Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis

Transcriptome analysis of Petunia axillaris flowers reveals genes involved in morphological differentiation and metabolite transport

The biosynthesis of plant secondary metabolites is associated with morphological and metabolic differentiation. As a consequence, gene expression profiles can change drastically, and primary and secondary metabolites, including intermediate and end-products, move dynamically within and between cells. However, little is known about the molecular mechanisms underlying differentiation and transport mechanisms. In this study, we performed a transcriptome analysis of Petunia axillaris subsp. parodii, which produces various volatiles in its corolla limbs and emits metabolites to attract pollinators. RNA-sequencing from leaves, buds, and limbs identified 53,243 unigenes. Analysis of differentially expressed genes, combined with gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, showed that many biological processes were highly enriched in limbs. These included catabolic processes and signaling pathways of hormones, such as gibberellins, and metabolic pathways, including phenylpropanoids and fatty acids. Moreover, we identified five transporter genes that showed high expression in limbs, and we performed spatiotemporal expression analyses and homology searches to infer their putative functions. Our systematic analysis provides comprehensive transcriptomic information regarding morphological differentiation and metabolite transport in the Petunia flower and lays the foundation for establishing the specific mechanisms that control secondary metabolite biosynthesis in plants.

The early inflorescence of Arabidopsis thaliana demonstrates positional effects in floral organ growth and meristem patterning

Linear modelling approaches detected significant gradients in organ growth and patterning across early flowers of the Arabidopsis inflorescence and uncovered evidence of new roles for gibberellin in floral development. Most flowering plants, including the genetic model Arabidopsis thaliana, produce multiple flowers in sequence from a reproductive shoot apex to form a flower spike (inflorescence). The development of individual flowers on an Arabidopsis inflorescence has typically been considered as highly stereotypical and uniform, but this assumption is contradicted by the existence of mutants with phenotypes visible in early flowers only. This phenomenon is demonstrated by mutants partially impaired in the biosynthesis of the phytohormone gibberellin (GA), in which floral organ growth is retarded in the first flowers to be produced but has recovered spontaneously by the 10th flower. We presently lack systematic data from multiple flowers across the Arabidopsis inflorescence to explain such changes. Using mutants of the GA 20-OXIDASE (GA20ox) GA biosynthesis gene family to manipulate endogenous GA levels, we investigated the dynamics of changing floral organ growth across the early Arabidopsis inflorescence (flowers 1-10). Modelling of floral organ lengths identified a significant, GA-independent gradient of increasing stamen length relative to the pistil in the wild-type inflorescence that was separable from other, GA-dependent effects. It was also found that the first flowers exhibited unstable organ patterning in contrast to later flowers and that this instability was prolonged by exogenous GA treatment. These findings indicate that the development of individual flowers is influenced by hitherto unknown factors acting across the inflorescence and also suggest novel functions for GA in floral patterning.

Developmental transcriptome analysis of floral transition in Rosa odorata var. gigantea

Expression analyses revealed that floral transition of Rosa odorata var. gigantea is mainly regulated by VRN1, COLs, DELLA and KSN, with contributions by the effects of phytohormone and starch metabolism. Seasonal plants utilize changing environmental and developmental cues to control the transition from vegetative growth to flowering at the correct time of year. This study investigated global gene expression profiles at different developmental stages of Rosa odorata var. gigantea by RNA-sequencing, combined with phenotypic characterization and physiological changes. Gene ontology enrichment analysis of the differentially expressed genes (DEGs) between four different developmental stages (vegetative meristem, pre-floral meristem, floral meristem and secondary axillary buds) indicated that DNA methylation and the light reaction played a large role in inducing the rose floral transition. The expression of SUF and FLC, which are known to play a role in delaying flowering until vernalization, was down-regulated from the vegetative to the pre-floral meristem stage. In contrast, the expression of VRN1, which promotes flowering by repressing FLC expression, increased. The expression of DELLA proteins, which function as central nodes in hormone signaling pathways, and probably involve interactions between GA, auxin, and ABA to promote the floral transition, was well correlated with the expression of floral integrators, such as AGL24, COL4. We also identified DEGs associated with starch metabolism correlated with SOC1, AGL15, SPL3, AGL24, respectively. Taken together, our results suggest that vernalization and photoperiod are prominent cues to induce the rose floral transition, and that DELLA proteins also act as key regulators. The results summarized in the study on the floral transition of the seasonal rose lay a foundation for further functional demonstration, and have profound economic and ornamental values.

Screening of Genes Related to Early and Late Flowering in Tree Peony Based on Bulked Segregant RNA Sequencing and Verification by Quantitative Real-Time PCR

Tree peony (Paeonia suffruticosa Andrews) is a perennial woody shrub bearing large and colorful flowers. However, the flowering period is short and relatively uniform, which to an important extent hinders the cultivation and exploitation of ornamental peonies. In this study, the segregation of an F₁ population derived from P. ostti ‘Feng Dan’ (an early-flowering cultivar) × P. suffruticosa ‘Xin Riyuejin’ (a late-flowering cultivar) was used to screen and analyze candidate genes associated with flowering period of the two parents. Extreme early- and late-flowering genotypes of the F₁ population at full-bloom stage were sampled to establish an early-flowering mixed pool (T03), a late-flowering mixed pool (T04), a late-flowering male pool (T01), and an early-flowering female pool (T02), using the Sequencing By Synthesis (SBS) technology on the Illumina HiSeq TM2500 platform. A total of 56.51 Gb of clean reads data, comprising at least 87.62% of Quality30 (Q30), was generated, which was then combined into 173,960 transcripts (N50 = 1781) and 78,645 (N50 = 1282) unigenes, with a mean length of 1106.76 and 732.27 base pairs (bp), respectively. Altogether, 58,084 genes were annotated by comparison with public databases, based on an E-value parameter of less than 10⁻⁵ and 10⁻¹⁰ for BLAST and HMMER, respectively. In total, 291 unigene sequences were finally screened out by BSR-seq (bulked segregant RNA-seq) association analysis. To validate these unigenes, we finally confirmed seven unigenes that were related to early and late flowering, which were then verified by quantitative real-time PCR (qRT-PCR). This is the first reported study to screen genes associated with early and late flowering of tree peony by the BSA (bulked sample analysis) method of transcriptome sequencing, and to construct a high-quality transcriptome database. A set of candidate functional genes related to flowering time was successfully obtained, providing an important genetic resource for further studies of flowering in peony and the mechanism of regulation of flowering time in tree peony.

Regulation of floral meristem activity through the interaction of AGAMOUS, SUPERMAN, and CLAVATA3 in Arabidopsis

Floral meristem size is redundantly controlled by CLAVATA3, AGAMOUS , and SUPERMAN in Arabidopsis. The proper regulation of floral meristem activity is key to the formation of optimally sized flowers with a fixed number of organs. In Arabidopsis thaliana, multiple regulators determine this activity. A small secreted peptide, CLAVATA3 (CLV3), functions as an important negative regulator of stem cell activity. Two transcription factors, AGAMOUS (AG) and SUPERMAN (SUP), act in different pathways to regulate the termination of floral meristem activity. Previous research has not addressed the genetic interactions among these three genes. Here, we quantified the floral developmental stage-specific phenotypic consequences of combining mutations of AG, SUP, and CLV3. Our detailed phenotypic and genetic analyses revealed that these three genes act in partially redundant pathways to coordinately modulate floral meristem sizes in a spatial and temporal manner. Analyses of the ag sup clv3 triple mutant, which developed a mass of undifferentiated cells in its flowers, allowed us to identify downstream targets of AG with roles in reproductive development and in the termination of floral meristem activity. Our study highlights the role of AG in repressing genes that are expressed in organ initial cells to control floral meristem activity.

Molecular Characterization of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family in Betula luminifera

As a major family of plant-specific transcription factors, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes play vital regulatory roles in plant growth, development and stress responses. In this study, 18 SPL genes were identified and cloned from Betula luminifera. Two zinc finger-like structures and a nuclear location signal (NLS) segments were existed in the SBP domains of all BlSPLs. Phylogenetic analysis showed that these genes were clustered into nine groups (group I-IX). The intron/exon structure and motif composition were highly conserved within the same group. 12 of the 18 BlSPLs were experimentally verified as the targets of miR156, and two cleavage sites were detected in these miR156-targeted BlSPL genes. Many putative cis-elements, associated with light, stresses and phytohormones response, were identified in the promoter regions of BlSPLs, suggesting that BlSPL genes are probably involved in important physiological processes and developmental events. Tissue-specific expression analysis showed that miR156-targeted BlSPLs exhibited a more differential expression pattern, while most miR156-nontargeted BlSPLs tended to be constitutively expressed, suggesting the distinct roles of miR156-targeted and nontargeted BlSPLs in development and growth of B. luminifera. Further expression analysis revealed that miR156-targeted BlSPLs were dramatically up-regulated with age, whereas mature BlmiR156 level was apparently declined with age, indicating that miR156/SPL module plays important roles in vegetative phase change of B. luminifera. Moreover, yeast two-hybrid assay indicated that several miR156-targeted and nontargeted BlSPLs could interact with two DELLA proteins (BlRGA and BlRGL), which suggests that certain BlSPLs take part in the GA regulated processes through protein interaction with DELLA proteins. All these results provide an important basis for further exploring the biological functions of BlSPLs in B. luminifera.

Gene Expression and Transcription Factor Binding Tests Using Mutated-Promoter Reporter Lines

To control the expression of their target genes, plant transcription factors bind to specific DNA sequences (called cis-elements) adjacent to the genes they regulate, thereby promoting or blocking the recruitment of RNA polymerase. Functional analysis of cis-elements is therefore essential for understanding transcriptional regulation, which underlies developmental programs and environmental responses. Using transgenic promoters containing mutations in their cis-elements, the roles of cis-elements in both transcriptional activity and transcription factor binding can be analyzed. To generate mutated promoters, site-directed mutagenesis is used. Site-directed mutagenesis is an in vitro method that confers the desired mutation in a target through performing PCR of native DNA using a mutated oligonucleotide primer. In this chapter, we describe detailed protocols for cloning of promoter regions, PCR-based site-directed mutagenesis, the generation of Arabidopsis transgenic lines, and expression analysis. In addition, we describe an in vivo method to test the binding of transcription factors to promoters with wild-type or mutated cis-elements. This protocol mainly focuses on the use of transgenic lines generated by site-directed mutagenesis, but it can readily be adapted for use with lines generated by CRISPR/Cas9.

Using CRISPR/Cas9 System to Introduce Targeted Mutation in Arabidopsis

Gene editing enables the modification of genetic information in a targeted manner. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a gene editing approach that has been widely used in both the animal and plant studies. Plant transcription factors play critical roles in plant development. Recent studies have used the CRISPER/Cas9 system to disrupt transcription factors and cis-elements in plants. In this chapter, we describe a protocol of using the CRISPR/Cas9 system to generate transcription factor mutants in the model plant species Arabidopsis thaliana. Our protocol contains five different steps: (1) adaptor primers design, (2) cloning of sgRNA expression cassettes, (3) Golden Gate cloning, (4) E. coli and Agrobacterium transformation, and (5) Arabidopsis transformation.

Alterations of CorTFL1 and CorAP1 expression correlate with major evolutionary shifts of inflorescence architecture in Cornus (Cornaceae) - a proposed model for variation of closed inflorescence forms

TFL1-, AP1- and LFY-like genes are known to be key regulators of inflorescence development. However, it remains to be tested whether the evolutionary modifications of inflorescence morphology result from shifts in their expression patterns. We compared the spatiotemporal expression patterns of CorTFL1, CorAP1 and CorLFY in six closely related Cornus species that display four types of closed inflorescence morphology using quantitative real-time polymerase chain reaction (qRT-PCR) and RNA in situ hybridization. Character mapping on the phylogeny was conducted to identify evolutionary changes and to assess the correlation between changes in gene expression and inflorescence morphology. Results demonstrated variation of gene expression patterns among species and a strong correlation between CorTFL1 expression and the branch index of the inflorescence type. Evolutionary changes in CorTFL1 and CorAP1 expression co-occurred on the phylogeny with the morphological changes underpinning inflorescence divergence. The study found a clear correlation between the expression patterns of CorTFL1 and CorAP1 and the inflorescence architecture in a natural system displaying closed inflorescences. The results suggest a role for the alteration in CorTFL1 and CorAP1 expression during the evolutionary modification of inflorescences in Cornus. We propose that a TFL1-like and AP1-like gene-based model may explain variation of closed inflorescences in Cornus and other lineages.

Genetic Regulation of GA Metabolism during Vernalization, Floral Bud Initiation and Development in Pak Choi (Brassica rapa ssp. chinensis Makino)

Pak choi (Brassica rapa ssp. chinensis Makino) is a representative seed vernalization vegetable and premature bolting in spring can cause significant economic loss. Thus, it is critical to elucidate the mechanism of molecular regulation of vernalization and floral bud initiation to prevent premature bolting. Gibberellin (GA) is the key plant hormone involved in regulating plant development. To gain a better understanding of GA metabolism in pak choi, the content of GA in pak choi was measured at different stages of plant development using enzyme-linked immunosorbent assay. The results showed that the GA content increased significantly after low-temperature treatment (4°C) and then decreased rapidly with vegetative growth. During floral bud initiation, the GA content increased rapidly until it peaked upon floral bud differentiation. To elucidate these changes in GA content, the expression of homologous genes encoding enzymes directly involved in GA metabolism were analyzed. The results showed that the changes in the expression of four genes involved in GA synthesis (Bra035120 encoding ent-kaurene synthase, Bra009868 encoding ent-kaurene oxidase, Bra015394 encoding ent-kaurenoic acid oxidase, and Bra013890 encoding GA20-oxidase) were correlated with the changes in GA content. In addition, by comparing the expression of genes involved in GA metabolism at different growth stages, seven differentially expressed genes (Bra005596, Bra009285, Bra022565, Bra008362, Bra033324, Bra010802, and Bra030500) were identified. The differential expression of these genes were directly correlated with changes in GA content, suggesting that these genes were directly related to vernalization, floral bud initiation and development. These results contribute to the understanding of the molecular mechanism of changes in GA content during different developmental phases in pak choi.

Comparative transcriptome analysis of the floral transition in Rosa chinensis 'Old Blush' and R. odorata var. gigantea

The floral transition is a crucial developmental event, but little is known about the underlying regulatory networks in seasonally and continuously flowering roses. In this study, we compared the genetic basis of flowering in two rose species, Rosa chinensis ‘Old Blush’, which flowers continuously, and R. odorata var. gigantea, which blooms in early spring. Gene ontology (GO) terms related to methylation, light reaction, and starch metabolism were enriched in R. odorata var. gigantea and terms associated with sugar metabolism were enriched in R. chinensis ‘Old Blush’ during the floral transition. A MapMan analysis revealed that genes involved in hormone signaling mediate the floral transition in both taxa. Furthermore, differentially expressed genes (DEGs) involved in vernalization, photoperiod, gibberellin (GA), and starch metabolism pathways converged on integrators, e.g., LFY, AGL24, SOC1, CAL, and COLs, to regulate the floral transition in R. odorata var. gigantea, while DEGs related to photoperiod, sugar metabolism, and GA pathways, including COL16, LFY, AGL11, 6PGDH, GASA4, and BAM, modulated the floral transition in R. chinensis ‘Old Blush.’ Our analysis of the genes underlying the floral transition in roses with different patterns of flowering provides a basis for further functional studies.

Short and Solid Culm/RFL/APO2 for culm development in rice

The culm development of rice is characterized by elongation and medullary cavity (MC) formation, which are determined by node formation meristem and residual meristem, respectively. Although many factors have been shown to affect culm elongation, molecules involved in MC formation remained to be identified. In this study, we show that a point mutation in SHORT and SOLID CULM (SSC), the rice homologue of Arabidopsis LFY, resulted in plants with drastically reduced culm length and completely abolished MC formation. Analysis of transgenic plants with moderately enhanced SSC expression revealed significant decreases in plant height and MC size in contrast to slight changes in heading date, indicating that the culm developmental process is much more tightly monitored by the gene. Transcriptomic analysis revealed the differential expression of knotted-1 like homeobox (KNOX) protein genes and gibberellin (GA) metabolic genes in the ssc mutant background, and most of the genes contained well-conserved LFY-binding cis-elements that could be effectively recognized by SSC. Genetic analysis found that the reduced culm length of the mutant could be largely rescued by the GA-accumulating mutation eui, whereas MC formation remained unchanged in the double mutant plants. Taken together, our results suggest that SSC affects culm elongation mainly through maintaining GA homeostasis, while functions in MC formation by mediating residual meristem activity possibly via the KNOX pathway. The present study provides a potential strategy for improving the culm morphology and plant architecture in rice by manipulating SSC and/or its downstream components.

GA as a regulatory link between the showy floral traits color and scent

Emission of volatiles at advanced stages of flower development is a strategy used by plants to lure pollinators to the flower. We reveal that GA negatively regulates floral scent production in petunia. We used Agrobacterium-mediated transient expression of GA-20ox in petunia flowers and a virus-induced gene silencing approach to knock down DELLA expression, measured volatile emission, internal pool sizes and GA levels by GC-MS or LC-MS/MS, and analyzed transcript levels of scent-related phenylpropanoid-pathway genes. We show that GA has a negative effect on the concentrations of accumulated and emitted phenylpropanoid volatiles in petunia flowers; this effect is exerted through transcriptional/post-transcriptional downregulation of regulatory and biosynthetic scent-related genes. Both overexpression of GA20-ox, a GA-biosynthesis gene, and suppression of DELLA, a repressor of GA-signal transduction, corroborated GA's negative regulation of floral scent. We present a model in which GA-dependent timing of the sequential activation of different branches of the phenylpropanoid pathway during flower development may represent a link between the showy traits controlling pollinator attraction, namely color and scent.

Making Flowers at the Right Time

Different plant species flower in different seasons, but there is also annual variability depending on environmental conditions. In this issue of Developmental Cell, Hyun et al. (2016) show that Arabidopsis plants can flower without proper seasonal cues if they have developed past the juvenile phase and have high levels of gibberellin.

Integrated mRNA and microRNA transcriptome variations in the multi-tepal mutant provide insights into the floral patterning of the orchid Cymbidium goeringii

Background

Cymbidium goeringii is a very famous traditional orchid plant in China, which is well known for its spectacular and diverse flower morphology. In particular, the multi-tepal mutants have considerable ecological and cultural value. However, the current understanding of the molecular mechanisms of floral patterning and multi-tepal development is limited. In this study, we performed expression profiling of both microRNA (miRNA) and mRNA from wild-type and typical multi-tepal-mutant flowers of C. goeringii for the first time, to identify the genes and pathways regulating floral morphogenesis in C. goeringii.

Results

Total clean reads of 98,988,774 and 100,188,534 bp were obtained from the wild-type and mutant library, respectively, and de novo assembled into 98,446 unigenes, with an average length of 989 bp. Among them, 18,489 were identified as differentially expressed genes between the two libraries according to comparative transcript profiling. The majority of the gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathway enrichment responses were for membrane-building and ploidy-related processes, consistent with the excessive floral organs and altered cell size observed in the mutant. There were 29 MADS-box genes, as well as a large number of floral-related regulators and hormone-responsive genes, considered as candidates regulating floral patterning of C. goeringii. Small RNA sequencing revealed 132 conserved miRNA families expressed in flowers of C. goeringii, and 11 miRNAs corresponding to 455 putative target genes were considered to be responsible for multi-tepal development. Importantly, integrated analysis of mRNA and miRNA sequencing data showed two transcription factor/microRNA-based genetic pathways contributing to the multi-tepal trait: well-known floral-related miR156/SPL and miR167/ARF regulatory modes involved in reproductive organ development; and the miR319/TCP4–miR396/GRF regulatory cascade probably regulating cell proliferation of the multi-tepal development.

Conclusions

Integrated mRNA and miRNA profiling data provided comprehensive gene expression information on the wild-type and multi-tepal mutant at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral patterning of C. goeringii. These data could also be used as an important resource for investigating the genetics of floral morphogenesis and various biological mechanisms of orchid plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3756-9) contains supplementary material, which is available to authorized users.

Identification, Classification, and Expression Analysis of GRAS Gene Family in Malus domestica

GRAS genes encode plant-specific transcription factors that play important roles in plant growth and development. However, little is known about the GRAS gene family in apple. In this study, 127 GRAS genes were identified in the apple (Malus domestica Borkh.) genome and named MdGRAS1 to MdGRAS127 according to their chromosomal locations. The chemical characteristics, gene structures and evolutionary relationships of the MdGRAS genes were investigated. The 127 MdGRAS genes could be grouped into eight subfamilies based on their structural features and phylogenetic relationships. Further analysis of gene structures, segmental and tandem duplication, gene phylogeny and tissue-specific expression with ArrayExpress database indicated their diversification in quantity, structure and function. We further examined the expression pattern of MdGRAS genes during apple flower induction with transcriptome sequencing. Eight higher MdGRAS (MdGRAS6, 26, 28, 44, 53, 64, 107, and 122) genes were surfaced. Further quantitative reverse transcription PCR indicated that the candidate eight genes showed distinct expression patterns among different tissues (leaves, stems, flowers, buds, and fruits). The transcription levels of eight genes were also investigated with various flowering related treatments (GA₃, 6-BA, and sucrose) and different flowering varieties (Yanfu No. 6 and Nagafu No. 2). They all were affected by flowering-related circumstance and showed different expression level. Changes in response to these hormone or sugar related treatments indicated their potential involvement during apple flower induction. Taken together, our results provide rich resources for studying GRAS genes and their potential clues in genetic improvement of apple flowering, which enriches biological theories of GRAS genes in apple and their involvement in flower induction of fruit trees.

Ascorbic Acid-A Potential Oxidant Scavenger and Its Role in Plant Development and Abiotic Stress Tolerance

Over-production of reactive oxygen species (ROS) in plants under stress conditions is a common phenomenon. Plants tend to counter this problem through their ability to synthesize ROS neutralizing substances including non-enzymatic and enzymatic antioxidants. In this context, ascorbic acid (AsA) is one of the universal non-enzymatic antioxidants having substantial potential of not only scavenging ROS, but also modulating a number of fundamental functions in plants both under stress and non-stress conditions. In the present review, the role of AsA, its biosynthesis, and cross-talk with different hormones have been discussed comprehensively. Furthermore, the possible involvement of AsA-hormone crosstalk in the regulation of several key physiological and biochemical processes like seed germination, photosynthesis, floral induction, fruit expansion, ROS regulation and senescence has also been described. A simplified and schematic AsA biosynthetic pathway has been drawn, which reflects key intermediates involved therein. This could pave the way for future research to elucidate the modulation of plant AsA biosynthesis and subsequent responses to environmental stresses. Apart from discussing the role of different ascorbate peroxidase isoforms, the comparative role of two key enzymes, ascorbate peroxidase (APX) and ascorbate oxidase (AO) involved in AsA metabolism in plant cell apoplast is also discussed particularly focusing on oxidative stress perception and amplification. Limited progress has been made so far in terms of developing transgenics which could over-produce AsA. The prospects of generation of transgenics overexpressing AsA related genes and exogenous application of AsA have been discussed at length in the review.

Comparative Transcriptomic Analysis of Vernalization- and Cytokinin-Induced Floral Transition in Dendrobium nobile

Vernalization is required for floral initiation in Dendrobium. Interestingly, those beneficial effects can also be achieved by exogenous cytokinin application in greenhouses. Thus, an as yet unknown crosstalk/interaction may exist between vernalization and cytokinin signaling pathways. In this study, we showed, by de novo transcriptome assembly using RNA-seq data from both vegetative and reproductive tissue samples, that some floral transition-related genes—DnVRN1, FT, SOC1, LFY and AP1—were differentially expressed in low-temperature-challenged (LT) or thidiazuron (TDZ)-treated plants, compared to those mock-treated (CK). Both LT and TDZ upregulated SOC1, LFY and AP1, while the upregulation of DnVRN1 and FT was only LT-induced. We further found that LT promoted the upregulation of some key cytokinin signaling regulators, including several cytokinin biosynthesis-related genes and type-B response regulator (RR)-encoding genes, and that both LT and TDZ triggered the significant upregulation of some marker genes in the gibberellin (GA) signaling pathway, indicating an important low temperature-cytokinin-GA axis in flowering. Our data thus have revealed a cytokinin-GA signal network underlying vernalization, providing a novel insight into further investigation of the molecular mechanism of floral initiation in Dendrobium.

Hormonal control of the floral transition: Can one catch them all?

The transition to flowering marks a key adaptive developmental switch in plants which impacts on their survival and fitness. Different signaling pathways control the floral transition, conveying both endogenous and environmental cues. These cues are often relayed and/or modulated by different hormones, which might confer additional developmental flexibility to the floral process in the face of varying conditions. Among the different hormonal pathways, the phytohormone gibberellic acid (GA) plays a dominant role. GA is connected with the other floral pathways through the GA-regulated DELLA proteins, acting as versatile interacting modules for different signaling proteins. In this review, I will highlight the role of DELLAs as spatial and temporal modulators of different consolidated floral pathways. Next, building on recent data, I will provide an update on some emerging themes connecting other hormone signaling cascades to flowering time control. I will finally provide examples for some established as well as potential cross-regulatory mechanisms between hormonal pathways mediated by the DELLA proteins.

Key developmental transitions during flower morphogenesis and their regulation

The arrangement of flowers on flowering stems called inflorescences contributes to the beauty of the natural world and enhances seed yield, impacting species survival and human sustenance. During the reproductive phase, annual/monocarpic plants like Arabidopsis and most crops form two types of lateral structures: indeterminate lateral inflorescences and determinate flowers. Their stereotypical arrangement on the primary inflorescence stem determines the species-specific inflorescence architecture. This architecture can be modulated in response to environmental cues to enhance reproductive success. Early botanists already appreciated that flowers and lateral inflorescences are analogous structures that are interconvertible. Here I will discuss the molecular underpinnings of these observations and explore the regulatory logic of the developmental fate transitions that lead to the formation of a flower.

Transcriptome of the floral transition in Rosa chinensis 'Old Blush'

BACKGROUND

The floral transition plays a vital role in the life of ornamental plants. Despite progress in model plants, the molecular mechanisms of flowering regulation remain unknown in perennial plants. Rosa chinensis 'Old Blush' is a unique plant that can flower continuously year-round. In this study, gene expression profiles associated with the flowering transition were comprehensively analyzed during floral transition in the rose.

RESULTS

According to the transcriptomic profiles, 85,663 unigenes and 1,637 differentially expressed genes (DEGs) were identified, among which 32 unigenes were involved in the circadian clock, sugar metabolism, hormone, and autonomous pathways. A hypothetical model for the regulation of floral transition was proposed in which the candidate genes function synergistically the floral transition process. Hormone contents and biosynthesis and metabolism genes fluctuated during the rose floral transition process. Gibberellins (GAs) inhibited rose floral transition, the content of GAs gradually decreased and GA2ox and SCL13 were upregulated from vegetative (VM) meristem to floral meristem (FM). Auxin plays an affirmative part in mediating floral transition, auxin content and auxin-related gene expression levels were gradually upregulated during the floral transition of the rose. However, ABA content and ABA signal genes were gradually downregulated, suggesting that ABA passively regulates the rose floral transition by participating in sugar signaling. Furthermore, sugar content and sugar metabolism genes increased during floral transition in the rose, which may be a further florigenic signal that activates floral transition. Additionally, FRI, FY, DRM1, ELIP, COP1, CO, and COL16 are involved in the circadian clock and autonomous pathway, respectively, and they play a positively activating role in regulating floral transition. Overall, physiological changes associated with genes involved in the circadian clock or autonomous pathway collectively regulated the rose floral transition.

CONCLUSIONS

Our results summarize a valuable collective of gene expression profiles characterizing the rose floral transition. The DEGs are candidates for functional analyses of genes affecting the floral transition in the rose, which is a precious resource that reveals the molecular mechanism of mediating floral transition in other perennial plants.

Early histological, hormonal, and molecular changes during pineapple (Ananas comosus (L.) Merrill) artificial flowering induction

Natural flowering can cause serious scheduling problems in the pineapple (Ananas comosus) industry and increase harvest costs. Pineapple flowering is thought to be triggered by increased ethylene levels and artificial forcing of pineapple flowering is a common practice to promote flowering synchronisation. However, little is known about the early hormonal and molecular changes of pineapple flowering induction and development. Here, we aimed to analyse the molecular, hormonal, and histological changes during artificial pineapple flowering by Ethrel^®48 treatment. Histological analyses of the shoot apical meristem, leaf gibberellic acid (GA₃), and ethylene quantification were carried out during the first 72h after Ethrel^®48 treatment. Expression profiles from ethylene biosynthesis (AcACS2 and AcACO1), gibberellin metabolism (AcGA2-ox1 and AcDELLA1), and flower development (FT-like gene (AcFT), LFY-like gene (AcLFY), and a PISTILLATA-like gene (AcPI)) genes were analysed during the first 24h after Ethrel^®48 treatment. Differentiation processes of the shoot apical meristem into flower buds were already present in the first 72h after Ethrel^®48 treatment. Ethrel^®48 lead to a reduction in GA₃ levels, probably triggered by elevated ethylene levels and the positive regulation AcGA2-ox1. AcLFY activation upon Ethrel^®48 may also have contributed to the reduction of GA₃ levels and, along with the up-regulation of AcPI, are probably associated with the flower induction activation. AcFT and AcDELLA1 do not seem to be regulated by GA₃ and ethylene. Decreased GA₃ and increased ethylene levels suggest an accumulation of AcDELLA1, which may display an important role in pineapple flowering induction. Thus, this study shows that molecular, hormonal, and histological changes are present right after Ethrel^®48 treatment, providing new insights into how pineapple flowering occurs under natural conditions.

Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation

Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the expression of the corresponding gene in an additive fashion or cooperate by physical interactions, forming larger protein complexes. The importance of protein-protein interactions between members of a particular plant TF family has long been recognised; however, a significant number of interfamily TF interactions has recently been reported. The biological implications and the molecular mechanisms involved in cross-family interactions have now started to be elucidated and the examples illustrate potential roles in the bridging of biological processes. Hence, cross-family TF interactions expand the molecular toolbox for plants with additional mechanisms to control and fine-tune robust gene expression patterns and to adapt to their continuously changing environment.

Overexpression of Jatropha Gibberellin 2-oxidase 6 (JcGA2ox6) Induces Dwarfism and Smaller Leaves, Flowers and Fruits in Arabidopsis and Jatropha

Gibberellins (GAs) are plant hormones that play fundamental roles in plant growth and development. Gibberellin 2-oxidase (GA2ox) plays a direct role in determining the levels of bioactive GAs by catalyzing bioactive GAs or their immediate precursors to inactive forms. In this study, a GA2ox gene, designated JcGA2ox6, was isolated from Jatropha curcas. JcGA2ox6 is expressed in all tissues of adult Jatropha, with the highest expression level in male flowers and the lowest expression level in young leaves. Overexpression of JcGA2ox6 in Arabidopsis resulted in a typical dwarf phenotype, along with late flowering, smaller leaves and flowers, shorter siliques and smaller seeds. Similarly, when JcGA2ox6 was overexpressed in Jatropha, the transgenic plants exhibited a dwarf phenotype with dark-green leaves and smaller inflorescences, flowers, fruits and seeds. However, the flowering time of Jatropha was not affected by overexpression of JcGA2ox6, unlike that in the transgenic Arabidopsis. Moreover, the number of flowers per inflorescence, the weight of 10 seeds and the seed oil content were significantly decreased in transgenic Jatropha. The results indicated that overexpression of JcGA2ox6 had a great impact on the vegetative and reproductive growth of transgenic Jatropha. Furthermore, we found that the dwarf phenotype of transgenic Jatropha was caused by a decrease in endogenous bioactive GA₄, which was correlated with the degree of dwarfism.

Evolutionary Analysis of DELLA-Associated Transcriptional Networks

DELLA proteins are transcriptional regulators present in all land plants which have been shown to modulate the activity of over 100 transcription factors in Arabidopsis, involved in multiple physiological and developmental processes. It has been proposed that DELLAs transduce environmental information to pre-wired transcriptional circuits because their stability is regulated by gibberellins (GAs), whose homeostasis largely depends on environmental signals. The ability of GAs to promote DELLA degradation coincides with the origin of vascular plants, but the presence of DELLAs in other land plants poses at least two questions: what regulatory properties have DELLAs provided to the behavior of transcriptional networks in land plants, and how has the recruitment of DELLAs by GA signaling affected this regulation. To address these issues, we have constructed gene co-expression networks of four different organisms within the green lineage with different properties regarding DELLAs: Arabidopsis thaliana and Solanum lycopersicum (both with GA-regulated DELLA proteins), Physcomitrella patens (with GA-independent DELLA proteins) and Chlamydomonas reinhardtii (a green alga without DELLA), and we have examined the relative evolution of the subnetworks containing the potential DELLA-dependent transcriptomes. Network analysis indicates a relative increase in parameters associated with the degree of interconnectivity in the DELLA-associated subnetworks of land plants, with a stronger effect in species with GA-regulated DELLA proteins. These results suggest that DELLAs may have played a role in the coordination of multiple transcriptional programs along evolution, and the function of DELLAs as regulatory 'hubs' became further consolidated after their recruitment by GA signaling in higher plants.

Chemical control of flowering time

Flowering at the right time is of great importance; it secures seed production and therefore species survival and crop yield. In addition to the genetic network controlling flowering time, there are a number of much less studied metabolites and exogenously applied chemicals that may influence the transition to flowering as well as flower opening. Increased emphasis on research within this area has the potential to counteract the negative effects of global warming on flowering time, especially in perennial crop plants. Perennial crops have a requirement for winter chill, but winters become increasingly warm in temperate regions. This has dramatic effects on crop yield. Different strategies are therefore being developed to engineer flowering time to match local growing conditions. The majority of these efforts are within plant breeding, which benefits from a substantial amount of knowledge on the genetic aspects of flowering time regulation in annuals, but less so in perennials. An alternative to plant breeding approaches is to engineer flowering time chemically via the external application of flower-inducing compounds. This review discusses a variety of exogenously applied compounds used in fruit farming to date, as well as endogenous growth substances and metabolites that can influence flowering time of annuals and perennials.

SPL3/4/5 Integrate Developmental Aging and Photoperiodic Signals into the FT-FD Module in Arabidopsis Flowering

Environmental sensitivity varies across developmental phases in flowering plants. In the juvenile phase, microRNA156 (miR156)-mediated repression of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) transcription factors renders Arabidopsis plants incompetent to floral inductive signals, including long-day (LD) photoperiod. During the vegetative phase transition, which accompanies a reduction of miR156 and a concomitant elevation of its targets, plants acquire reproductive competence such that LD signals promote flowering. However, it remains largely unknown how developmental signals are associated with photoperiodic flowering. Here, we show that SPL3, SPL4, and SPL5 (SPL3/4/5) potentiate the FLOWERING LOCUS T (FT)-FD module in photoperiodic flowering. SPL3/4/5 function as transcriptional activators through the interaction with FD, a basic leucine zipper transcription factor which plays a critical role in photoperiodic flowering. SPL3/4/5 can directly bind to the promoters of APETALA1, LEAFY, and FRUITFULL, thus mediating their activation by the FT-FD complex. Our findings demonstrate that SPL3/4/5 act synergistically with the FT-FD module to induce flowering under LDs, providing a long-sought molecular knob that links developmental aging and photoperiodic flowering.

Trichome patterning control involves TTG1 interaction with SPL transcription factors

Epidermal cell differentiation is a paramount and conserved process among plants. In Arabidopsis, a ternary complex formed by MYB, bHLH transcription factors and TTG1 modulates unicellular trichome morphogenesis. The formation of multicellular glandular trichomes of the xerophytic shrub Cistus creticus that accumulate labdane-type diterpenes, has attained much attention renowned for its medicinal properties. Here, we show that C. creticus TTG1 (CcTTG1) interacts with the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPLA/B) proteins, putative homologs of AtSPL4/5 that in turn interact with AtTTG1. These interactions occur between proteins from evolutionarily distant species supporting the conserved function of TTG1-SPL complex. Overexpression of AtSPL4 and AtSPL5 decreased the expression of GLABRA2 (AtGL2), the major regulator of trichome morphogenesis, resulting in trichome reduction on the adaxial surface of cauline leaves, thereby illuminating the significance of TTG1-SPLs interactions in trichome formation control. AtGL2 and AtSPL4 have opposite expression patterns during early stages of leaf development. We postulate an antagonistic effect between SPLs and the heterogeneous MYB-bHLH factors binding to TTG1. Hence, the SPLs potentially rearrange the complex, attenuating its transcriptional activity to control trichome distribution.

An ortholog of LEAFY in Jatropha curcas regulates flowering time and floral organ development

Jatropha curcas seeds are an excellent biofuel feedstock, but seed yields of Jatropha are limited by its poor flowering and fruiting ability. Thus, identifying genes controlling flowering is critical for genetic improvement of seed yield. We isolated the JcLFY, a Jatropha ortholog of Arabidopsis thaliana LEAFY (LFY), and identified JcLFY function by overexpressing it in Arabidopsis and Jatropha. JcLFY is expressed in Jatropha inflorescence buds, flower buds, and carpels, with highest expression in the early developmental stage of flower buds. JcLFY overexpression induced early flowering, solitary flowers, and terminal flowers in Arabidopsis, and also rescued the delayed flowering phenotype of lfy-15, a LFY loss-of-function Arabidopsis mutant. Microarray and qPCR analysis revealed several flower identity and flower organ development genes were upregulated in JcLFY-overexpressing Arabidopsis. JcLFY overexpression in Jatropha also induced early flowering. Significant changes in inflorescence structure, floral organs, and fruit shape occurred in JcLFY co-suppressed plants in which expression of several flower identity and floral organ development genes were changed. This suggests JcLFY is involved in regulating flower identity, floral organ patterns, and fruit shape, although JcLFY function in Jatropha floral meristem determination is not as strong as that of Arabidopsis.

Gibberellins regulate the stem elongation rate without affecting the mature plant height of a quick development mutant of winter wheat (Triticum aestivum L.)

Gibberellin (GA) is essential for determining plant height. Alteration of GA content or GA signaling results in a dwarf or slender phenotype. Here, we characterized a novel wheat mutant, quick development (qd), in which GA regulates stem elongation but does not affect mature plant height. qd and wild-type plants did not exhibit phenotypic differences at the seedling stage. From jointing to heading stage, qd plants were taller than wild-type plants due to elongated cells. However, wild-type and qd plants were the same height at heading. Unlike wild-type plants, qd plants were sensitive to exogenous GA due to mutation of Rht-B1. With continuous GA stimulation, qd seedlings and adult plants were taller than wild-type. Thus, the GA content of qd plants might differ from that of wild-type during the growth process. Analysis of GA biosynthetic gene expression verified this hypothesis and showed that TaKAO, which is involved in catalyzing the early steps of GA biosynthesis, was differentially expressed in qd plants compared with wild-type. The bioactive GA associated gene TaGA20ox was downregulated in qd plants during the late growth stages. Measurements of endogenous GA content were consistent with the gene-expression analysis results. Consistent with the GA content variation, the first three basal internodes were longer and the last two internodes were shorter in qd than in wild-type plants. The qd mutant might be useful in dissecting the mechanism by which GA regulates stem-growing process, and it may be serve as a GA responsive semi-dwarf germplasm in breeding programs.

Effect of exogenous GA3 and its inhibitor paclobutrazol on floral formation, endogenous hormones, and flowering-associated genes in 'Fuji' apple (Malus domestica Borkh.)

Gibberellins (GAs) reduce apple (Malus domestica) flowering rates; however, the mechanism of their action is not fully understood. To gain a better insight into gibberellin-regulated flowering, here, 5 year-old 'Fuji' apple trees were used to explore the responses of hormones [GA1+3, GA4+7, indole-3-acetic acid (IAA), zeatin-riboside (ZR), and abscisic acid (ABA)], and gibberellin- and flowering-associated genes, to applications of gibberellin acid (GA3) and paclobutrazol (PAC). Results showed that GA3 relatively stimulated vegetative growth and delayed floral induction. Moreover, GA3 spraying significantly affected contents of all endogenous hormones and all the genes tested in at least one time points: the content of endogenous GAs was increased instantly and that of ZR was reduced at 44 days after fullbloom (DAF), which might constitute an unfavorable factor for flower formation; MdKO (ent-kaurene oxidase gene) and MdGA20ox (GA20 oxidase gene) were significantly repressed by a high level of GAs through the negative feedback regulation of GA; additionally, the MdSPLs (SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE) in this study were all significantly repressed by GA3 but promoted by PAC; the expression of MdFT1/2 (FLOWERING LOCUS T), MdSOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1) and MdAP1 (APETALA1) in GA3-treated buds changed in the same way, and they were repressed at 44 DAF. We suppose that GA3 spraying disrupts the balance between ZR and GAs, and inhibits floral induction, probably by suppressing MdSPLs and the floral integrators in flower induction, which ultimately contributed to inhibiting flower formation.

Integrative effect of drought and low temperature on litchi (Litchi chinensis Sonn.) floral initiation revealed by dynamic genome-wide transcriptome analysis

Floral induction in litchi is influenced by multiple environment cues including temperature and soil water condition. In the present study, we determined that a combined treatment consisting of 14-day drought imposed prior to exposure to 35-day low temperature (T3) significantly promoted litchi flowering relative to the low temperature alone (T2), suggesting an integrative effect of drought and low temperature on litchi floral initiation. Analysis of transcriptomic changes in leaves from different treatments showed that 2,198 and 4,407 unigenes were differentially expressed in response to drought and low temperature, respectively. 1,227 of these unigenes were expressed in response to both treatments, implying an interaction of drought and low temperature on expression of genes involved in litchi floral initiation. Additionally, 932 unigenes were consistently differentially expressed during floral induction between T2 and T3 plants, which potentially accounts for the difference of flowering time. Thirty-eight transcription factors out of these 932 unigenes were identified as hub genes with central roles in regulation of litchi floral induction. The expression of litchi homologs of well-known flowering genes was also investigated, and one Flowering Locus T (FT) homolog may play a crucial role in litchi flowering in responses to drought and low temperature.

Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana

Correct developmental timing is essential for plant fitness and reproductive success. Two important transitions in shoot development-the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition-are mediated by a group of genes targeted by miR156, SQUAMOSA PROMOTER BINDING PROTEIN (SBP) genes. To determine the developmental functions of these genes in Arabidopsis thaliana, we characterized their expression patterns, and their gain-of-function and loss-of-function phenotypes. Our results reveal that SBP-LIKE (SPL) genes in Arabidopsis can be divided into three functionally distinct groups: 1) SPL2, SPL9, SPL10, SPL11, SPL13 and SPL15 contribute to both the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition, with SPL9, SP13 and SPL15 being more important for these processes than SPL2, SPL10 and SPL11; 2) SPL3, SPL4 and SPL5 do not play a major role in vegetative phase change or floral induction, but promote the floral meristem identity transition; 3) SPL6 does not have a major function in shoot morphogenesis, but may be important for certain physiological processes. We also found that miR156-regulated SPL genes repress adventitious root development, providing an explanation for the observation that the capacity for adventitious root production declines as the shoot ages. miR156 is expressed at very high levels in young seedlings, and declines in abundance as the shoot develops. It completely blocks the expression of its SPL targets in the first two leaves of the rosette, and represses these genes to different degrees at later stages of development, primarily by promoting their translational repression. These results provide a framework for future studies of this multifunctional family of transcription factors, and offer new insights into the role of miR156 in Arabidopsis development.

Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana

Reproductive development in plants is controlled by complex and intricate gene-regulatory networks of transcription factors. These networks integrate the information from endogenous, hormonal and environmental regulatory pathways. Many of the key players have been identified in Arabidopsis and other flowering plant species, and their interactions and molecular modes of action are being elucidated. An emerging theme is that there is extensive crosstalk between different pathways, which can be accomplished at the molecular level by modulation of transcription factor activity or of their downstream targets. In this review, we aim to summarize current knowledge on transcription factors and epigenetic regulators that control basic developmental programs during inflorescence and flower morphogenesis in the model plant Arabidopsis thaliana. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

Expression of ZmGA20ox cDNA alters plant morphology and increases biomass production of switchgrass (Panicum virgatum L.)

Switchgrass (Panicum virgatum L.) is considered a model herbaceous energy crop for the USA, for its adaptation to marginal land, low rainfall and nutrient-deficient soils; however, its low biomass yield is one of several constraints, and this might be rectified by modulating plant growth regulator levels. In this study, we have determined whether the expression of the Zea mays gibberellin 20-oxidase (ZmGA20ox) cDNA in switchgrass will improve biomass production. The ZmGA20ox gene was placed under the control of constitutive CaMV35S promoter with a strong TMV omega enhancer, and introduced into switchgrass via Agrobacterium-mediated transformation. The transgene integration and expression levels of ZmGA20ox in T0 plants were analysed using Southern blot and qRT-PCR. Under glasshouse conditions, selected transgenic plants exhibited longer leaves, internodes and tillers, which resulted in twofold increased biomass. These phenotypic alterations correlated with the levels of transgene expression and the particular gibberellin content. Expression of ZmGA20ox also affected the expression of genes coding for key enzymes in lignin biosynthesis. Our results suggest that the employment of ectopic ZmGA20ox and selection for natural variants with high level expression of endogenous GA20ox are appropriate approaches to increase biomass production of switchgrass and other monocot biofuel crops.

Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum

Epipremnum aureum is an extremely popular houseplant belonging to the Araceae family of angiosperms, but it does not flower either in the wild or under cultivation. We uncovered the potential causes of its shy-flowering nature by building the transcriptome using next-generation sequencing and identifying floral-related genes that are differentially expressed between vertical growth (VG, adult) and horizontal growth (HG, juvenile) plants. Transcripts of the gibberellin (GA) biosynthetic gene EaGA3ox1 and GA-responsive floral meristem identity gene EaLFY were absent in both VG and HG plants, suggesting that a deficiency of bioactive GAs may be responsible for its shy-flowering nature. This hypothesis is supported by undetectable or low levels of three bioactive GAs, and exogenous GA3 triggered flowering in both plants. Our study resolves the mystery why E. aureum fails to flower, and reveals the positive role of GAs in floral transition in perennials.

Light-Mediated Hormonal Regulation of Plant Growth and Development

Light is crucial for plant life, and perception of the light environment dictates plant growth, morphology, and developmental changes. Such adjustments in growth and development in response to light conditions are often established through changes in hormone levels and signaling. This review discusses examples of light-regulated processes throughout a plant's life cycle for which it is known how light signals lead to hormonal regulation. Light acts as an important developmental switch in germination, photomorphogenesis, and transition to flowering, and light cues are essential to ensure light capture through architectural changes during phototropism and the shade avoidance response. In describing well-established links between light perception and hormonal changes, we aim to give insight into the mechanisms that enable plants to thrive in variable light environments.

Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem

Flowering is initiated in response to environmental and internal cues that are integrated at the shoot apical meristem (SAM). We show that SPL15 coordinates the basal floral promotion pathways required for flowering of Arabidopsis in non-inductive environments. SPL15 directly activates transcription of the floral regulators FUL and miR172b in the SAM during floral induction, whereas its paralog SPL9 is expressed later on the flanks of the SAM. The capacity of SPL15 to promote flowering is regulated by age through miR156, which targets SPL15 mRNA, and gibberellin (GA), which releases SPL15 from DELLAs. Furthermore, SPL15 and the MADS-box protein SOC1 cooperate to promote transcription of their target genes. SPL15 recruits RNAPII and MED18, a Mediator complex component, in a GA-dependent manner, while SOC1 facilitates active chromatin formation with the histone demethylase REF6. Thus, we present a molecular basis for assimilation of flowering signals and transcriptional control at the SAM during flowering.

Paralogous SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes differentially regulate leaf initiation and reproductive phase change in petunia

MAIN CONCLUSION

Duplicated petunia clade-VI SPL genes differentially promote the timing of inflorescence and flower development, and leaf initiation rate. The timing of plant reproduction relative to favorable environmental conditions is a critical component of plant fitness, and is often associated with variation in plant architecture and habit. Recent studies have shown that overexpression of the microRNA miR156 in distantly related annual species results in plants with perennial characteristics, including late flowering, weak apical dominance, and abundant leaf production. These phenotypes are largely mediated through the negative regulation of a subset of genes belonging to the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors. In order to determine how and to what extent paralogous SPL genes have partitioned their roles in plant growth and development, we functionally characterized petunia clade-VI SPL genes under different environmental conditions. Our results demonstrate that PhSBP1and PhSBP2 differentially promote discrete stages of the reproductive transition, and that PhSBP1, and possibly PhCNR, accelerates leaf initiation rate. In contrast to the closest homologs in annual Arabidopsis thaliana and Mimulus guttatus, PhSBP1 and PhSBP2 transcription is not mediated by the gibberellic acid pathway, but is positively correlated with photoperiod and developmental age. The developmental functions of clade-VI SPL genes have, thus, evolved following both gene duplication and speciation within the core eudicots, likely through differential regulation and incomplete sub-functionalization.

The Arabidopsis RING Domain Protein BOI Inhibits Flowering via CO-dependent and CO-independent Mechanisms

BOTRYTIS SUSCEPTIBLE1 INTERACTOR (BOI) and its three homologs (BOIs) are RING domain-containing proteins that repress flowering. Here, we investigated how BOIs repress flowering. Genetic analysis of the boiQ quadruple mutant indicates that BOIs repress flowering mainly through FLOWERING LOCUS T (FT). BOIs repress the expression of FT by CONSTANS (CO)-dependent and -independent mechanisms: in the CO-dependent mechanism, BOIs bind to CO, inhibit the targeting of CO to the FT locus, and thus repress the expression of FT; in the CO-independent mechanism, BOIs target the FT locus via a mechanism that requires DELLAs but not CO. This dual repression of FT makes BOIs strong repressors of flowering in both CO-dependent and CO-independent pathways in Arabidopsis thaliana. Our finding that BOIs inhibit CO targeting further suggests that, in addition to modulating CO mRNA expression and CO protein stability, flowering regulation can also modulate the targeting of CO to FT.

Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana

Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15°C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process.

Transcription Profiles Reveal Sugar and Hormone Signaling Pathways Mediating Flower Induction in Apple (Malus domestica Borkh.)

Flower induction in apple (Malus domestica Borkh.) is regulated by complex gene networks that involve multiple signal pathways to ensure flower bud formation in the next year, but the molecular determinants of apple flower induction are still unknown. In this research, transcriptomic profiles from differentiating buds allowed us to identify genes potentially involved in signaling pathways that mediate the regulatory mechanisms of flower induction. A hypothetical model for this regulatory mechanism was obtained by analysis of the available transcriptomic data, suggesting that sugar-, hormone- and flowering-related genes, as well as those involved in cell-cycle induction, participated in the apple flower induction process. Sugar levels and metabolism-related gene expression profiles revealed that sucrose is the initiation signal in flower induction. Complex hormone regulatory networks involved in cytokinin (CK), abscisic acid (ABA) and gibberellic acid pathways also induce apple flower formation. CK plays a key role in the regulation of cell formation and differentiation, and in affecting flowering-related gene expression levels during these processes. Meanwhile, ABA levels and ABA-related gene expression levels gradually increased, as did those of sugar metabolism-related genes, in developing buds, indicating that ABA signals regulate apple flower induction by participating in the sugar-mediated flowering pathway. Furthermore, changes in sugar and starch deposition levels in buds can be affected by ABA content and the expression of the genes involved in the ABA signaling pathway. Thus, multiple pathways, which are mainly mediated by crosstalk between sugar and hormone signals, regulate the molecular network involved in bud growth and flower induction in apple trees.

Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley

Early flowering is an important trait influencing grain yield and quality in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) in short-season cropping regions. However, due to large and complex genomes of these species, direct identification of flowering genes and their molecular characterization remain challenging. Here, we used a bioinformatic approach to predict flowering-related genes in wheat and barley from 190 known Arabidopsis (Arabidopsis thaliana (L.) Heynh.) flowering genes. We identified 900 and 275 putative orthologs in wheat and barley, respectively. The annotated flowering-related genes were clustered into 144 orthologous groups with one-to-one, one-to-many, many-to-one, and many-to-many orthology relationships. Our approach was further validated by domain and phylogenetic analyses of flowering-related proteins and comparative analysis of publicly available microarray data sets for in silico expression profiling of flowering-related genes in 13 different developmental stages of wheat and barley. These further analyses showed that orthologous gene pairs in three critical flowering gene families (PEBP, MADS, and BBX) exhibited similar expression patterns among 13 developmental stages in wheat and barley, suggesting similar functions among the orthologous genes with sequence and expression similarities. The predicted candidate flowering genes can be confirmed and incorporated into molecular breeding for early flowering wheat and barley in short-season cropping regions.

Transcriptional programs regulated by both LEAFY and APETALA1 at the time of flower formation

Two key regulators of the switch to flower formation and of flower patterning in Arabidopsis are the plant-specific helix-turn-helix transcription factor LEAFY (LFY) and the MADS box transcription factor APETALA1 (AP1). The interactions between these two transcriptional regulators are complex. AP1 is both a direct target of LFY and can act in parallel with LFY. Available genetic and molecular evidence suggests that LFY and AP1 together orchestrate the switch to flower formation and early events during flower morphogenesis by altering transcriptional programs. However, very little is known about target genes regulated by both transcription factors. Here, we performed a meta-analysis of public datasets to identify genes that are likely to be regulated by both LFY and AP1. Our analyses uncovered known and novel direct LFY and AP1 targets with a role in the control of onset of flower formation. It also identified additional families of proteins and regulatory pathways that may be under transcriptional control by both transcription factors. In particular, several of these genes are linked to response to hormones, to transport and to development. Finally, we show that the gibberellin catabolism enzyme ELA1, which was recently shown to be important for the timing of the switch to flower formation, is positively feedback-regulated by AP1. Our study contributes to the elucidation of the regulatory network that leads to formation of a vital plant organ system, the flower.

Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins

The ability of plants to provide a plastic response to environmental cues relies on the connectivity between signaling pathways. DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis.

Plants respond to environmental cues by modulating transcriptional circuits. One mechanism for such modulation involves DELLA proteins. They are promiscuous interactors of transcription factors and, in most cases, this interaction impairs the recognition of the DNA target sequences. Here we show that DELLA proteins are also recruited to multiple locations of the genome where they act as transcriptional coactivators, and we demonstrate how physical interaction with type-B ARRs is relevant for the regulation of meristem maintenance and photomorphogenesis.

Plant development regulation: Overview and perspectives

Plant development, as occur in other eukaryotes, is conducted through a complex network of hormones, transcription factors, enzymes and micro RNAs, among other cellular components. They control developmental processes such as embryo, apical root and shoot meristem, leaf, flower, or seed formation, among others. The research in these topics has been very active in last decades. Recently, an explosion of new data concerning regulation mechanisms as well as the response of these processes to environmental changes has emerged. Initially, most of investigations were carried out in the model eudicot Arabidopsis but currently data from other plant species are available in the literature, although they are still limited. The aim of this review is focused on summarize the main molecular actors involved in plant development regulation in diverse plant species. A special attention will be given to the major families of genes and proteins participating in these regulatory mechanisms. The information on the regulatory pathways where they participate will be briefly cited. Additionally, the importance of certain structural features of such proteins that confer ductility and flexibility to these mechanisms will also be reported and discussed.