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The pseudanthial inflorescences of the sunflower family, Asteraceae, mimic a solitary flower but are composed of multiple flowers. Our studies in Gerbera hybrida indicate functional diversification for SEPALLATA (SEP)-like MADS box genes that often function redundantly in other core eudicots. We conducted phylogenetic and expression analysis for eight SEP-like GERBERA REGULATOR OF CAPITULUM DEVELOPMENT (GRCD) genes, including previously unstudied gene family members. Transgenic gerbera plants were used to infer gene functions. Adding to the previously identified stamen and carpel functions for GRCD1 and GRCD2, two partially redundant genes, GRCD4 and GRCD5, were found to be indispensable for petal development. Stepwise conversion of floral organs into leaves in the most severe RNA interference lines suggest redundant and additive GRCD activities in organ identity regulation. We show conserved and redundant functions for several GRCD genes in regulation of flower meristem maintenance, while functional diversification for three SEP1/2/4 clade genes in regulation of inflorescence meristem patterning was observed. GRCD genes show both specialized and pleiotropic functions contributing to organ differentiation and flower meristem fate, and uniquely, to patterning of the inflorescence meristem. Altogether, we provide an example of how plant reproductive evolution has used conserved genetic modules for regulating the elaborate inflorescence architecture in Asteraceae.

Stem cells (SCs) are undifferentiated cells of multicellular organisms that can divide, self-renew, and differentiate. Despite the differences in their properties, the general principles of the existence of SCs can be distinguished in all multicellular organisms. In plants, SCs are found in meristems, structures that ensure the continuous growth of a plant and provide material for the formation of various specialized tissues. There are numerous types of meristems: shoot apical meristem (SAM) and root apical meristem (RAM), and lateral meristems (LMs) (procambium, cambium, and pericycle), as well as the so-called irregular meristems, developing under certain conditions (callus, meristems of symbiotic nodules, spontaneous and pathogen-induced tumors, etc.). Specific mechanisms of regulation, which are based on the interaction of plant hormones and the major groups of transcription factors, were identified for each meristem. The activity of meristems is determined by two opposing processes: proliferation and self-renewal of SCs in the central part of the meristem and differentiation of specialized cells in the periphery. WOX-CLAVATA systems are a regulatory component conservative for different meristems, which ensures the consistency of the composition of the meristem, as well as the balance of SC proliferation and differentiation. In this review, we consider the similarities and differences between the principles of the organization of SC niches in plants and animals, as well as in a variety of meristems of higher plants; special attention will be paid to the role of WOX-CLAVATA systems in maintaining meristems and their interaction with other meristem regulators.

Plant meristem cells divide and differentiate in a spatially and temporally regulated manner, ultimately giving rise to organs. In this study, we isolated the Arabidopsis jing he sheng 1 (jhs1) mutant, which exhibited retarded growth, an abnormal pattern of meristem cell division and differentiation, and morphological defects such as fasciation, an irregular arrangement of siliques, and short roots. We identified JHS1 as a homolog of human and yeast DNA Replication Helicase/Nuclease2, which is known to be involved in DNA replication and damage repair. JHS1 is strongly expressed in the meristem of Arabidopsis. The jhs1 mutant was sensitive to DNA damage stress and had an increased DNA damage response, including increased expression of genes involved in DNA damage repair and cell cycle regulation, and a higher frequency of homologous recombination. In the meristem of the mutant plants, cell cycle progression was delayed at the G2 or late S phase and genes essential for meristem maintenance were misregulated. These results suggest that JHS1 plays an important role in DNA replication and damage repair, meristem maintenance, and development in plants.

The floral organ identity gene APETALA3 (AP3) is a MADS-box transcription factor involved in stamen and petal identity that belongs to the B-class of the ABC model of flower development. Thalictrum (Ranunculaceae), an emerging model in the non-core eudicots, has AP3 homologs derived from both ancient and recent gene duplications. Prior work has shown that petals have been lost repeatedly and independently in Ranunculaceae in correlation with the loss of a specific AP3 paralog, and Thalictrum represents one of these instances. The main goal of this study was to conduct a functional analysis of the three AP3 orthologs present in Thalictrum thalictroides, representing the paleoAP3 gene lineage, to determine the degree of redundancy versus divergence after gene duplication. Because Thalictrum lacks petals, and has lost the petal-specific AP3, we also asked whether heterotopic expression of the remaining AP3 genes contributes to the partial transference of petal function to the first whorl found in insect-pollinated species. To address these questions, we undertook functional characterization by virus-induced gene silencing (VIGS), protein-protein interaction and binding site analyses. Our results illustrate partial redundancy among Thalictrum AP3s, with deep conservation of B-class function in stamen identity and a novel role in ectopic petaloidy of sepals. Certain aspects of petal function of the lost AP3 locus have apparently been transferred to the other paralogs. A novel result is that the protein products interact not only with each other, but also as homodimers. Evidence presented here also suggests that expression of the different ThtAP3 paralogs is tightly integrated, with an apparent disruption of B function homeostasis upon silencing of one of the paralogs that codes for a truncated protein. To explain this result, we propose two testable alternative scenarios: that the truncated protein is a dominant negative mutant or that there is a compensational response as part of a back-up circuit. The evidence for promiscuous protein-protein interactions via yeast two-hybrid combined with the detection of AP3 specific binding motifs in all B-class gene promoters provide partial support for these hypotheses.

Crocus sativus, a monocot triploid species belonging to the Iridaceae family, is cultivated for its red stigmatic lobes of the carpel that constitute saffron. Flower development has been extensively studied in different plants. Different floral developmental pathways have been deciphered in many plants. In Crocus sativus, flower is the most important part and understanding the pathway underlying the flower development can pave the way for new avenues to improve its productivity and quality. The combination of class A genes (including APETALA1; CsAP1 and APETALA2; CsAP2), class B genes (including APETALA3; CsAP3 and PISTILLATA; CsPI) and class C genes (including AGAMOUS; CsAG) that are active in each whorl, determines the identity of the organs that will later develop in that whorl. CsAP3 is a class B homeotic gene which promotes petal and stamen formation and has a very important role in flower development. It also activates other genes playing pivotal role in flower development. It has been earlier reported that CsAP3 gene has direct role in activation of CsNAP gene which promotes senescence in plants. Present work was focused on study of relative gene expression changes of CsAP3 and CsNAP gene during different stages of flower development. CsAP3 gene expression was found maximum during late-preanthesis stages of stigma development. Expression increases from stage 5 to stage 6 of flower development and then reduces again from stage 6 to stage 7. CsNAP gene had moderate expression during stage 3 to stage 4 transition and its expression increased abruptly from stage 6 to stage 7 of flower development. There is no direct concordance in the expression of CsAP3 and CsNAP gene expression in saffron. We may conclude that some other factor(s) may be responsible for initiation of CsNAP expression and CsAP3 gene may directly/indirectly be involved in regulating the factors responsible for CsNAP activation.

The shoot apical meristem contains a pool of undifferentiated stem cells and controls initiation of all aerial plant organs. In maize (Zea mays), leaves are formed throughout vegetative development; on transition to floral development, the shoot meristem forms the tassel. Due to the regulated balance between stem cell maintenance and organogenesis, the structure and morphology of the shoot meristem are constrained during vegetative development. Previous work identified loci controlling meristem architecture in a recombinant inbred line population. The study presented here expanded on this by investigating shoot apical meristem morphology across a diverse set of maize inbred lines. Crosses of these lines to common parents showed varying phenotypic expression in the F1, with some form of heterosis occasionally observed. An investigation of meristematic growth throughout vegetative development in diverse lines linked the timing of reproductive transition to flowering time. Phenotypic correlations of meristem morphology with adult plant traits showed an association between the meristem and flowering time, leaf shape, and yield traits, revealing links between the control and architecture of undifferentiated and differentiated plant organs. Finally, quantitative trait loci mapping was utilized to map the genetic architecture of these meristem traits in two divergent populations. Control of meristem architecture was mainly population-specific, with 15 total unique loci mapped across the two populations with only one locus identified in both populations.

The paper described a new mutation that causes the development of multiple meristematic foci as part of shoot apical meristem, which can give rise to new stem axes or cause stem fasciation. The wus-1 mutation represses development of additional apical meristem in fas5 mutant, indicating to the sequential action of the genes in the formation of the shoot apical meristem and FAS5 gene participation in spatial restriction of the WUS gene expression. This function gene FAS5 performs independently of other negative regulators of WUS gene--namely genes CLV, as demonstrated by additive phenotype of double mutants fas5 clv2-1 and fas5 clv3-2. Besides the effect on the development of the shoot apical meristem fas5 mutation causes a change in the shape and number of leaves, accelerates the plant transition to the reproductive stage and leads to the development of cell neoplasms on the stem (buds, stigmatic tissues and ovule-like structures). The mutation also causes changes in apical meristems and leaf cell morphology indicating the activation in cells of DNA endoreduplication. Pleiotropic effect of the fas5 mutation on different stages of ontogeny and different organs suggests that the FAS5 gene plays a complex regulatory role at all stages of the A. thaliana shoot development, and affects many direct or indirect target genes.

Identification of new genes involved in the control of flower initiation and development, is an important problem of the plant developmental genetics. Central approach to solve it is the study of mutants with changes in these characters. The effect of pleiotropic mutation fasciata5 on the transition to the reproductive stage and flower development was studied. By analyzing double mutants we identified interactions of FASCIATA5 gene with LEAFY, APETALA1 and APETALA2, which control the floral meristem identity. The results indicate an important role of gene FASCIATA5 in upregulation of these genes.

Flower development is one of the major developmental processes that governs seed setting in angiosperms. However, little is known about the molecular mechanisms underlying flower development in legumes. Employing RNA-seq for various stages of flower development and few vegetative tissues in chickpea, we identified differentially expressed genes in flower tissues/stages in comparison to vegetative tissues, which are related to various biological processes and molecular functions during flower development. Here, we provide details of experimental methods, RNA-seq data (available at Gene Expression Omnibus database under GSE42679) and analysis pipeline published by Singh and colleagues in the Plant Biotechnology Journal (Singh et al., 2013), along with additional analysis for discovery of genes involved in shoot apical meristem (SAM) development. Our data provide a resource for exploring the complex molecular mechanisms underlying SAM and flower development and identification of gene targets for functional and applied genomics in legumes.

The wild sunflower (Helianthus annuus) plants develop a highly branched form with numerous small flowering heads. The origin of a no branched sunflower, producing a single large head, has been a key event in the domestication process of this species. The interaction between hormonal factors and several genes organizes the initiation and outgrowth of axillary meristems (AMs). From sunflower, we have isolated two genes putatively involved in this process, LATERAL SUPPRESSOR (LS)-LIKE (Ha-LSL) and REGULATOR OF AXILLARY MERISTEM FORMATION (ROX)-LIKE (Ha-ROXL), encoding for a GRAS and a bHLH transcription factor (TF), respectively. Typical amino acid residues and phylogenetic analyses suggest that Ha-LSL and Ha-ROXL are the orthologs of the branching regulator LS and ROX/LAX1, involved in the growth habit of both dicot and monocot species. qRT-PCR analyses revealed a high accumulation of Ha-LSL transcripts in roots, vegetative shoots, and inflorescence shoots. By contrast, in internodal stems and young leaves, a lower amount of Ha-LSL transcripts was observed. A comparison of transcription patterns between Ha-LSL and Ha-ROXL revealed some analogies but also remarkable differences; in fact, the gene Ha-ROXL displayed a low expression level in all organs analyzed. In situ hybridization (ISH) analysis showed that Ha-ROXL transcription was strongly restricted to a small domain within the boundary zone separating the shoot apical meristem (SAM) and the leaf primordia and in restricted regions of the inflorescence meristem, beforehand the separation of floral bracts from disc flower primordia. These results suggested that Ha-ROXL may be involved to establish a cell niche for the initiation of AMs as well as flower primordia. The accumulation of Ha-LSL transcripts was not restricted to the boundary zones in vegetative and inflorescence shoots, but the mRNA activity was expanded in other cellular domains of primary shoot apical meristem as well as AMs. In addition, Ha-LSL transcript accumulation was also detected in leaves and floral primordia at early stages of development. These results were corroborated by qRT-PCR analyses that evidenced high levels of Ha-LSL transcripts in very young leaves and disc flowers, suggesting a role of Ha-LSL for the early outgrowth of lateral primordia.

During very early stages of flower development in Arabidopsis thaliana, a series of key decisions are taken. Indeed, the position and the basic patterning of new flowers are determined in less than 4 days. Given that the scientific literature provides hard evidence for the function of only 10% of A. thaliana genes, we hypothesized that although many essential genes have already been identified, many poorly characterized genes are likely to be involved in floral patterning. In the current study, we use high-throughput sequencing to describe the transcriptome of the native inflorescence meristem, the floral meristem and the new flower immediately after the start of organ differentiation. We provide evidence that our experimental system is reliable and less affected by experimental artefacts than a widely used floral induction system. Furthermore, we show how these data can be used to identify candidate genes for functional studies, and to generate hypotheses of functional redundancies and regulatory interactions.

The shoot apical meristem contains a pool of undifferentiated stem cells and generates all above-ground organs of the plant. During vegetative growth, cells differentiate from the meristem to initiate leaves while the pool of meristematic cells is preserved; this balance is determined in part by genetic regulatory mechanisms. To assess vegetative meristem growth and genetic control in Zea mays, we investigated its morphology at multiple time points and identified three stages of growth. We measured meristem height, width, plastochron internode length, and associated traits from 86 individuals of the intermated B73 × Mo17 recombinant inbred line population. For meristem height-related traits, the parents exhibited markedly different phenotypes, with B73 being very tall, Mo17 short, and the population distributed between. In the outer cell layer, differences appeared to be related to number of cells rather than cell size. In contrast, B73 and Mo17 were similar in meristem width traits and plastochron internode length, with transgressive segregation in the population. Multiple loci (6−9 for each trait) were mapped, indicating meristem architecture is controlled by many regions; none of these coincided with previously described mutants impacting meristem development. Major loci for height and width explaining 16% and 19% of the variation were identified on chromosomes 5 and 8, respectively. Significant loci for related traits frequently coincided, whereas those for unrelated traits did not overlap. With the use of three near-isogenic lines, a locus explaining 16% of the parental variation in meristem height was validated. Published expression data were leveraged to identify candidate genes in significant regions.

One of the most remarkable manifestations of plant evolution is the diversity for floral branching systems. These “inflorescences” arise from stem cell populations in shoot meristems that mature gradually to reproductive states in response to environmental and endogenous signals. The morphology of the shoot meristem maturation process is conserved across distantly related plants, raising the question of how diverse inflorescence architectures arise from seemingly common maturation programs. In tomato and related nightshades (Solanaceae), inflorescences range from solitary flowers to highly branched structures bearing hundreds of flowers. Since reproductive barriers between even closely related Solanaceae have precluded a genetic dissection, we captured and compared meristem maturation transcriptomes from five domesticated and wild species reflecting the evolutionary continuum of inflorescence complexity. We find these divergent species share hundreds of dynamically expressed genes, enriched for transcription factors. Meristem stages are defined by distinct molecular states and point to modified maturation schedules underlying architectural variation. These modified schedules are marked by a peak of transcriptome expression divergence during the reproductive transition, driven by heterochronic shifts of dynamic genes, including transcriptional regulators with known roles in flowering. Thus, evolutionary diversity in Solanaceae inflorescence complexity is determined by subtle modifications of transcriptional programs during a critical transitional window of meristem maturation, which we propose underlies similar cases of plant architectural variation. More broadly, our findings parallel the recently described transcriptome “inverse hourglass” model for animal embryogenesis, suggesting both plant and animal morphological variation is guided by a mid-development period of transcriptome divergence.

Background Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using DORNRÖSCHEN-LIKE::GFP to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in apetala1 cauliflower double mutants, which overproliferate IMs. Results Within the lateral organ founder-cell population at the inflorescence meristem, floral primordium identity genes are upregulated and stem-cell identity markers are downregulated. Additional differentially expressed transcripts are involved in polarity generation and boundary formation, and in epigenetic and post-translational changes. However, only subtle transcriptional reprogramming within the global auxin network was observed. Conclusions The transcriptional network of differentially expressed genes supports the hypothesis that lateral organ founder-cell specification involves the creation of polarity from the centre to the periphery of the IM and the establishment of a boundary from surrounding cells, consistent with bract initiation. However, contrary to the established paradigm that sites of auxin response maxima pre-pattern lateral organ initiation in the IM, auxin response might play a minor role in the earliest stages of lateral floral initiation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3189-x) contains supplementary material, which is available to authorized users.

The control of organ growth by coordinating cell proliferation and differentiation is a fundamental developmental process. In plants, postembryonic root growth is sustained by the root meristem. For maintenance of root meristem size, the rate of cell differentiation must equal the rate of cell division. Cytokinin and auxin interact to affect the cell proliferation and differentiation balance and thus control root meristem size. However, the genetic and molecular mechanisms that determine root meristem size still remain largely unknown. Here, we report that da1-related protein2 (dar2) mutants produce small root meristems due to decreased cell division and early cell differentiation in the root meristem of Arabidopsis (Arabidopsis thaliana). dar2 mutants also exhibit reduced stem cell niche activity in the root meristem. DAR2 encodes a Lin-11, Isl-1, and Mec-3 domain-containing protein and shows an expression peak in the border between the transition zone and the elongation zone. Genetic analyses show that DAR2 functions downstream of cytokinin and SHORT HYPOCOTYL2 to maintain normal auxin distribution by influencing auxin transport. Further results indicate that DAR2 acts through the PLETHORA pathway to influence root stem cell niche activity and therefore control root meristem size. Collectively, our findings identify the role of DAR2 in root meristem size control and provide a novel link between several key regulators influencing root meristem size.

A long-standing question in plants and animals is how spatial patterns are maintained within stem cell niches despite ongoing cell divisions. Here we address how, during shoot meristem formation in Arabidopsis thaliana, the three apical cell layers acquire stem cell identity. Using a sensitized mutant screen, we identified miR394 as a mobile signal produced by the surface cell layer (the protoderm) that confers stem cell competence to the distal meristem by repressing the F box protein LEAF CURLING RESPONSIVENESS. This repression is required to potentiate signaling from underneath the stem cells by the transcription factor WUSCHEL, maintaining stem cell pluripotency. The interaction of two opposing signaling centers provides a mechanistic framework of how stem cells are localized at the tip of the meristem. Although the constituent cells change, the surface layer provides a stable point of reference in the self-organizing meristem.

For successful molecular breeding it is important to identify targets to the gene family level, and in the specific species of interest, in this case Pisum sativum L. The cytokinins have been identified as a key breeding target due to their influence on plant architecture, and on seed size and sink activity. We focused on the cytokinin biosynthetic gene family (the IPTs) and the gene family key to the destruction of cytokinins (the CKXs), as well as other gene families potentially affected by changing cytokinin levels. These included key meristem genes (WUS and BAM1) and the transporter gene families, sucrose transporters (SUTs) and amino acid permeases (AAPs). We used reverse transcription quantitative PCR (RT-qPCR) to monitor gene expression in the vegetative meristem and in pre- and post-fertilisation young pea fruits. PsWUS expression was specific to the shoot apical meristem while PsBAM1 was highly expressed in the shoot apical meristem (SAM) but was also expressed at a low level in the young fruit. Differential expression was shown between genes and within gene families for IPT, CKX, SUT, and AAP. PsCKX7 showed strong gene family member-specific expression in the SAM, and was also expressed in young pea fruits. We suggest that PsCKX7 is a potential target for downregulation via molecular breeding or gene editing.

Plant meristems are responsible for the generation of all plant tissues and organs. Here we show that the transcription factor (TF) FAR-RED ELONGATED HYPOCOTYL3 (FHY3) plays an important role in both floral meristem (FM) determinacy and shoot apical meristem maintenance in Arabidopsis, in addition to its well-known multifaceted roles in plant growth and development during the vegetative stage. Through genetic analyses, we show that WUSCHEL (WUS) and CLAVATA3 (CLV3), two central players in the establishment and maintenance of meristems, are epistatic to FHY3 Using genome-wide ChIP-seq and RNA-seq data, we identify hundreds of FHY3 target genes in flowers and find that FHY3 mainly acts as a transcriptional repressor in flower development, in contrast to its transcriptional activator role in seedlings. Binding motif-enrichment analyses indicate that FHY3 may coregulate flower development with three flower-specific MADS-domain TFs and four basic helix-loop-helix TFs that are involved in photomorphogenesis. We further demonstrate that CLV3, SEPALLATA1 (SEP1), and SEP2 are FHY3 target genes. In shoot apical meristem, FHY3 directly represses CLV3, which consequently regulates WUS to maintain the stem cell pool. Intriguingly, CLV3 expression did not change significantly in fhy3 and phytochrome B mutants before and after light treatment, indicating that FHY3 and phytochrome B are involved in light-regulated meristem activity. In FM, FHY3 directly represses CLV3, but activates SEP2, to ultimately promote FM determinacy. Taken together, our results reveal insights into the mechanisms of meristem maintenance and determinacy, and illustrate how the roles of a single TF may vary in different organs and developmental stages.

Background Plant profilin genes encode core cell-wall structural proteins and are evidenced for their up-regulation under cotton domestication. Notwithstanding striking discoveries in the genetics of cell-wall organization in plants, little is explicit about the manner in which profilin-mediated molecular interplay and corresponding networks are altered, especially during cellular signalling of apical meristem determinacy and flower development. Results Here we show that the ectopic expression of GhPRF1 gene in tobacco resulted in the hyperactivation of apical meristem and early flowering phenotype with increased flower number in comparison to the control plants. Spatial expression alteration in CLV1, a key meristem-determinacy gene, is induced by the GhPRF1 overexpression in a WUS-dependent manner and mediates cell signalling to promote flowering. But no such expression alterations are recorded in the GhPRF1-RNAi lines. The GhPRF1 transduces key positive flowering regulator AP1 gene via coordinated expression of FT4, SOC1, FLC1 and FT1 genes involved in the apical-to-floral meristem signalling cascade which is consistent with our in silico profilin interaction data. Remarkably, these positive and negative flowering regulators are spatially controlled by the Actin-Related Protein (ARP) genes, specifically ARP4 and ARP6 in proximate association with profilins. This study provides a novel and systematic link between GhPRF1 gene expression and the flower primordium initiation via up-regulation of the ARP genes, and an insight into the functional characterization of GhPRF1 gene acting upstream to the flowering mechanism. Also, the transgenic plants expressing GhPRF1 gene show an increase in the plant height, internode length, leaf size and plant vigor. Conclusions Overexpression of GhPRF1 gene induced early and increased flowering in tobacco with enhanced plant vigor. During apical meristem determinacy and flower development, the GhPRF1 gene directly influences key flowering regulators through ARP-genes, indicating for its role upstream in the apical-to-floral meristem signalling cascade. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0798-0) contains supplementary material, which is available to authorized users.

In rice, inflorescence architecture is established at early stages of reproductive development and contributes directly to grain yield potential. After induction of flowering, the complexity of branching, and therefore the number of seeds on the panicle, is determined by the activity of different meristem types and the timing of transitions between them. Although some of the genes involved in these transitions have been identified, an understanding of the network of transcriptional regulators controlling this process is lacking. To address this we used a precise laser microdissection and RNA-sequencing approach in Oryza sativa ssp. japonica cv. Nipponbare to produce quantitative data that describe the landscape of gene expression in four different meristem types: the rachis meristem, the primary branch meristem, the elongating primary branch meristem (including axillary meristems), and the spikelet meristem. A switch in expression profile between apical and axillary meristem types followed by more gradual changes during transitions in axillary meristem identity was observed, and several genes potentially involved in branching were identified. This resource will be vital for a mechanistic understanding of the link between inflorescence development and grain yield., This project was jointly supported by Fondation Agropolis through the Investissements d'avenir programme (ANR-10-LABX-0001-01) and Fondazione Cariplo under the EVOREPRICE 1201-004 project. Israr Ud Din's Ph.D. fellowship was funded by IBGE, The University of Agriculture Peshawar, KPK, Pakistan.

Plants produce new organs from a population of pluripotent cells which are located in specific tissues called meristems. One of these meristems, the shoot apical meristem (SAM), gives rise to leaves during the vegetative phase and flowers during the reproductive phase. The transition from vegetative SAM to an inflorescence meristem (IM) is a dramatic developmental switch, which has been particularly well studied in the model species Arabidopsis thaliana. This developmental switch is controlled by multiple environmental signals such as day length (or photoperiod), and it is accompanied by changes in expression of hundreds of genes. A major interest in plant biology is to identify and characterize those genes which are regulated in the stem cells of the SAM in response to the photoperiodic signals. In this sense, techniques such as RNA in situ hybridization (RNA ISH) have been very successfully employed to detect the temporal and spatial expression patterns of genes in the SAM. This method can be specifically optimized for photoperiodic-flowering studies. In this chapter, we describe improved methods to generate plant material and histological samples to be combined with RNA ISH in flowering-related studies.

SUMMARY The shoot apical meristem, a small dome-shaped structure at the shoot apex, is responsible for the initiation of all post-embryonic shoot organs. Pluripotent stem cells within the meristem replenish themselves and provide daughter cells that become incorporated into lateral organ primordia around the meristem periphery. We have identified three novel regulators of shoot apical meristem activity in Arabidopsis thaliana that encode related AIL/PLT transcription factors: AINTEGUMENTA (ANT), AINTEGUMENTA-LIKE6 (AIL6)/PLETHORA3 (PLT3) and AINTEGUMENTA-LIKE7 (AIL7)/PLETHORA7 (PLT7). Loss of these genes results in plants that initiate only a few leaves prior to termination of shoot apical meristem activity. In 7-day-old ant ail6 ail7 seedlings, we observed reduced cell division in the meristem region, differentiation of meristematic cells and altered expression of the meristem regulators WUSCHEL (WUS), CLAVATA3 (CLV3) and SHOOT MERISTEMLESS (STM). Genetic experiments suggest that these three AIL genes do not act specifically in either the WUS/CLV or STM pathway regulating meristem function. Furthermore, these studies indicate that ANT, AIL6 and AIL7 have distinct functions within the meristem rather than acting in a strictly redundant manner. Our study thus identifies three new genes whose distinct functions are together required for continuous shoot apical meristem function.

Alstroemeria sp. cv. Green Coral has numerous bracts instead of flowers, and its cyme structures are repeated eternally. Observations of the development and morphology of inflorescence in cv. Green Coral revealed that transition from inflorescence to floral meristem was restricted. We isolated and characterized floral meristem identity genes LEAFY-like (AlsLFY) and SQUAMOSA-like (AlsSQa and AlsSQb) genes from Alstroemeria ligtu. In situ hybridization results indicated that AlsSQa and AlsSQb were expressed in the dome-shaped floral meristems and all floral organ primordia in A. ligtu. Transcripts of AlsLFY accumulated early in the dome-shaped floral meristems; the signals were restricted later to the outer region of the floral meristem. These results indicate that AlsLFY, AlsSQa, and AlsSQb function as floral meristem identity genes. Expression profiles of AlsLFY, AlsSQa, AlsSQb, and other MADS-box genes were compared between A. ligtu and cv. Green Coral. AlsLFY, AlsDEFa, and AlsAGL6 transcripts were not detected at the shoot apices of cv. Green Coral but were detected in A. ligtu. The early induction and accumulation of AlsLFY transcripts in the inflorescence meristem of A. ligtu prior to development of the floral meristem suggest that downregulation of AlsLFY is likely to restrict the inflorescence-to-floral meristem transition in cv. Green Coral.

The indeterminate growth pattern displayed by shoots is mediated by the proper maintenance of the shoot meristem. Meristem maintenance is dependent upon the balance of stem cell perpetuation in the central zone (CZ) and organogenesis in the peripheral zone (PZ). Although the mechanisms that coordinate CZ and PZ function is not understood, meristem cell fate is likely achieved by the spatial interplay between gene regulatory networks and hormone signaling pathways. During shoot maturation, the identity of the shoot meristem as well as the lateral organs are transformed during the vegetative and reproductive transitions. Studies in model plant systems indicate that three amino acid extension (TALE) homeodomain proteins integrate signaling events that transform the identity of the shoot meristem and establish reproductive patterns of growth. This review will highlight the function of TALE homeodomain transcription factors that regulate shoot meristem cell fate and also function with phase specific regulators to maintain shoot meristem identity.

PpMADS1, a member of the euAP1 clade of the class A genes, was previously cloned from peach. In this study, PpMADS1 was constitutively expressed in Arabidopsis thaliana to study its function in plant development. The transgenic A. thaliana plants containing 35S::PpMADS1 showed severe phenotype variation including early flowering, conversion of inflorescence branches to solitary flowers, formation of terminal flowers, production of higher number of carpels, petals, and stamens than non-transgenic plants, and prevention of pod shatter. Significantly, the transgenic plants produced more than one silique from a single flower. The results obtained by using cDNA microarray and real-time PCR analyses in the transgenic Arabidopsis indicated that PpMADS1 might play dual roles in regulating the floral meristem development by activating or repressing different sets of genes that would determine the different fate of a floral meristem. In addition, the PpMADS1 gene promoter was further cloned, and deletion analyses were conducted by using fused GUS as a reporter gene in transgenic A. thaliana. Histochemical staining of different organs from transgenic plants revealed the region between −197 and −454 bp was specific for GUS expression in flower primordium, and the region between −454 and −678 bp was specific for GUS expression in sepals and petals. In contrast, a negative regulatory element present between −678 and −978 bp could suppress GUS expression in filament.

Post-embryonic development depends on the activity of meristems in plants, and thus control of cell fate in the meristem is crucial to plant development and its architecture. In grasses such as rice and maize, the fate of reproductive meristems changes from indeterminate meristems, such as inflorescence and branch meristems, to determinate meristems, such as the spikelet meristem. Here we analyzed a recessive mutant of rice, aberrant spikelet and panicle1 (asp1), that showed pleiotropic phenotypes such as a disorganized branching pattern, aberrant spikelet morphology, and disarrangement of phyllotaxy. Close examination revealed that regulation of meristem fate was compromised in asp1: degeneration of the inflorescence meristem was delayed, transition from the branch meristem to the spikelet meristem was accelerated, and stem cell maintenance in both the branch meristem and the spikelet meristem was compromised. The genetic program was also disturbed in terms of spikelet development. Gene isolation revealed that ASP1 encodes a transcriptional co-repressor that is related to TOPLESS (TPL) in Arabidopsis and RAMOSA ENHANCER LOCUS2 (REL2) in maize. It is likely that the pleiotropic defects are associated with de-repression of multiple genes related to meristem function in the asp1 mutant. The asp1 mutant also showed de-repression of axillary bud growth and disturbed phyllotaxy in the vegetative phase, suggesting that the function of this gene is closely associated with auxin action. Consistent with these observations and the molecular function of Arabidopsis TPL, auxin signaling was also compromised in the rice asp1 mutant. Taken together, these results indicate that ASP1 regulates various aspects of developmental processes and physiological responses as a transcriptional co-repressor in rice.

In recent years, the role of WOX genes encoding homeodomain transcription factors in the development of the apical meristem of shoots and roots has been actively investigated. However, the role of WOX genes in the control of the cell proliferation in other meristem types is poorly studied. In our work, we have studied the role of the WOX5 gene in the development of the meristem in nitrogen-fixing nodules developing on the roots of legumes in a symbiosis with rhizobia. We have shown that the WOX5 gene is involved in the development of the nodule meristem in legumes, have quantitatively evaluated the gene’s expression at different nodule formation stages, and have studied the localization of its expression using a construct containing the WOX5 promoter fused with a reporter gene. The role of the WOX5 transcription factor in the nodule organogenesis and its possible interaction with the hormonal system in the course of the nodule development has been discussed.

An indeterminate developmental program allows plant organs to grow continuously by maintaining functional meristems over time. The molecular mechanisms involved in the maintenance of the root apical meristem are not completely understood. We have identified a new Arabidopsis thaliana mutant named moots koom 1 (mko1) that showed complete root apical meristem exhaustion of the primary root by 9 days post-germination. MKO1 is essential for maintenance of root cell proliferation. In the mutant, cell division is uncoupled from cell growth in the region corresponding to the root apical meristem. We established the sequence of cellular events that lead to meristem exhaustion in this mutant. Interestingly, the SCR and WOX5 promoters were active in the mko1 quiescent center at all developmental stages. However, during meristem exhaustion, the mutant root tip showed defects in starch accumulation in the columella and changes in auxin response pattern. Therefore, contrary to many described mutants, the determinate growth in mko1 seedlings does not appear to be a consequence of incorrect establishment or affected maintenance of the quiescent center but rather of cell proliferation defects both in stem cell niche and in the rest of the apical meristem. Our results support a model whereby the MKO1 gene plays an important role in the maintenance of the root apical meristem proliferative capacity and indeterminate root growth, which apparently acts independently of the SCR/SHR and WOX5 regulatory pathways.

AGAMOUS-LIKE6 (AGL6) genes play essential roles in flower development, but whether and how they work with floral organ identity genes remain less understood. Here, we describe interactions of the rice (Oryza sativa) AGL6 gene MADS6 with other rice floral homeotic genes in flower development. Genetic analyses revealed that MADS6 specifies the identity of the three inner whorls and floral meristem determinacy redundantly with SUPERWOMAN1/MADS16 (B-gene) or MADS3 (C-gene). MADS6 was shown to define carpel/ovule development and floral determinacy by interacting with MADS13 (D-gene) and control the palea and floral meristem identities together with the YABBY gene DROOPING LEAF. Expression analyses revealed that the transcript levels of six B-, C-, and E-class genes were reduced in mads6-1 at the early flower developmental stage, suggesting that MADS6 is a key regulator of early flower development. Moreover, MADS6 can directly bind to a putative regulatory motif on MADS58 (C-gene), and mads6-1 mads58 displayed phenotypes similar to that of mads6-1. These results suggest that MADS6 is a key player in specifying flower development via interacting with other floral homeotic genes in rice, thus providing new insights into the mechanism by which flower development is controlled.

In plants, the meristem has to maintain a separate population of pluripotent cells that serve two main tasks, i.e., self-maintenance and organ initiation, which are separated spatially in meristem. Prior to our study, WUS and WUS-like WOX genes had been reported as essential for the development of the SAM. In this study, the consequences of gain of WOX1 function are described. Here we report the identification of an Arabidopsis gain-of-function mutant wox1-D, in which the expression level of the WOX1 (WUSCHEL HOMEOBOX 1) was elevated and subtle defects in meristem development were observed. The wox1-D mutant phenotype is dwarfed and slightly bushy, with a smaller shoot apex. The wox1-D mutant also produced small and dark green leaves, and exhibited a failure in anther dehiscence and male sterility. Molecular evidences showed that the transcription of the stem cell marker gene CLV3 was down-regulated in the meristem of wox1-D but accumulated in the other regions, i.e., in the root-hypocotyl junction and at the sites for lateral root initiation. The fact that the organ size and cell size in leaves of wox1-D are smaller than those in wild type suggests that cell expansion is possibly affected in order to have partially retarded the development of lateral organs, possibly through alteration of CLV3 expression pattern in the meristem. An S-adenosylmethionine decarboxylase (SAMDC) protein, SAMDC1, was found able to interact with WOX1 by yeast two-hybrid and pull-down assays in vitro. HPLC analysis revealed a significant reduction of polyamine content in wox1-D. Our results suggest that WOX1 plays an important role in meristem development in Arabidopsis, possibly via regulation of SAMDC activity and polyamine homeostasis, and/or by regulating CLV3 expression.

The family of MADS box genes is involved in a number of processes besides controlling floral development. In addition to supplying homeotic functions defined by the ABC model, they influence flowering time and transformation of vegetative meristem into inflorescence meristem, and have functions in roots and leaves. Three Gerbera hybrida At-SOC1-like genes (Gh-SOC1-Gh-SOC3) were identified among gerbera expressed sequence tags.Evolutionary relationships between SOC1-like genes from gerbera and other plants were studied by phylogenetic analysis. The function of the gerbera gene Gh-SOC1 in gerbera floral development was studied using expression analysis, protein-protein interaction assays and reverse genetics. Transgenic gerbera lines over-expressing or downregulated for Gh-SOC1 were obtained using Agrobacterium transformation and investigated for their floral phenotype.Phylogenetic analysis revealed that the closest paralogues of At-SOC1 are Gh-SOC2 and Gh-SOC3. Gh-SOC1 is a more distantly related paralogue, grouping together with a number of other At-SOC1 paralogues from arabidopsis and other plant species. Gh-SOC1 is inflorescence abundant and no expression was seen in vegetative parts of the plant. Ectopic expression of Gh-SOC1 did not promote flowering, but disturbed the development of floral organs. The epidermal cells of ray flower petals appeared shorter and their shape was altered. The colour of ray flower petals differed from that of the wild-type petals by being darker red on the adaxial side and greenish on the abaxial surface. Several protein-protein interactions with other gerbera MADS domain proteins were identified.The At-SOC1 paralogue in gerbera shows a floral abundant expression pattern. A late petal expression might indicate a role in the final stages of flower development. Over-expression of Gh-SOC1 led to partial loss of floral identity, but did not affect flowering time. Lines where Gh-SOC1 was downregulated did not show a phenotype. Several gerbera MADS domain proteins interacted with Gh-SOC1.

Grass plants develop unique floral patterns that determine grain production. However, the molecular mechanism underlying the specification of floral organ identities and meristem determinacy, including the interaction among floral homeotic genes, remains largely unknown in grasses. Here, we report the interactions of rice (Oryza sativa) floral homeotic genes, OsMADS3 (a C-class gene), OsMADS13 (a D-class gene), and DROOPING LEAF (DL), in specifying floral organ identities and floral meristem determinacy. The interaction among these genes was revealed through the analysis of double mutants. osmads13-3 osmads3-4 displayed a loss of floral meristem determinacy and generated abundant carpelloid structures containing severe defective ovules in the flower center, which were not detectable in the single mutant. In addition, in situ hybridization and yeast two-hybrid analyses revealed that OsMADS13 and OsMADS3 did not regulate each other’s transcription or interact at the protein level. This indicates that OsMADS3 plays a synergistic role with OsMADS13 in both ovule development and floral meristem termination. Strikingly, osmads3-4 dl-sup6 displayed a severe loss of floral meristem determinacy and produced supernumerary whorls of lodicule-like organs at the forth whorl, suggesting that OsMADS3 and DL synergistically terminate the floral meristem. Furthermore, the defects of osmads13-3 dl-sup6 flowers appeared identical to those of dl-sup6, and the OsMADS13 expression was undetectable in dl-sup6 flowers. These observations suggest that DL and OsMADS13 may function in the same pathway specifying the identity of carpel/ovule and floral meristem. Collectively, we propose a model to illustrate the role of OsMADS3, DL, and OsMADS13 in the specification of flower organ identity and meristem determinacy in rice.

Floral homeotic genes encode transcription factors and act as master regulators of flower development. The homeotic protein complex is expressed in a specific whorl of the floral primordium and determines floral organ identity by the combinatorial action. Homeotic proteins continue to be expressed until late in flower development to coordinate growth and organogenesis. Recent genomic studies have shown that homeotic proteins bind thousands of target sites in the genome and regulate the expression of transcription factors, chromatin components and various proteins involved in hormone biosynthesis and signaling and other physiological activities. Further, homeotic proteins program chromatin to direct the developmental coordination of stem cell maintenance and differentiation in shaping floral organs.

We identify a gene, ORGAN BOUNDARY1 ( OBO1 ), by its unique pattern of enhancer- driven GFP expression at the boundaries between the apical meristems and lateral organs in Arabidopsis embryos, seedlings, and mature plants. OBO1 also is expressed at the root apical meristem and in distinct cell files surrounding this area. OBO1 is one of a 10-member plant-specific gene family encoding a single small domain (133 amino acids) with unknown function. One member of this gene family, OBO2 , is identical to a previously studied gene, LIGHT-SENSITIVE HYPOCOTYL1 . Overexpression of OBO1 causes an abnormal number and size of petals and petal–stamen fusions. The patterns of OBO1 gene expression are distinct but overlap with other genes involved in boundary formation in the Arabidopsis shoot apical meristem, including CUP-SHAPED COTYLEDON , LATERAL ORGAN BOUNDARIES , BLADE-ON-PETIOLE , ASYMMETRIC LEAVES , and LATERAL ORGAN FUSION. Nuclear localization of OBO1 suggests that it might act with one or more of the transcription factors encoded by the foregoing genes. Ablation of the specific cells expressing OBO1 leads to loss of the shoot apical meristem and lateral organs. Thus, the cells expressing OBO1 are important for meristem maintenance and organogenesis in Arabidopsis .

A MADS-box gene was isolated using the suppressive subtractive hybridization library between early-flowering mutant and wild-type trifoliate orange (Poncirus trifoliata L. Raf.). This gene is highly homologous with Arabidopsis SHORT VEGETATIVE PHASE (SVP). Based on real-time PCR and in situ hybridization during bud differentiation, PtSVP was expressed intensively in dormant tissue and vegetative meristems. PtSVP transcripts were detected in apical meristems before floral transition, then down-regulated during the transition. PtSVP expression was higher in differentiated (flower primordium) than in undifferentiated cells (apical meristems). The PtSVP expression pattern during apical meristem determination suggested that its function is not to depress flower initiation but to maintain meristem development. Transcription of PtSVP in Arabidopsis svp-41 showed partially rescued SVP function. Ectopic overexpression of PtSVP in wild-type Arabidopsis induced late flowering similar to the phenotypes induced by other SVP/StMADS-11-like genes, but transformants produced additional trichomes and floral defects, such as flower-like structures instead of carpels. Ectopic expression of PtSVP in tobacco also caused additional florets. Overexpression of PtSVP in tobacco inhibited early transition of the coflorescence and prolonged coflorescence development, thus causing additional florets at the later stage. A yeast two-hybrid assay indicated that PtSVP significantly interacted with PtAP1, a homolog of Arabidopsis APETALA1 (AP1). These findings suggest that citrus SVP homolog genes are involved in flowering time regulation and may influence inflorescence meristem identity in some conditions or genetic backgrounds. SVP homologs might have evolved among plant species, but the protein functions are conserved between Arabidopsis and citrus.

The shoot meristem is a group of self-perpetuating cells that ultimately gives rise to the aerial parts of plants. The Arabidopsis thaliana SHOOT MERISTEMLESS (STM) gene, which encodes a knotted1-like homeobox transcription factor, is required for shoot meristem formation and maintenance, and loss-of-function mutations in the gene result in complete loss or premature termination of the shoot meristem. Here, we report a novel missense allele of STM, gorgon (gor), which displays striking differences in shoot meristem defects compared with known stm alleles. The gor phenotype results from substitution of the highly conserved arginine at position 53 of the homeodomain, which is important for DNA binding in other homeodomain proteins. In gor, the shoot meristem enlarges continuously during post-embryonic development and the floral meristems frequently develop additional whorls. These phenotypes, together with enlarged expression domains of meristem markers, indicate that the mutation affects shoot meristem activity in the opposite direction to other loss-of-function alleles. However, detailed genetic analyses and overexpression studies indicate that gor represents a novel type of hypomorphic alleles rather than the hypermorph that is suggested by the phenotype. Consistently, the gor allele strictly requires the functional PENNYWISE (PNY) gene, which encodes a known binding partner of the STM protein, to maintain shoot meristem activity, whereas the wild-type allele efficiently maintains the meristem even in the absence of PNY. Our results suggest a critical role for Arg53 of the homeodomain in STM function and that the gor mutation at this residue impairs shoot meristem homeostasis.

Floral organ identity and meristem determinacy in plants are controlled by combinations of activities mediated by MADS box genes. AGAMOUS-LIKE6 (AGL6)-like genes are MADS box genes expressed in floral tissues, but their biological functions are mostly unknown. Here, we describe an AGL6-like gene in rice (Oryza sativa), MOSAIC FLORAL ORGANS1 (MFO1/MADS6), that regulates floral organ identity and floral meristem determinacy. In the flower of mfo1 mutants, the identities of palea and lodicule are disturbed, and mosaic organs were observed. Furthermore, the determinacy of the floral meristem was lost, and extra carpels or spikelets developed in mfo1 florets. The expression patterns of floral MADS box genes were disturbed in the mutant florets. Suppression of another rice AGL6-like gene, MADS17, caused no morphological abnormalities in the wild-type background, but it enhanced the phenotype in the mfo1 background, indicating that MADS17 has a minor but redundant function with that of MFO1. Whereas single mutants in either MFO1 or the SEPALLATA-like gene LHS1 showed moderate phenotypes, the mfo1 lhs1 double mutant showed a severe phenotype, including the loss of spikelet meristem determinacy. We propose that rice AGL6-like genes help to control floral organ identity and the establishment and determinacy of the floral meristem redundantly with LHS1.

A central question in biology is to understand how gene expression is precisely regulated to give rise to a variety of forms during the process of development. Epigenetic effects such as DNA methylation or histone modification have been increasingly shown to play a critical role in regulation of genome function. GCN5 is a prototypical histone acetyltransferase that participates in regulating developmental gene expression in several metazoan species. In Arabidopsis thaliana, plants with T-DNA insertions in GCN5 (also known as HAG1) display a variety of pleiotropic effects including dwarfism, loss of apical dominance, and floral defects affecting fertility. We sought to determine when during early development floral abnormalities first arise. Using scanning electron microscopy, we demonstrate that gcn5-1/hag1-1 and gcn5-5/hag1-5 mutants display overproliferation of young buds and development of abnormal structures around the inflorescence meristem. gcn5 mutants also display defects in stamen number and arrangement at later stages. This analysis provides temporal and spatial information to aid in the identification of GCN5 target genes in the developing flower. Preliminary studies of putative targets using reverse transcriptase PCR suggest that the floral meristem identity gene LEAFY is among factors upregulated in gcn5-1 mutants.

Plant organs are generated from meristems throughout development. Patterning and elaboration of organ primordia occur as a result of organized cell division and expansion, processes that are likely to be controlled, in part, by meristem-derived signals. Communication between the meristem and lateral organs is crucial for meristem maintenance and organ patterning, and organ boundaries are thought to be important for mediating this communication. Arabidopsis thaliana LATERAL ORGAN FUSION1 (LOF1) encodes a MYB-domain transcription factor that is expressed in organ boundaries. lof1 mutants display defects in organ separation as a result of abnormal cell division and expansion during early boundary formation. lof1 mutants also fail to form accessory shoot meristems. Mutations in the closely related LATERAL ORGAN FUSION2 (LOF2) gene enhance the lof1 phenotype, such that lof1 lof2 double mutants display additional fusion defects. Genetic interactions with the CUP-SHAPED COTYLEDON genes CUC2 and CUC3 revealed a role for LOF1 in both organ separation and axillary meristem formation. Expression of the meristem determinant STM was reduced in lof1 mutant paraclade junctions and lof1 enhanced the weak stm-10 mutant, such that double mutants had severe defects in meristem maintenance and organ separation. Our data implicate LOF1and LOF2 in boundary specification, meristem initiation and maintenance, and organ patterning.

During the floral transition the shoot apical meristem changes its identity from a vegetative to an inflorescence state. This change in identity can be promoted by external signals, such as inductive photoperiod conditions or vernalization, and is accompanied by changes in expression of key developmental genes. The change in meristem identity is usually not reversible, even if the inductive signal occurs only transiently. This implies that at least some of the key genes must possess an intrinsic memory of the newly acquired expression state that ensures irreversibility of the process. In this review, we discuss different molecular scenarios that may underlie a molecular memory of gene expression.

EMBRYONIC FLOWER (EMF) genes are required to maintain vegetative development via repression of flower homeotic genes in Arabidopsis. Removal of EMF gene function caused plants to flower upon germination, producing abnormal and sterile flowers. The pleiotropic effect of emf1 mutation suggests its requirement for gene programs involved in diverse developmental processes. Transgenic plants harboring EMF1 promoter::glucuronidase (GUS) reporter gene were generated to investigate the temporal and spatial expression pattern of EMF1. These plants displayed differential GUS activity in vegetative and flower tissues, consistent with the role of EMF1 in regulating multiple gene programs. EMF1::GUS expression pattern in emf mutants suggests organ-specific auto-regulation. Sense- and antisense (as) EMF1 cDNA were expressed under the control of stage- and tissue-specific promoters in transgenic plants. Characterization of these transgenic plants showed that EMF1 activity is required in meristematic as well as differentiating tissues to rescue emf mutant phenotype. Temporal removal or reduction of EMF1 activity in the embryo or shoot apex of wild-type seedlings was sufficient to cause early flowering and terminal flower formation in adult plants. Such reproductive cell memory is reflected in the flower MADS-box gene activity expressed prior to flowering in these early flowering plants. However, temporal removal of EMF1 activity in flower meristem did not affect flower development. Our results are consistent with EMF1's primary role in repressing flowering in order to allow for vegetative growth.

Two types of branches, rachis branches (i.e. nonfloral) and spikelets (i.e. floral), are produced during rice (Oryza sativa) inflorescence development. We previously reported that the ABERRANT PANICLE ORGANIZATION1 (APO1) gene, encoding an F-box-containing protein orthologous to Arabidopsis (Arabidopsis thaliana) UNUSUAL FLORAL ORGANS, suppresses precocious conversion of rachis branch meristems to spikelets to ensure generation of certain number of spikelets. Here, we identified four dominant mutants producing an increased number of spikelets and found that they are gain-of-function alleles of APO1. The APO1 expression levels are elevated in all four mutants, suggesting that an increase of APO1 activity caused the delay in the program shift to spikelet formation. In agreement with this result, ectopic overexpression of APO1 accentuated the APO1 gain-of-function phenotypes. In the apo1-D dominant alleles, the inflorescence meristem starts to increase in size more vigorously than the wild type when switching to the reproductive development phase. This alteration in growth rate is opposite to what is observed with the apo1 mutants that have a smaller inflorescence meristem. The difference in meristem size is caused by different rates of cell proliferation. Collectively, these results suggest that the level of APO1 activity regulates the inflorescence form through control of cell proliferation in the meristem.

A new morphogenetic mutation of the shoot, FLORAL MERISTEM UNDETERMINATION, was found in Papaver somniferum L. with monocarpic shoot. The expression of the DFM (determination of floral meristem) gene, which limits the proliferative activity of stem cells in the floral meristem, was affected. The mutation displayed spontaneous phenotypic instability in ontogeny, variation in the mutant character expression on different flowers of the same plant in the same genotypic environment. The mutation phenotype varied from no expression or formation of individual phyllomes in the center of the primary ovary to formation of a new flower and a new capsule with viable seeds.

The floral meristem identity gene LEAFY (LFY) in Arabidopsis plays a key role in flower development. We isolated two LFY-like genes from radish, designated RsLFY1 and RsLFY2. Comparison of genomic and cDNA sequences revealed that the number and positions of introns are precisely conserved in RsLFY1, RsLFY2 and LFY. Using RsLFY1 full- length cDNA as a probe, genomic DNA blot hybridization analysis detected two hybridizing fragments under high stringency, suggesting that there are two RsLFY loci within radish genome. Both genes were expressed during vegetative growth, reproductive growth, flower development and seed development. RsLFY1 was expressed slightly in leaf primordia and strongly in early floral meristem. It was expressed successively in primordia of sepals, petals, stamens, gynoecium, ovule integument and mature seeds. These results suggest that RsLFY1 plays a similar role to LFY in floral initiation and the developmental stages of floral organs, and that it also may regulate radish seed development, unlike LFY.

In maize (Zea mays), sex determination occurs through abortion of female carpels in the tassel and arrest of male stamens in the ear. The Tasselseed6 (Ts6) and tasselseed4 (ts4) mutations permit carpel development in the tassel while increasing meristem branching, showing that sex determination and acquisition of meristem fate share a common pathway. We show that ts4 encodes a mir172 microRNA that targets APETALA2 floral homeotic transcription factors. Three lines of evidence suggest that indeterminate spikelet1 (ids1), an APETALA2 gene required for spikelet meristem determinacy, is a key target of ts4. First, loss of ids1 suppresses the ts4 sex determination and branching defects. Second, Ts6 mutants phenocopy ts4 and possess mutations in the microRNA binding site of ids1. Finally, IDS1 protein is expressed more broadly in ts4 mutants compared to wild type. Our results demonstrate that sexual identity in maize is acquired by limiting floral growth through negative regulation of the floral homeotic pathway.

During the last 15 years enormous progress had been made in understanding the genetic and molecular regulation of flower development. The classical A-B-C model, which describes how the activities of three classes of genes coding for transcription factors (A, B, C) alone or coordinately specify the different floral organs, has been expanded by class D genes involved in ovule development and class E genes required for the identities of all floral organs. The molecular quartet model advances the genetic A-B-C-D-E model by describing the presumed interactions between floral MADS-domain proteins. Although the basic developmental program appears to be quite conserved, in non-core eudicots modifications such as ``sliding-boundary'' and ``fading borders'' models had to be established. Since the identity of floral organs is strictly dependent on the activity of the MADS-box genes, duplication and diversification within these genes must have been key processes in flower evolution. Hence, insights into the phylogeny of the floral homeotic genes may help to better understand the evolution of flowers (``evo-devo'').

Through multifaceted genome-scale research involving phylogenomics, targeted gene surveys, and gene expression analyses in diverse basal lineages of angiosperms, our studies provide insights into the most recent common ancestor of all extant flowering plants. MADS-box gene duplications have played an important role in the origin and diversification of angiosperms. Furthermore, early angiosperms possessed a diverse tool kit of floral genes and exhibited developmental 'flexibility', with broader patterns of expression of key floral organ identity genes than are found in eudicots. In particular, homologs of B-function MADS-box genes are more broadly expressed across the floral meristem in basal lineages. These results prompted formulation of the 'fading borders' model, which states that the gradual transitions in floral organ morphology observed in some basal angiosperms (e.g. Amborella) result from a gradient in the level of expression of floral organ identity genes across the developing floral meristem.

In Arabidopsis, two floral homeotic genes APETALA2 (AP2) and AGAMOUS (AG) specify the identities of perianth and reproductive organs, respectively, in flower development. The two genes act antagonistically to restrict each other to their proper domains of action within the floral meristem. In addition to AG, which antagonizes AP2, miR172, a microRNA, serves as a negative regulator of AP2. In this study, we showed that AG and miR172 have distinct functions in flower development and that they largely act independently in the negative regulation of AP2. We uncovered functions of miR172-mediated repression of AP2 in the regulation of floral stem cells and in the delineation of the expression domain of another class of floral homeotic genes. Given the antiquity of miR172 in land plants, our findings have implications for the recruitment of a microRNA in the building of a flower in evolution.

Postembryonic growth and development in higher plants are ultimately reliant on the activity of meristems, where the cells divide frequently to provide source cells for new organs and tissues while in part maintain their pluripotent nature as stem cells. The shoot apical meristem (SAM) is maintained throughout the life of plants and responsible for the development of all areal tissues. In Arabidopsis thaliana, the size of SAM is controlled by a peptide ligand, CLAVATA3 (CLV3). Previously, genetic studies have identified several genes that function downstream of CLV3, many of which, intriguingly, encode receptors. Recently we identified an E3 ubiquitin ligase, PLANT U-BOX 4 (PUB4), as a key regulatory component of root meristem maintenance that functions downstream of an exogenous synthetic CLV3 peptide. Here, we report an additional function of PUB4 in the SAM.

Background The ABC model of flower development describes the molecular basis for specification of floral organ identity in model eudicots such as Arabidopsis and Antirrhinum. According to this model, expression of C-class genes is linked to stamen and gynoecium organ identity. The Zingiberales is an order of tropical monocots in which the evolution of floral morphology is characterized by a marked increase in petaloidy in the androecium. Petaloidy is a derived characteristic of the ginger families and seems to have arisen in the common ancestor of the ginger clade. We hypothesize that duplication of the C-class AGAMOUS (AG) gene followed by divergence of the duplicated AG copies during the diversification of the ginger clade lineages explains the evolution of petaloidy in the androecium. In order to address this hypothesis, we carried out phylogenetic analyses of the AG gene family across the Zingiberales and investigated patterns of gene expression within the androecium. Results Phylogenetic analysis supports a scenario in which Zingiberales-specific AG genes have undergone at least one round of duplication. Gene duplication was immediately followed by divergence of the retained copies. In particular, we detect positive selection in the third alpha-helix of the K domain of Zingiberales AGAMOUS copy 1 (ZinAG-1). A single fixed amino acid change is observed in ZinAG-1 within the ginger clade when compared to the banana grade. Expression analyses of AG and APETALA1/FRUITFULL (AP1/FUL) in Musa basjoo is similar to A- and C-class gene expressions in the Arabidopsis thaliana model, while Costus spicatus exhibits simultaneous expression of AG and AP1/FUL in most floral organs. We propose that this novel expression pattern could be correlated with the evolution of androecial petaloidy within the Zingiberales. Conclusions Our results present an intricate story in which duplication of the AG lineage has lead to the retention of at least two diverged Zingiberales-specific copies, ZinAG-1 and Zingiberales AGAMOUS copy 2 (ZinAG-2). Positive selection on ZinAG-1 residues suggests a mechanism by which AG gene divergence may explain observed morphological changes in Zingiberales flowers. Expression data provides preliminary support for the proposed mechanism, although further studies are required to fully test this hypothesis.