of meristematic cells is initiated but fails to progress into the formation of AM. The difference in sites of LAX1 mRNA expression and its action suggests non-cell-autonomous characteristics of LAX1 function. We found that LAX1 protein is trafficked to AM in a stage- and direction-specific manner. Furthermore, we present evidence that LAX1 protein movement is required for the full function of LAX1. Thus, we propose that LAX1 protein accumulates transiently in the initiating AM at P4 stage by a strict regulation of mRNA expression and a subsequent control of protein trafficking. This two-step regulation is crucial to the establishment of the new AM.

Fine mapping of Spr3, a locus for spreading panicle from African cultivated rice (Oryza glaberrima Steud.)

A CSSL (chromosome segment substitution line), SG-64, carrying a segment of chromosome 4 from African cultivated rice (CG-14) in the genetic background of var. Wuyujing-7 (japonica), showed a spreading panicle, which was different significantly from that of Wuyujing-7 with an erect compact panicle. The gene controlling a spreading panicle is referred to as Spr3, and is mapped on chromosome 4. To uncover the genetic basis of Spr3, a large F(2) population derived from cross between SG-64 and Wuyujing-7 was constructed for fine mapping of the Spr3 locus. The high-resolution linkage analysis revealed that the Spr3 locus was narrowed down to a 4.6-kb region. The delimited genomic DNA regions of Wuyujing-7 and CG-14 were sequenced and compared. Sequence mutations between Wuyujing-7 and CG-14 were evident and the candidate genes for the locus were predicted. Publicly available databases were searched for homologous cDNA sequences. However, any coding regions or other meaningful sequences for the Spr3 locus were not found within this delimited region. This result suggested that Spr3 is an unknown genetic factor in controlling the outspreading of the primary branches in rice inflorescence. In addition, NIL(Spr3) exhibited seed shattering. The formation of spreading panicle was accompanied by a few undesirable traits and the spreading panicle links with seed shattering suggest that the spreading panicle was likely lost during the domestication and selection for high seed productivity of cultivated rice.

The role of auxin transport during inflorescence development in maize (Zea mays, Poaceae)

Axillary meristems play a fundamental role in inflorescence architecture. Maize (Zea mays) inflorescences are highly branched panicles because of the production of multiple types of axillary meristems. We used auxin transport inhibitors to show that auxin transport is required for axillary meristem initiation in the maize inflorescence. The phenotype of plants treated with auxin transport inhibitors is very similar to that of barren inflorescence2 (bif2) and barren stalk1 (ba1) mutants, suggesting that these genes function in the same auxin transport pathway. To dissect this pathway, we performed RNA in situ hybridization on plants treated with auxin transport inhibitors. We determined that bif2 is expressed upstream and that ba1 is expressed downstream of auxin transport, enabling us to integrate the genetic and hormonal control of axillary meristem initiation. In addition, treatment of maize inflorescences with auxin transport inhibitors later in development results in the production of single instead of paired spikelets. Paired spikelets are a key feature of the Andropogoneae, a group of over 1000 grasses that includes maize, sorghum, and sugarcane. Because all other grasses bear spikelets singly, these results implicate auxin transport in the evolution of inflorescence architecture. Furthermore, our results provide insight into mechanisms of inflorescence branching that are relevant to all plants.

barren inflorescence2 Encodes a co-ortholog of the PINOID serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize

Organogenesis in plants is controlled by meristems. Axillary meristems, which give rise to branches and flowers, play a critical role in plant architecture and reproduction. Maize (Zea mays) and rice (Oryza sativa) have additional types of axillary meristems in the inflorescence compared to Arabidopsis (Arabidopsis thaliana) and thus provide an excellent model system to study axillary meristem initiation. Previously, we characterized the barren inflorescence2 (bif2) mutant in maize and showed that bif2 plays a key role in axillary meristem and lateral primordia initiation in the inflorescence. In this article, we cloned bif2 by transposon tagging. Isolation of bif2-like genes from seven other grasses, along with phylogenetic analysis, showed that bif2 is a co-ortholog of PINOID (PID), which regulates auxin transport in Arabidopsis. Expression analysis showed that bif2 is expressed in all axillary meristems and lateral primordia during inflorescence and vegetative development in maize and rice. Further phenotypic analysis of bif2 mutants in maize illustrates additional roles of bif2 during vegetative development. We propose that bif2/PID sequence and expression are conserved between grasses and Arabidopsis, attesting to the important role they play in development. We provide further support that bif2, and by analogy PID, is required for initiation of both axillary meristems and lateral primordia.

Morphological and molecular characterization of a new frizzy panicle mutant, "fzp-9(t)", in rice (Oryza sativa L.)

The spikelet identity gene "fzp" (frizzy panicle) is required for transformation of the floral meristems to inflorescent shoots. In fzp mutants, spikelets are replaced by branches and spikelet meristems produce massive numbers of branch meristems. We have isolated and characterized a new fzp mutant derived from anther culture lines in rice and designated as fzp-9(t). The fzp-9(t) mutant showed retarded growth habit and developed fewer tillers than those of the wild-type plant. The primary and secondary rachis branches of fzp-9(t) appeared to be normal, but higher-order branches formed continuous bract-like structures without developing spikelets. The genetic segregation of fzp-9(t) showed a good fit to the expected ratio of 3: 1. The sequence analysis of fzp-9(t) revealed that there is a single nucleotide base change upstream of the ERF (ethylene-responsive element-binding factor) domain compare to wild-type plant. The mutation point of fzp-9(t) (W66G) was one of the six amino acids of the ERF domain that contributed to GCC box-specific binding. The premature formation of a stop codon at the beginning of the ERF domain might cause a non-functional product.

Genome-wide analysis of spatial and temporal gene expression in rice panicle development

The basic structure of a rice inflorescence (the panicle) is determined by the pattern of branch formation, which is established at the early stages of panicle development. In this study we conducted global transcriptome profiling of the early stages of rice panicle development from phase transition to floral organ differentiation. To generate a meristem-specific gene-expression profile, shoot apical meristems (SAMs) and subsequently formed, very young panicles were collected manually and used for cDNA microarray analysis. We identified 357 out of 22,000 genes that are expressed differentially in the early stages of panicle development, and the 357 genes were classified into seven groups based on their temporal expression patterns. The most noticeable feature is that a fairly small number of genes, which are extensively enriched in transcription factors, are upregulated in the SAM immediately after phase transition. In situ hybridization analysis showed that each gene analysed exhibits a unique and interesting localization of mRNA. Remarkably, one of the transcription factors was proven to be a close downstream component of the pathway in which LAX, a major regulator of panicle branching, acts. These results suggest that our strategy--careful collection of meristems, global transcriptome analysis and subsequent in situ hybridization analysis--is useful not only to obtain a genome-wide view of gene expression, but also to reveal genetic networks controlling rice panicle development.

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.

Something on the side: axillary meristems and plant development

Axillary meristems allow the production of secondary growth axes in the shoot systems of plants. As such they make a large contribution to the plastic developmental potential of plants, allowing them to alter their architecture to suit the prevailing environment conditions. This review focuses on the formation and activity of axillary meristems, across several model species. Current topics and problems in the field are discussed.

Cloning, characterization and expression of a Lateral suppressor-like gene from chrysanthemum (Dendranthema grandiflorum Kitamura)

Conventionally, the lateral shoots of chrysanthemum are removed manually, which is time consuming and uneconomical. The development of branchless chrysanthemum will economize its commercial cultivation. To investigate the regulatory mechanism of branchlessness, we undertook cloning of Dendranthema grandiflorum Kitamura Lateral suppressor-like (DgLsL) gene for development of lateral shoot in chrysanthemum. A full-length cDNA of DgLsL gene was isolated by screening cDNA library and performing Rapid Amplification of cDNA Ends (RACE) PCR. Phylogenetic analysis showed that the DgLsL gene is closely related to Lateral suppressor that encodes transcriptional regulator proteins belonging to GRAS family of known transcription factor. Southern blot analysis revealed that DgLsL gene in chrysanthemum genome has one copy. DgLsL expression was apparently up-regulated by ethephon treatment. The expression patterns revealed that DgLsL transcripts were detected in all organs, but showed their highest level in stems.

The plant architecture of rice (Oryza sativa)

Plant architecture, a collection of the important agronomic traits that determine grain production in rice, is mainly affected by factors including tillering, plant height and panicle morphology. Recently, significant progress has been made in isolating and collecting of mutants that are defective in rice plant architecture. Although our understanding of the molecular mechanisms that control rice tillering, panicle development and plant height are still limited, new findings have begun to emerge. This review, therefore, summarizes the recent progress in exploring the mechanisms that control rice plant architecture.

ABERRANT PANICLE ORGANIZATION 1 temporally regulates meristem identity in rice

We report a recessive mutation of rice, aberrant panicle organization 1 (apo1), which severely affects inflorescence architecture, floral organ identity, and leaf production rate. In the wild-type inflorescence, the main-axis meristem aborts after forming 10-12 primary branch primordia. However, in apo1, the main-axis meristem was converted to a spikelet meristem after producing a small number of branch primordia. In addition, the branch meristems in apo1 became spikelet meristems earlier than in wild type. Therefore, in the inflorescence, the apo1 mutation caused the precocious conversion of the meristem identity. In the apo1 flower, lodicules were increased at the expense of stamens, and carpels were formed indeterminately by the loss of meristem determinacy. Vegetative development is also affected in the apo1. Leaves were formed rapidly throughout the vegetative phase, indicating that APO1 is also involved in temporal regulation of leaf production. These phenotypes suggest that the APO1 plays an important role in the temporal regulation of both vegetative and reproductive development.

Regulation of developmental transitions

Plants undergo a series of profound developmental changes throughout their lifetimes in response to both external environmental factors and internal intrinsic ones. When these changes are abrupt and dramatic, the process is referred to as phase change. Recently, several genes have been discovered that play a role in these developmental transitions. Their sequence and expression patterns shed new light on the mechanisms of phase change, and provide a link between the external and internal factors that control them. Examples of these transitions include changes from juvenile to adult leaf formation, vegetative to inflorescence meristem development, and inflorescence to floral meristem initiation.

Rice mutants and genes related to organ development, morphogenesis and physiological traits

Recent advances in genomic studies and the sequenced genome information have made it possible to utilize phenotypic mutants for characterizing relevant genes at the molecular level and reveal their functions. Various mutants and strains expressing phenotypic and physiological variations provide an indispensable source for functional analysis of genes. In this review, we cover almost all of the rice mutants found to date and the variant strains that are important in developmental, physiological and agronomical studies. Mutants and genes showing defects in vegetative organs, i.e. leaf, culm and root, inflorescence reproductive organ and seeds with an embryo and endosperm are described with regards to their phenotypic and molecular characteristics. A variety of alleles detected by quantitative trait locus analysis, such as heading date, disease/insect resistance and stress tolerance, are also shown.

Rice plant development: from zygote to spikelet

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 on the morphological and anatomical viewpoints. Recent advancement in genetics and molecular biology has given us new aspects of developmental processes. In this review, we first describe the phasic development of the rice plant, and then describe in detail the developmental courses of major organs, leaf, root and spikelet, and specific organs/tissues. Also, for the facility of future studies, we propose a staging system for each organ.

Genetics and evolution of inflorescence and flower development in grasses

Inflorescences and flowers in the grass species have characteristic structures that are distinct from those in eudicots. Owing to the availability of genetic tools and their genome sequences, rice and maize have become model plants for the grasses and for the monocots in general. Recent studies have provided much insight into the genetic control of inflorescence and flower development in grasses, especially in rice and maize. Progress in elucidating the developmental mechanisms in each of these plants may contribute greatly to our understanding of the evolution of development in higher plants.

Shoot branching

All plant shoots can be described as a series of developmental modules termed phytomers, which are produced from shoot apical meristems. A phytomer generally consists of a leaf, a stem segment, and a secondary shoot meristem. The fate and activity adopted by these secondary, axillary shoot meristems is the major source of evolutionary and environmental diversity in shoot system architecture. Axillary meristem fate and activity are regulated by the interplay of genetic programs with the environment. Recent results show that these inputs are channeled through interacting hormonal and transcription factor regulatory networks. Comparison of the factors involved in regulating the function of diverse axillary meristem types both within and between species is gradually revealing a pattern in which a common basic program has been modified to produce a range of axillary meristem types.

A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.)

Two large-scale ethylmethanesulfonate (EMS) mutant populations from barley (Hordeum vulgare L.) cv. Optic have been developed to promote both forward and reverse genetics in this crop. Leaf material and seed from approximately 20 000 M(2) plants were individually harvested, freeze-dried and archived. DNA was isolated from 9216 plants from the 20 and 30 mm EMS treatments and assembled into 1152 eight-plant pools. To facilitate PCR-based mutation scanning an approach has been employed that combines cleavage of heteroduplexes using the Cel nuclease (Cel I), post-cleavage intercalating dye labeling and the subsequent detection of cleaved products on a Transgenomic WAVE-HS. The populations were evaluated by screening for induced mutations in two genes of interest and the induced mutations were validated by sequence analysis. To enhance the screening process, 12-16 M(3) progeny from each of the M(2) plants were assessed for visible phenotypes and the data entered into a web accessible database (http://bioinf.scri.sari.ac.uk/distilling/distilling.html).

Ectopic expression of OsYAB1 causes extra stamens and carpels in rice

Members in the YABBY gene family of proteins are plant-specific transcription factors that play critical roles in determining organ polarity. We have isolated a cDNA clone from rice that encodes a YABBY protein. This protein, OsYAB1, is similar to Arabidopsis YAB2 (50.3%) and YAB5 (47.6%). It carries a zinc-finger motif and a YABBY domain, as do those in Arabidopsis . A fusion protein between OsYAB1 and GFP is located in the nucleus. RNA gel-blot analysis showed that the OsYAB1 gene is preferentially expressed in flowers. In-situ hybridization experiments also indicated that the transcript accumulated in the stamen and carpel primordia. Unlike the Arabidopsis YABBY genes, however, the OsYAB1 gene does not show polar expression pattern in the tissues of floral organs. Our transgenic plants that ectopically expressed OsYAB1 were normal during the vegetative growth period, but then showed abnormalities in their floral structures. Spikelets contained supernumerary stamens and carpels compared with those of the wild types. These results suggest that OsYAB1 plays a major role in meristem development and maintenance of stamens and carpels, rather than in determining polarity.

LAX and SPA: major regulators of shoot branching in rice

The aerial architecture of plants is determined primarily by the pattern of shoot branching. Although shoot apical meristem initiation during embryogenesis has been extensively studied by molecular genetic approaches using Arabidopsis, little is known about the genetic mechanisms controlling axillary meristem initiation, mainly because of the insufficient number of mutants that specifically alter it. We identified the LAX PANICLE (LAX) and SMALL PANICLE (SPA) genes as the main regulators of axillary meristem formation in rice. LAX encodes a basic helix-loop-helix transcription factor and is expressed in the boundary between the shoot apical meristem and the region of new meristem formation. This pattern of LAX expression was repeatedly observed in every axillary meristem, consistent with our observation that LAX is involved in the formation of all types of axillary meristems throughout the ontogeny of a rice plant. Ectopic LAX expression in rice caused pleiotropic effects, including dwarfing, an altered pattern of stem elongation, darker color, bending of the lamina joint, absence of the midribs of leaves, and severe sterility.

Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L)

BACKGROUND

The genetics of spikelet formation, a feature unique to grasses such as rice and maize, is yet to be fully understood, although a number of meristem and organ identity mutants have been isolated and investigated in Arabidopsis and maize. Using a two-element Ac/Ds transposon tagging system we have isolated a rice mutant, designated branched floretless 1 (bfl1) which is defective in the transition from spikelet meristem to floret meristem.

RESULTS

The bfl1 mutant shows normal differentiation of the primary rachis-branches leading to initial spikelet meristem (bract-like structure equivalent to rudimentary glumes) formation but fails to develop empty glumes and florets. Instead, axillary meristems in the bract-like structure produce sequential alternate branching, thus resulting in a coral shaped morphology of the branches in the developing panicle. The bfl1 mutant harbours a single Ds insertion in the upstream region of the BFL1 gene on chromosome 7 corresponding to PAC clone P0625E02 (GenBank Acc No. message URL http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=34395191&dopt=GenBank&term=ap004570AP004570). RT-PCR analyses revealed a drastic reduction of BFL1 transcript levels in the bfl1 mutant compared to that in the wild-type. In each of the normal panicle-bearing progeny plants, from occasional revertant seeds of the vegetatively-propagated mutant plant, Ds was shown to be excised from the bfl1 locus. BFL1 contains an EREBP/AP2 domain and is most likely an ortholog of the maize transcription factor gene BRANCHED SILKLESS1 (BD1).

CONCLUSIONS

bfl1 is a Ds-tagged rice mutant defective in the transition from spikelet meristem (SM) to floret meristem (FM). BFL1 is most probably a rice ortholog of the maize ERF (EREBP/AP2) transcription factor gene BD1. Based on the similarities in mutant phenotypes bfl1 is likely to be an allele of the previously reported frizzy panicle locus.

FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets

Inflorescences of grass species have a distinct morphology in which florets are grouped in compact branches called spikelets. Although many studies have shown that the molecular and genetic mechanisms that control floret organ formation are conserved between monocots and dicots, little is known about the genetic pathway leading to spikelet formation. In the frizzy panicle (fzp) mutant of rice, the formation of florets is replaced by sequential rounds of branching. Detailed analyses revealed that several rudimentary glumes are formed in each ectopic branch, indicating that meristems acquire spikelet identity. However, instead of proceeding to floret formation, axillary meristems are formed in the axils of rudimentary glumes and they either arrest or develop into branches of higher order. The fzp mutant phenotype suggests that FZP is required to prevent the formation of axillary meristems within the spikelet meristem and permit the subsequent establishment of floral meristem identity. The FZP gene was isolated by transposon tagging. FZP encodes an ERF transcription factor and is the rice ortholog of the maize BD1 gene. Consistent with observations from phenotypic analyses, FZP expression was found to be restricted to the time of rudimentary glumes differentiation in a half-ring domain at the base of which the rudimentary glume primordium emerged.

MISSING FLOWERS gene controls axillary meristems initiation in sunflower

The initiation and growth of axillary meristems are fundamental components of plant architecture. Here, we describe the mutant missing flowers (mf) of Helianthus annuus characterized by the lack of axillary shoots. Decapitation experiments and histological analysis indicate that this phenotype is the result of a defect in axillary meristem initiation. In addition to shoot branching, mutation affects floral differentiation. The indeterminate inflorescence of sunflower (capitulum) is formed of a large flat meristem which produces floret primordia in multiple spirals. In wildtype plants a bisecting crease divides each primordium in two distinct bumps that adopt different fate. The peripheral (abaxial) part of the primordium becomes a small leaf-like bract and the adaxial part becomes a flower. In the mf mutant, the formation of flowers at the axil of bracts is precluded. Histological analyses show that in floret primordia of the mutant a clear subdivision in dyads is not established. The primordia progressively bend inside and only large involucral floral bracts are developed. The results suggest that the MISSING FLOWERS gene is essential to provide or perceive an appropriate signal to the initiation of axillary meristems during both vegetative and reproductive phases.

The maize mutant barren stalk1 is defective in axillary meristem development

barren stalk1 is a recessive mutant of maize that has no tassel branches, spikelets, tillers, or ears. Here we present a detailed characterization of the ba1 mutant phenotype, including scanning electron microscopy of developing inflorescences, in situ hybridization analysis using a meristem marker, molecular mapping, and genetic analysis demonstrating an epistatic relationship between ba1 and teosinte branched1 (tb1). These data show that the primary defect in the ba1 mutant is a failure in axillary meristem development.

Rice as a model for comparative genomics of plants

Rapid progress in rice genomics is making it possible to undertake detailed structural and functional comparisons of genes involved in various biological processes among rice and other plant species, such as Arabidopsis. In this review, we summarize the current status of rice genomics. We then select two important areas of research, reproductive development and defense signaling, and compare the functions of rice and orthologous genes in other species involved in these processes. The analysis revealed that apparently orthologous genes can also display divergent functions. Changes in functions and regulation of orthologous genes may represent a basis for diversity among plant species. Such comparative genomics in other plant species will provide important information for future work on the evolution of higher plants.

barren inflorescence2 regulates axillary meristem development in the maize inflorescence

Organogenesis in plants is controlled by meristems. Shoot apical meristems form at the apex of the plant and produce leaf primordia on their flanks. Axillary meristems, which form in the axils of leaf primordia, give rise to branches and flowers and therefore play a critical role in plant architecture and reproduction. To understand how axillary meristems are initiated and maintained, we characterized the barren inflorescence2 mutant, which affects axillary meristems in the maize inflorescence. Scanning electron microscopy, histology and RNA in situ hybridization using knotted1 as a marker for meristematic tissue show that barren inflorescence2 mutants make fewer branches owing to a defect in branch meristem initiation. The construction of the double mutant between barren inflorescence2 and tasselsheath reveals that the function of barren inflorescence2 is specific to the formation of branch meristems rather than bract leaf primordia. Normal maize inflorescences sequentially produce three types of axillary meristem: branch meristem, spikelet meristem and floral meristem. Introgression of the barren inflorescence2 mutant into genetic backgrounds in which the phenotype was weaker illustrates additional roles of barren inflorescence2 in these axillary meristems. Branch, spikelet and floral meristems that form in these lines are defective, resulting in the production of fewer floral structures. Because the defects involve the number of organs produced at each stage of development, we conclude that barren inflorescence2 is required for maintenance of all types of axillary meristem in the inflorescence. This defect allows us to infer the sequence of events that takes place during maize inflorescence development. Furthermore, the defect in branch meristem formation provides insight into the role of knotted1 and barren inflorescence2 in axillary meristem initiation.