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

An insertion of oleate desaturase homologous sequence silences via siRNA the functional gene leading to high oleic acid content in sunflower seed oil

Classical sunflower varieties display a high linoleic acid content in their seeds [low oleic (LO) varieties] whereas genotypes carrying the Pervenets mutation display an increased oleic acid content of above 83% [high oleic (HO) varieties]. Despite the advantage in health terms of oleic acid, the nature of the mutation was still unknown. Previous work reported that HO genotypes carried a specific oleate desaturase (OD) allele. This enzyme catalyses the desaturation of oleic acid into linoleic acid. The present work demonstrates that this allele is organised in two parts: the first section present in both HO and LO genotypes carries a normal OD gene, the second section is specific to HO genotypes and carries OD duplications. The study of mRNA accumulation in LO and HO seeds revealed that the mutation is dominant and induces an OD mRNA down-regulation. Furthermore, OD small interfering RNA, characteristic of gene silencing, accumulated specifically in HO seeds. Considered together, these observations show that the mutation is associated with OD duplications leading to gene silencing of the OD gene and consequently, to oleic acid accumulation. This finding allowed the development of molecular markers characterising the mutation that can be used in breeding programmes to facilitate the selection of HO genotypes.

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.

Floral meristem initiation and meristem cell fate are regulated by the maize AP2 genes ids1 and sid1

Grass flowers are organized on small branches known as spikelets. In maize, the spikelet meristem is determinate, producing one floral meristem and then converting into a second floral meristem. The APETALA2 (AP2)-like gene indeterminate spikelet1 (ids1) is required for the timely conversion of the spikelet meristem into the floral meristem. Ectopic expression of ids1 in the tassel, resulting from a failure of regulation by the tasselseed4 microRNA, causes feminization and the formation of extra floral meristems. Here we show that ids1 and the related gene, sister of indeterminate spikelet1 (sid1), play multiple roles in inflorescence architecture in maize. Both genes are needed for branching of the inflorescence meristem, to initiate floral meristems and to control spikelet meristem determinacy. We show that reducing the levels of ids1 and sid1 fully suppresses the tasselseed4 phenotype, suggesting that these genes are major targets of this microRNA. Finally, sid1 and ids1 repress AGAMOUS-like MADS-box transcription factors within the lateral organs of the spikelet, similar to the function of AP2 in Arabidopsis, where it is required for floral organ fate. Thus, although the targets of the AP2 genes are conserved between maize and Arabidopsis, the genes themselves have adopted novel meristem functions in monocots.

Towards molecular breeding of reproductive traits in cereal crops

The transition from vegetative to reproductive phase, flowering per se, floral organ development, panicle structure and morphology, meiosis, pollination and fertilization, cytoplasmic male sterility (CMS) and fertility restoration, and grain development are the main reproductive traits. Unlocking their genetic insights will enable plant breeders to manipulate these traits in cereal germplasm enhancement. Multiple genes or quantitative trait loci (QTLs) affecting flowering (phase transition, photoperiod and vernalization, flowering per se), panicle morphology and grain development have been cloned, and gene expression research has provided new information about the nature of complex genetic networks involved in the expression of these traits. Molecular biology is also facilitating the identification of diverse CMS sources in hybrid breeding. Few Rf (fertility restorer) genes have been cloned in maize, rice and sorghum. DNA markers are now used to assess the genetic purity of hybrids and their parental lines, and to pyramid Rf or tms (thermosensitive male sterility) genes in rice. Transgene(s) can be used to create de novo CMS trait in cereals. The understanding of reproductive biology facilitated by functional genomics will allow a better manipulation of genes by crop breeders and their potential use across species through genetic transformation.

The art and design of genetic screens: maize

Maize (Zea mays) is an excellent model for basic research. Genetic screens have informed our understanding of developmental processes, meiosis, epigenetics and biochemical pathways--not only in maize but also in other cereal crops. We discuss the forward and reverse genetic screens that are possible in this organism, and emphasize the available tools. Screens exploit the well-studied behaviour of transposon systems, and the distinctive chromosomes allow an integration of cytogenetics into mutagenesis screens and analyses. The imminent completion of the maize genome sequence provides the essential resource to move seamlessly from gene to phenotype and back.

Distinct regulatory role for RFL, the rice LFY homolog, in determining flowering time and plant architecture

Activity of axillary meristems dictates the architecture of both vegetative and reproductive parts of a plant. In Arabidopsis thaliana, a model eudicot species, the transcription factor LFY confers a floral fate to new meristems arising from the periphery of the reproductive shoot apex. Diverse orthologous LFY genes regulate vegetative-to-reproductive phase transition when expressed in Arabidopsis, a property not shared by RFL, the homolog in the agronomically important grass, rice. We have characterized RFL by knockdown of its expression and by its ectopic overexpression in transgenic rice. We find that reduction in RFL expression causes a dramatic delay in transition to flowering, with the extreme phenotype being no flowering. Conversely, RFL overexpression triggers precocious flowering. In these transgenics, the expression levels of known flowering time genes reveal RFL as a regulator of OsSOC1 (OsMADS50), an activator of flowering. Aside from facilitating a transition of the main growth axis to an inflorescence meristem, RFL expression status affects vegetative axillary meristems and therefore regulates tillering. The unique spatially and temporally regulated RFL expression during the development of vegetative axillary bud (tiller) primordia and inflorescence branch primordia is therefore required to produce tillers and panicle branches, respectively. Our data provide mechanistic insights into a unique role for RFL in determining the typical rice plant architecture by regulating distinct downstream pathways. These results offer a means to alter rice flowering time and plant architecture by manipulating RFL-mediated pathways.

Molecular basis of plant architecture

Higher plants display a variety of architectures that are defined by the degree of branching, internodal elongation, and shoot determinancy. Studies on the model plants of Arabidopsis thaliana and tomato and on crop plants such as rice and maize have greatly strengthened our understanding on the molecular genetic bases of plant architecture, one of the hottest areas in plant developmental biology. The identification of mutants that are defective in plant architecture and characterization of the corresponding and related genes will eventually enable us to elucidate the molecular mechanisms underlying plant architecture. The achievements made so far in studying plant architecture have already allowed us to pave a way for optimizing the plant architecture of crops by molecular design and improving grain productivity.

WFL, a wheat FLORICAULA/LEAFY ortholog, is associated with spikelet formation as lateral branch of the inflorescence meristem

FLORICAULA (FLO) of Antirrhinum and LEAFY (LFY) of Arabidopsis encode plant-specific transcription factors, which are necessary and sufficient to specify floral meristem identity. We isolated WFL, a wheat FLO/LFY ortholog, and analyzed its expression pattern. RT-PCR analysis indicated that WFL is expressed predominantly in young spike. The WFL expression pattern during reproductive development was analyzed in more detail by using in situ hybridization technique. WFL transcripts were observed in all layers of the young spike excepting spikelet initiation sites as axillary meristem. In the double-ridge stage, WFL transcripts were localized in the lower ridge but were absent in the upper ridge, where spikelet meristem initiates. The WFL expression pattern indicated that WFL is associated with spikelet formation rather than floral meristem identity in wheat. As development of floret proceeds, the WFL transcripts were detectable in the developing palea, but not in other floral organs, suggesting that WFL may play a novel role in developing palea in the wheat floret.

The auxin-regulated AP2/EREBP gene PUCHI is required for morphogenesis in the early lateral root primordium of Arabidopsis

Organ primordia develop from founder cells into organs due to coordinated patterns of cell division. How patterned cell division is regulated during organ formation, however, is not well understood. Here, we show that the PUCHI gene, which encodes a putative APETALA2/ethylene-responsive element binding protein transcription factor, is required for the coordinated pattern of cell divisions during lateral root formation in Arabidopsis thaliana. Recessive mutations in PUCHI disturbed cell division patterns in the lateral root primordium, resulting in swelling of the proximal region of lateral roots. PUCHI expression was initially detected in all of the cells in early lateral root primordia, and later it was restricted to the proximal region of the primordia. Stable expression of PUCHI required auxin-responsive elements in its promoter region, and exogenous auxin increased the level of PUCHI mRNA accumulation. These results suggest that PUCHI acts downstream of auxin signaling and that this gene contributes to lateral root morphogenesis through affecting the pattern of cell divisions during the early stages of primordium development.

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.

Compact shoot and leafy head 1, a mutation affects leaf initiation and developmental transition in rice (Oryza sativa L)

The shoot apical meristem (SAM) produces lateral organs in a regular spacing (phyllotaxy) and at a regular interval (phyllochron) during the vegetative phase. In a Dissociation (Ds) insertion rice population, we identified a mutant, compact shoot and leafy head 1 (csl1), which produced massive number of leaves (~70) during the vegetative phase. In csl1, the transition from the vegetative to the reproductive phase was delayed by about 2 months under long-day conditions. With a reduced leaf size and severe dwarfism, csl1 failed to produce a normal panicle after the transition to reproductive growth. Instead, it produced a leafy panicle, in which all primary rachis-branches were converted to vegetative shoots. Phenotypically csl1 resembled pla mutants in short plastochron but was more severe in the conversion of the reproductive organs to vegetative organs. In addition, neither the expression nor the coding region of PLA1 or PLA2 was affected in csl1. csl1 is most likely a dominant mutation because no mutant segregant was observed in progeny of 67 siblings of the csl1 mutant. CSL1 may represent a novel gene, which functions downstream of PLA1 and/or PLA2, or alternatively functions in a separate pathway, involved in the regulation of leaf initiation and developmental transition via plant hormones or other mobile signals.

Two OsGASR genes, rice GAST homologue genes that are abundant in proliferating tissues, show different expression patterns in developing panicles

Two different types of genes for rice GA-stimulated transcript (GAST) homologue genes, Oryza sativa GA-stimulated transcript-related gene 1 (OsGASR1) and gene 2 (OsGASR2), were found. Both OsGASR proteins contain a cysteine-rich domain highly conserved among GAST family proteins in their C-terminal regions. Gibberellin A3 (GA3) stimulated expression of both OsGASRs in the wild-type Nipponbare and GA3 synthesis-deficient mutant. Expression of both OsGASRs apparently increased when cell proliferation entered the logarithmic phase, and rapidly reduced when cell proliferation was temporarily halted. RT-PCR analysis indicated different expression patterns of these genes in developing panicles. OsGASR1 was limitedly but strongly expressed in florets while OsGASR2 was expressed in both florets and branches. In situ hybridization showed that they were strongly expressed in the root apical meristem (RAM) and shoot apical meristem (SAM), but little signals were detected in mature leaves. Transient expression of OsGASR-GFP fusion proteins in onion epidermal cells revealed that both OsGASR proteins localized to the apoplasm or cell wall. These results suggest that OsGASR1 and OsGASR2 were involved in cell division and might play diverse roles in differentation of panicles.

The rice heterochronic gene SUPERNUMERARY BRACT regulates the transition from spikelet meristem to floral meristem

Regulating the transition of meristem identity is a critical step in reproductive development. After the shoot apical meristem (SAM) acquires inflorescence meristem identity, it goes through a sequential transition to second- and higher-order meristems that can eventually give rise to floral organs. Despite ample information on the molecular mechanisms that control the transition from SAM to inflorescence meristems, little is known about the mechanism for inflorescence development, especially in monocots. Here, we report the identification of the SUPERNUMERARY BRACT (SNB) gene controlling the transition from spikelet meristem to floral meristem and the floral organ development. This gene encodes a putative transcription factor carrying two AP2 domains. The SNB:GFP fusion protein is localized to the nucleus. SNB is expressed in all the examined tissues, but most strongly in the newly emerging spikelet meristems. In SNB knockout plants, the transition from spikelet meristems to floral meristems is delayed, resulting in the production of multiple rudimentary glumes in an alternative phyllotaxy. The development of additional bracts interferes with subsequent floral architecture. In some spikelets, the empty glumes and lodicules are transformed into lemma/palea-like organs. Occasionally, the number of stamens and carpels is altered and an ectopic floret occurs in the axil of the rachilla. These phenotypes suggest that snb is a heterochronic mutant, affecting the phase transition of spikelet meristems, the pattern formation of floral organs and spikelet meristem determinancy.

AtERF14, a member of the ERF family of transcription factors, plays a nonredundant role in plant defense

We had previously shown that several transcription factors of the ethylene (ET) response factor (ERF) family were induced with different but overlapping kinetics following challenge of Arabidopsis (Arabidopsis thaliana) with Pseudomonas syringae pv tomato DC3000 (avrRpt2). One of these genes, a transcriptional activator, AtERF14, was induced at the same time as ERF-target genes (ChiB, basic chitinase). To unravel the potential function of AtERF14 in regulating the plant defense response, we have analyzed gain- and loss-of-function mutants. We show here that AtERF14 has a prominent role in the plant defense response, since overexpression of AtERF14 had dramatic effects on both plant phenotype and defense gene expression and AtERF14 loss-of-function mutants showed impaired induction of defense genes following exogenous ET treatment and increased susceptibility to Fusarium oxysporum. Moreover, the expression of other ERF genes involved in defense and ET/jasmonic acid responses, such as ERF1 and AtERF2, depends on AtERF14 expression. A number of ERFs have been shown to function in the defense response through overexpression. However, the effect of loss of AtERF14 function on defense gene expression, pathogen resistance, and regulation of the expression of other ERF genes is unique thus far. These results suggest a unique role for AtERF14 in regulating the plant defense response.

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.

Inheritance of inflorescence architecture in sorghum

The grass inflorescence is the primary food source for humanity, and has been repeatedly shaped by human selection during the domestication of different cereal crops. Of all major cultivated cereals, sorghum [Sorghum bicolor (L.) Moench] shows the most striking variation in inflorescence architecture traits such as branch number and branch length, but the genetic basis of this variation is little understood. To study the inheritance of inflorescence architecture in sorghum, 119 recombinant inbred lines from an elite by exotic cross were grown in three environments and measured for 15 traits, including primary, secondary, and tertiary inflorescence branching. Eight characterized genes that are known to control inflorescence architecture in maize (Zea mays L.) and other grasses were mapped in sorghum. Two of these candidate genes, Dw3 and the sorghum ortholog of ramosa2, co-localized precisely with QTL of large effect for relevant traits. These results demonstrate the feasibility of using genomic and mutant resources from maize and rice (Oryza sativa L.) to investigate the inheritance of complex traits in related cereals.

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.

Evidence for distinct roles of the SEPALLATA gene LEAFY HULL STERILE1 in Eleusine indica and Megathyrsus maximus (Poaceae)

LEAFY HULL STERILE1 (LHS1) is an MIKC-type MADS-box gene in the SEPALLATA class. Expression patterns of LHS1 homologs vary among species of grasses, and may be involved in determining palea and lemma morphology, specifying the terminal floret of the spikelet, and sex determination. Here we present LHS1 expression data from Eleusine indica (subfamily Chloridoideae) and Megathyrsus maximus (subfamily Panicoideae) to provide further insights into the hypothesized roles of the gene. E. indica has spikelets with three to eight florets that mature acropetally; E. indica LHS1 (EiLHS1) is expressed in the palea and lemma of all florets. In contrast, M. maximus has spikelets with two florets that mature basipetally; M. maximus LHS1 (MmLHS1) is expressed in the palea and lemma of the distal floret only. These data are consistent with the hypothesis that LHS1 plays a role in determining palea and lemma morphology and specifies the terminal floret of basipetally maturing grass spikelets. However, LHS1 expression does not correlate with floret sex expression; MmLHS1 is restricted to the bisexual distal floret, whereas EiLHS1 is expressed in both sterile and bisexual floret meristems. Phylogenetic analyses reconstruct a complex pattern of LHS1 expression evolution in grasses. LHS1 expression within the gynoecium has apparently been lost twice, once before diversification of a major clade within tribe Paniceae, and once in subfamily Chloridoideae. These data suggest that LHS1 has multiple roles during spikelet development and may have played a role in the diversification of spikelet morphology.

Morphogenesis and patterning at the organ boundaries in the higher plant shoot apex

Formation of lateral organ primordia from the shoot apical meristem creates boundaries that separate the primordium from surrounding tissue. Morphological and gene expression studies indicate the presence of a distinct set of cells that define the boundaries in the plant shoot apex. Cells at the boundary usually display reduced growth activity that results in separation of adjacent organs or tissues and this morphological boundary coincides with the border of different cell identities. Such morphogenetic and patterning events and their spatial coordination are controlled by a number of boundary-specific regulatory genes. The boundary may also act as a reference point for the generation of new meristems such as axillary meristems. Many of the genes involved in meristem initiation are expressed in the boundary. This review summarizes the cellular characters of the shoot organ boundary and the roles of regulatory genes that control different aspects of this unique region in plant 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.

Candidate genes for barley mutants involved in plant architecture: an in silico approach

To individuate candidate genes (CGs) for a set of barley developmental mutants, a synteny approach comparing the genomes of barley and rice has been introduced. Based on map positions of mutants, sequenced RFLP markers linked to the target loci were selected. The markers were mapped in silico by BLAST searches against the rice genome sequence and chromosomal regions syntenous to barley target intervals were identified. Rice syntenous regions were defined for 15 barley chromosomal intervals hosting 23 mutant loci affecting plant height (brh1; brh2; sld4), shoot and inflorescence branching (als; brc1; cul-2, -3, -5, -15, -16; dub1; mnd6; vrs1), development of leaves (lig) and leaf-like organs (cal-b19, -C15, -d4; lks5; suKD-25; suKE-74; suKF-76; trd; trp). Annotation of 110 Mb of rice genomic sequence made it possible to screen for putative CGs which are listed together with the reasons supporting mutant-gene associations. For two loci, CGs were identified with a clear probability to represent the locus considered. These include FRIZZY PANICLE, a candidate for the brc1 barley mutant, and the rice ortholog of maize Liguleless1 (Lg1), a candidate for the barley lig locus on chromosome 2H. For this locus, the validity of the approach was supported by the PCR-amplification of a genomic fragment of the orthologous barley sequence. SNP mapping located this fragment on chromosome 2H in the region hosting the lig genetic locus.

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.

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.

Genetic control of shoot organ boundaries

The initiation of plant lateral organs from the shoot meristem is associated with the formation of boundaries that separate the primordia from surrounding tissue. A distinctive set of cells is present along the boundary, and these 'boundary cells' display characteristic patterns of cell division, morphology and gene expression. A certain class of the NAC transcription factors is important for growth suppression at the boundary, and auxin and microRNAs participate in boundary formation by regulating NAC gene expression. Other factors regulate different aspects of boundary functions, such as the establishment of the border of different cell identities, the initiation of axillary meristems, or the proper development of organs and tissues in adjacent regions.

Genome-wide analysis of the ERF gene family in Arabidopsis and rice

Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.

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.

OsMADS1, a rice MADS-box factor, controls differentiation of specific cell types in the lemma and palea and is an early-acting regulator of inner floral organs

Grass flowers are highly derived compared to their eudicot counterparts. To delineate OsMADS1 functions in rice floret organ development we have examined its evolution and the consequences of its knockdown or overexpression. Molecular phylogeny suggests the co-evolution of OsMADS1 with grass family diversification. OsMADS1 knockdown perturbs the differentiation of specific cell types in the lemma and palea, creating glume-like features, with severe derangements in lemma differentiation. Conversely, ectopic OsMADS1 expression suffices to direct lemma-like differentiation in the glume. Strikingly, in many OsMADS1 knockdown florets glume-like organs occupy all the inner whorls. Such effects in the second and third whorl are unexplained, as wild-type florets do not express OsMADS1 in these primordia and because transcripts for rice B and C organ-identity genes are unaffected by OsMADS1 knockdown. Through a screen for OsMADS1 targets we identify a flower-specific Nt-gh3 type gene, OsMGH3, as a downstream gene. The delayed transcription activation of OsMGH3 by dexamethasone-inducible OsMADS1 suggests indirect activation. The OsMGH3 floret expression profile suggests a novel role for OsMADS1 as an early-acting regulator of second and third whorl organ fate. We thus demonstrate the differential contribution of OsMADS1 for lemma versus palea development and provide evidence for its regulatory function in patterning inner whorl organs.

Reverse genetic approaches for functional genomics of rice

T-DNA and transposable elements e.g., Ds and Tos17, are used to generate a large number of insertional mutant lines in rice. Some carry the GUS or GFP reporter for gene trap or enhancer trap. These reporter systems are valuable for identifying tissue- or organ-preferential genes. Activation tagging lines have also been generated for screening mutants and isolating mutagenized genes. To utilize these resources more efficiently, tagged lines have been produced for reverse genetic approaches. DNA pools of the T-DNA tagged lines and Tos17 lines have been prepared for PCR screening of insertional mutants in a given gene. Tag end sequences (TES) of the inserts have also been produced. TES databases are beneficial for analyzing the function of a large number of rice genes.

Genetic analysis and high-resolution mapping of a premature senescence genePse(t)in rice (Oryza sativaL.)

A rice mutant, designated pse(t) (premature senescence, tentatively), was isolated from a T-DNA-inserted transgenic population. Senescence advanced more markedly in pse(t) than in wild-type ('Zhonghua 11', japonica) plants. Genetic analysis of pse(t) revealed that the premature senescence mutation was controlled by a single recessive nuclear gene, but that it was not induced by T-DNA insertion. In an effort to understand the genetic and molecular basis underlying premature senescence in rice, a map-based cloning strategy was used to localize Pse(t). High-resolution mapping of the Pse(t) locus was carried out using simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (CAPS) markers. An F2population, comprising 1691 pse(t) individuals derived from a cross of the pse(t) mutant with 'Longtepu' (indica), was constructed. Several new polymorphism markers were developed in this study. Genetic linkage analysis showed that the Pse(t) gene was located on the long arm of chromosome 7. It was found that the Pse(t) gene cosegregated with 3 markers and was flanked by markers SS22 and PP21. Thus, the Pse(t) gene is located within a genetic distance of 0.15 cM, corresponding to a physical distance of 220 kb. These findings provide the basic information that can be used for the final isolation of this gene in the rice premature-senescence pathway.Key words: genetic analysis, high-resolution mapping, Oryza sativa L., premature senescence.

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.

Identification and fine mapping of a mutant gene for palealess spikelet in rice

In grass, the evolutionary relationship between lemma and palea, and their relationship to the flower organs in dicots have been variously interpreted and wildely debated. In the present study, we carried out morphological and genetic analysis of a palealess mutant (pal) from rice (Oryza sativa L.), and fine mapping the gene responsible for the mutated trait. Together, our findings indicate that the palea is replaced by two leaf-like structures in the pal flowers, and this trait is controlled by one recessive gene, termed palealess1 (pal1). With a large F2 segregating population, the pal1 gene was finally mapped into a physical region of 35 kb. Our results also suggest that the lemma and palea of rice are not homologous organs, palea is likely evolutionarily equivalent to the eudicot sepal, and the pal1 should be an A function gene for rice floral organ identity.

AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or division-competent states

Although several members of the AP2/ERF family of transcription factors are important developmental regulators in plants, many genes in this large protein family remain uncharacterized. Here, we present a phylogenetic analysis of the 18 genes that make up the AP2 subgroup of this family. We report expression analyses of seven Arabidopsis genes most closely related to the floral development gene AINTEGUMENTA (ANT) and show that all AINTEGUMENTA-like (AIL) genes are transcribed in multiple tissues during development. They are expressed primarily in young actively dividing tissues of a plant and not in mature leaves or stems. The spatial distribution of AIL5, AIL6, and AIL7 mRNA in inflorescences was characterized by in situ hybridization. Each of these genes is expressed in a spatially and temporally distinct pattern within inflorescence meristems and flowers. Ectopic expression of AIL5 resulted in a larger floral organ phenotype, similar to that resulting from ectopic expression of ANT. Our results are consistent with AIL genes having roles in specification of meristematic or division-competent states.

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.

Suppression of tiller bud activity in tillering dwarf mutants of rice

In this study, we analyzed five tillering dwarf mutants that exhibit reduction of plant stature and an increase in tiller numbers. We show that, in the mutants, axillary meristems are normally established but the suppression of tiller bud activity is weakened. The phenotypes of tillering dwarf mutants suggest that they play roles in the control of tiller bud dormancy to suppress bud activity. However, tillering dwarf mutants show the dependence of both node position and planting density on their growth, which implies that the functions of tillering dwarf genes are independent of the developmental and environmental control of bud activity. Map-based cloning of the D3 gene revealed that it encodes an F-box leucine-trich repeat (LRR) protein orthologous to Arabidopsis MAX2/ORE9. This indicates the conservation of mechanisms controlling axillary bud activity between monocots and eudicots. We suggest that tillering dwarf mutants are suitable for the study of bud activity control in rice and believe that future molecular and genetic studies using them may enable significant progress in understanding the control of tillering and shoot branching.

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.

Heterogeneous expression patterns and separate roles of the SEPALLATA gene LEAFY HULL STERILE1 in grasses

SEPALLATA (SEP) genes exhibit distinct patterns of expression and function in the grass species rice (Oryza sativa) and maize (Zea mays), suggesting that the role of the genes has changed during the evolution of the family. Here, we examine expression of the SEP-like gene LEAFY HULL STERILE1 (LHS1) in phylogenetically disparate grasses, reconstruct the pattern of gene expression evolution within the family, and then use the expression patterns to test hypotheses of gene function. Our data support a general role for LHS1 in specifying determinacy of the spikelet meristem and also in determining the identity of lemmas and paleas; these two functions are separable, as is the role of the gene in specifying floret meristems. We find no evidence that LHS1 determines flower number; it is strongly expressed in all spikelet meristems even as they are producing flowers, and expression is not correlated with eventual flower number. LHS1 expression in only the upper flowers of the spikelet appears to be the ancestral state; expression in all flowers is derived in subfamily Pooideae. LHS1 expression in pistils, stamens, and lodicules varies among the cereals. We hypothesize that LHS1 may have affected morphological diversification of grass inflorescences by mediating the expression of different floral identity genes in different regions of the floret and spikelet.

Evolution of developmental traits

The evolution of plant development can be studied in many different ways, each of which provides new insights into how plants have been modified over evolutionary time. DNA sequencing shows that most developmental genes are under purifying selection and that obvious adaptive change in proteins is rare. This may indicate that most change occurs in cis-regulatory sequences, that tests for detecting selection lack power, or both. Gene duplications are common and often correlate with divergence of function, as predicted by theory. Studies of gene expression illuminate similarities among structures in disparate plant groups and indicate that the same genes have been deployed repeatedly for similar developmental ends. Comparative functional studies remain uncommon, but promise to illuminate how changing proteins lead to changes in development. Precise characterization of phenotypes by studies of developmental morphology is beginning to occur in some taxonomic groups. The genetic variation necessary for morphological change must originate as allelic polymorphism within populations; such polymorphism has been identified in grasses and in sunflowers, although it is often cryptic.

Partial conservation of LFY function between rice and Arabidopsis

The LFY/FLO genes encode plant-specific transcription factors and play major roles in the reproductive transition as well as floral development. In this study, we reconstructed the phylogenetic tree of the 49 LFY/FLO homologs from various plant species. The tree clearly shows that the LFY/FLO genes from the eudicots and monocots formed the two monophyletic clusters with very high bootstrap probabilities, respectively. Furthermore, grass LFY/FLO genes have experienced significant acceleration of amino acid replacement rate compared with the eudicot homolog. To test whether grass LFY/FLO genes have a conserved function with those of eudicots, we introduced RFL, a rice LFY homolog, into the Arabidopsis lfy mutant. The RFL gene driven by LFY promoter partially rescued the lfy mutation, suggesting that the functions of LFY and RFL partly overlap. Interestingly, the RFL but not LFY, strongly activated the expression of AP1 and AG, the downstream targets of LFY, even in the vegetative tissues. The LFY::RFL transgenic Arabidopsis plants exhibited abnormal patterns of development such as leaf curling, bushy appearance and the transformation of ovules into carpels. All of the results indicate that both the partial conservation and divergence of LFY function between rice and Arabidopsis.

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.