Arabidopsis HECATE genes function in phytohormone control during gynoecium development

The role of D3-type cyclins is related to cytokinin and the bHLH transcription factor SPATULA in Arabidopsis gynoecium development

MAIN CONCLUSION

We studied the D3-type cyclin function during gynoecium development in Arabidopsis and how they are related to the hormone cytokinin and the transcription factor SPATULA. Growth throughout the life of plants is sustained by cell division and differentiation processes in meristematic tissues. In Arabidopsis, gynoecium development implies a multiphasic process where the tissues required for pollination, fertilization, and seed development form. The Carpel Margin Meristem (CMM) is a mass of undifferentiated cells that gives rise to the gynoecium internal tissues, such as septum, ovules, placenta, funiculus, transmitting tract, style, and stigma. Different genetic and hormonal factors, including cytokinin, control the CMM function. Cytokinin regulates the cell cycle transitions through the activation of cell cycle regulators as cyclin genes. D3-type cyclins are expressed in proliferative tissues, favoring the mitotic cell cycle over the endoreduplication. Though the role of cytokinin in CMM and gynoecium development is highly studied, its specific role in regulating the cell cycle in this tissue remains unclear. Additionally, despite extensive research on the relationship between CYCD3 genes and cytokinin, the regulatory mechanism that connects them remains elusive. Here, we found that D3-type cyclins are expressed in proliferative medial and lateral tissues. Conversely, the depletion of the three CYCD3 genes showed that they are not essential for gynoecium development. However, the addition of exogenous cytokinin showed that they could control the division/differentiation balance in gynoecium internal tissues and outgrowths. Finally, we found that SPATULA can be a mechanistic link between cytokinin and the D3-type cyclins. The data suggest that the role of D3-type cyclins in gynoecium development is related to the cytokinin response, and they might be activated by the transcription factor SPATULA.

Arabidopsis transcription factor TCP4 controls the identity of the apical gynoecium

The style and stigma at the apical gynoecium are crucial for flowering plant reproduction. However, the mechanisms underlying specification of the apical gynoecium remain unclear. Here, we demonstrate that Class II TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors are critical for apical gynoecium specification in Arabidopsis (Arabidopsis thaliana). The septuple tcp2 tcp3 tcp4 tcp5 tcp10 tcp13 tcp17 (tcpSEP) and duodecuple tcp2 tcp3 tcp4 tcp5 tcp10 tcp13 tcp17 tcp24 tcp1 tcp12 tcp18 tcp16 (tcpDUO) mutants produce narrower and longer styles, while disruption of TCPs and CRABS CLAW (CRC) or NGATHAs (NGAs) in tcpDUO crc or tcpDUO nga1 nga2 nga4 causes the apical gynoecium to be replaced by lamellar structures with indeterminate growth. TCPs are predominantly expressed in the apex of the gynoecium. TCP4 interacts with CRC to synergistically upregulate the expression level of NGAs, and NGAs further form high-order complexes to control the expression of auxin-related genes in the apical gynoecium by directly interacting with TCP4. Our findings demonstrate that TCP4 physically associates with CRC and NGAs to control auxin biosynthesis in forming fine structures of the apical gynoecium.

Multi-locus genome-wide association studies reveal the dynamic genetic architecture of flowering time in chrysanthemum

KEY MESSAGE

The dynamic genetic architecture of flowering time in chrysanthemum was elucidated by GWAS. Thirty-six known genes and 14 candidate genes were identified around the stable QTNs and QEIs, among which ERF-1 was highlighted. Flowering time (FT) adaptation is one of the major breeding goals in chrysanthemum, a multipurpose ornamental plant. In order to reveal the dynamic genetic architecture of FT in chrysanthemum, phenotype investigation of ten FT-related traits was conducted on 169 entries in 2 environments. The broad-sense heritability of five non-conditional FT traits, i.e., budding (FBD), visible coloring (VC), early opening (EO), full-bloom (OF) and decay period (DP), ranged from 56.93 to 84.26%, which were higher than that of the five derived conditional FT traits (38.51-75.13%). The phenotypic variation coefficients of OF_EO and DP_OF were relatively large ranging from 30.59 to 36.17%. Based on 375,865 SNPs, the compressed variance component mixed linear model 3VmrMLM was applied for a multi-locus genome-wide association study (GWAS). As a result, 313 quantitative trait nucleotides (QTNs) were identified for the non-conditional FT traits in single-environment analysis, while 119 QTNs and 67 QTN-by-environment interactions (QEIs) were identified in multi-environment analysis. As for the conditional traits, 343 QTNs were detected in single-environment analysis, and 119 QTNs and 83 QEIs were identified in multi- environment analysis. Among the genes around stable QTNs and QEIs, 36 were orthologs of known FT genes in Arabidopsis and other plants; 14 candidates were mined by combining the transcriptomics data and functional annotation, including ERF-1, ACA10, and FOP1. Furthermore, the haplotype analysis of ERF-1 revealed six elite accessions with extreme FBD. Our findings contribute to the understanding of dynamic genetic architecture of FT and provide valuable resources for future chrysanthemum molecular breeding programs.

O-glycosylation of the transcription factor SPATULA promotes style development in Arabidopsis

O-linked β-N-acetylglucosamine (O-GlcNAc) and O-fucose are two sugar-based post-translational modifications whose mechanistic role in plant signalling and transcriptional regulation is still largely unknown. Here we investigated how two O-glycosyltransferase enzymes of Arabidopsis thaliana, SPINDLY (SPY) and SECRET AGENT (SEC), promote the activity of the basic helix-loop-helix transcription factor SPATULA (SPT) during morphogenesis of the plant female reproductive organ apex, the style. SPY and SEC modify amino-terminal residues of SPT in vivo and in vitro by attaching O-fucose and O-GlcNAc, respectively. This post-translational regulation does not impact SPT homo- and heterodimerization events, although it enhances the affinity of SPT for the kinase PINOID gene locus and its transcriptional repression. Our findings offer a mechanistic example of the effect of O-GlcNAc and O-fucose on the activity of a plant transcription factor and reveal previously unrecognized roles for SEC and SPY in orchestrating style elongation and shape.

Rice DSP controls stigma, panicle and tiller primordium initiation

Tiller and seed number are key determinants of rice (Oryza sativa) yield. These traits are mainly affected by tiller, panicle, spikelet and stigma formation, but to date, no single gene involved in the development of all these organs has been identified. Here, we found a rice mutant defective stigma and panicle (dsp) with greatly reduced numbers of tillers and panicle branches, and ovaries lacking stigmas, due to defects in primordium initiation. We cloned DSP using sequencing-based mapping and verified its function with the CRISPR/Cas9 system. DSP encodes a transcription factor containing an APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain that recognizes the GCC motif and a transcription-activating domain at the site of 244-314 that contains an angiosperm-related (AR) motif. Mutating the AR motif resulted in the dsp mutant phenotypes, whereas mutating the AP2/ERF domain led to seedling death. DSP directly regulated PINOID (PID) expression to determine the emergence of rice stigmas, and PID overexpression partially rescued the stigma defect in the dsp cr2-8 and dsp mutants. Moreover, DSP indirectly affected LAX PANICLE1 (LAX1) expression to determine tiller primordium formation and synergistically regulated panicle primordium development. Our results indicated that DSP was a key regulator that modulated different genetic pathways to control the initiation of stigma primordia, the axillary meristem formation of tillers and panicle branches, which revealed their molecular mechanisms and cross-networks, laying the vital foundation for rice yield and trait improvement.

Knockout of floral and meiosis genes using CRISPR/Cas9 produces male-sterility in Eucalyptus without impacts on vegetative growth

Eucalyptus spp. are widely cultivated for the production of pulp, energy, essential oils, and as ornamentals. However, their dispersal from plantings, especially when grown as an exotic, can cause ecological disruptions. To provide new tools for prevention of sexual dispersal by pollen as well as to induce male-sterility for hybrid breeding, we studied the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated knockout of three floral genes in both FT-expressing (early-flowering) and non-FT genotypes. We report male-sterile phenotypes resulting from knockout of the homologs of all three genes, including one involved in meiosis and two regulating early stages of pollen development. The targeted genes were Eucalyptus homologs of REC8 (EREC8), TAPETAL DEVELOPMENT AND FUNCTION 1 (ETDF1), and HECATE3 (EHEC3-like). The erec8 knockouts yielded abnormal pollen grains and a predominance of inviable pollen, whereas the etdf1 and ehec3-like knockouts produced virtually no pollen. In addition to male-sterility, both erec8 and ehec3-like knockouts may provide complete sterility because the failure of erec8 to undergo meiosis is expected to be independent of sex, and ehec3-like knockouts produce flowers with shortened styles and no visible stigmas. When comparing knockouts to controls in wild-type (non-early-flowering) backgrounds, we did not find visible morphological or statistical differences in vegetative traits, including average single-leaf mass, stem volume, density of oil glands, or chlorophyll in leaves. Loss-of-function mutations in any of these three genes show promise as a means of inducing male- or complete sterility without impacting vegetative development.

A model worker: Multifaceted modulation of AUXIN RESPONSE FACTOR3 orchestrates plant reproductive phases

The key phytohormone auxin is involved in practically every aspect of plant growth and development. Auxin regulates these processes by controlling gene expression through functionally distinct AUXIN RESPONSE FACTORs (ARFs). As a noncanonical ARF, ARF3/ETTIN (ETT) mediates auxin responses to orchestrate multiple developmental processes during the reproductive phase. The arf3 mutation has pleiotropic effects on reproductive development, causing abnormalities in meristem homeostasis, floral determinacy, phyllotaxy, floral organ patterning, gynoecium morphogenesis, ovule development, and self-incompatibility. The importance of ARF3 is also reflected in its precise regulation at the transcriptional, posttranscriptional, translational, and epigenetic levels. Recent studies have shown that ARF3 controls dynamic shoot apical meristem (SAM) maintenance in a non-cell autonomous manner. Here, we summarize the hierarchical regulatory mechanisms by which ARF3 is regulated and the diverse roles of ARF3 regulating developmental processes during the reproductive phase.

Transcriptome-wide characterization of bHLH transcription factor genes in Lycoris radiata and functional analysis of their response to MeJA

As one of the biggest plant specific transcription factor (TF) families, basic helix-loop-helix (bHLH) protein, plays significant roles in plant growth, development, and abiotic stress responses. However, there has been minimal research about the effects of methyl jasmonate (MeJA) treatment on the bHLH gene family in Lycoris radiata (L'Her.) Herb. In this study, based on transcriptome sequencing data, 50 putative L. radiata bHLH (LrbHLH) genes with complete open reading frames (ORFs), which were divided into 20 bHLH subfamilies, were identified. The protein motif analyses showed that a total of 10 conserved motifs were found in LrbHLH proteins and motif 1 and motif 2 were the most highly conserved motifs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of LrbHLH genes revealed their involvement in regulation of plant growth, jasmonic acid (JA) mediated signaling pathway, photoperiodism, and flowering. Furthermore, subcellular localization revealed that most LrbHLHs were located in the nucleus. Expression pattern analysis of LrbHLH genes in different tissues and at flower developmental stages suggested that their expression differed across lineages and might be important for plant growth and organ development in Lycoris. In addition, all LrbHLH genes exhibited specific spatial and temporal expression patterns under MeJA treatment. Moreover, protein-protein interaction (PPI) network analysis and yeast two-hybrid assay showed that numerous LrbHLHs could interact with jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins. This research provides a theoretical basis for further investigation of LrbHLHs to find their functions and insights for their regulatory mechanisms involved in JA signaling pathway.

Hormones and Flower Development in Arabidopsis

Sexual reproduction requires the participation of two gametes, female and male. In angiosperms, gametes develop in specialized organs, pollen (containing the male gametes) develops in the stamens, and the ovule (containing the female gamete) develops in the gynoecium. In Arabidopsis thaliana, the female and male sexual organs are found within the same structure called flower, surrounded by the perianth, which is composed of petals and sepals. During flower development, different organs emerge in an established order and throughout their development distinct tissues within each organ are differentiated. All this requires the coordination and synchronization of several biological processes. To achieve this, hormones and genes work together. These components can interact at different levels generating hormonal interplay and both positive and negative feedback loops, which in turn, gives robustness, stability, and flexibility to flower development. Here, we summarize the progress made on elucidating the role of different hormonal pathways during flower development in Arabidopsis thaliana.

BnaCRCs with domestication preference positively correlate with the seed-setting rate of canola

Canola (Brassica napus) is an important oil crop worldwide. The seed-setting rate (SS) is a critical factor in determining its yield, and the development of pistils affects pollination and seed sets. However, research on seed-setting defects has been limited owing to difficulties in the identification of phenotypes, mutations, and complex genetic mechanisms. In this study, we found a stigma defect (sd) mutant in B. napus, which had no nectary. The SS of sd mutants in the field was approximately 93.4% lower than that of the wild type. Scanning and transmission electron microscopy imaging of sd mutants showed a low density of stigma papillary cells and stigma papillary cell vacuoles that disappeared 16 h after flowering. Genetic analysis of segregated populations showed that two recessive nuclear genes are responsible for the mutant phenotype of sd. Based on re-sequencing and map-based cloning, we reduced the candidate sites on ChrA07 (BnaSSA07) and ChrC06 (BnaSSC06) to 30 and 67 kb, including six and eight predicted genes, respectively. Gene analyses showed that a pair of CRABS CLAW (CRC) homeologous genes at BnaSSA07 and BnaSSC06 were associated with the development of carpel and nectary. BnaSSA07.CRC and BnaSSC06.CRC candidate genes were found to be expressed in flower organs only, with significant differences in their expression in the pistils of the near-isogenic lines. DNA sequencing showed transposon insertions in the upstream region and intron of the candidate gene BnaSSA07.crc. We also found that BnaSSC06.crc exists widely in the natural population and we give possible reasons for its widespread existence.

Floral symmetry: the geometry of plant reproduction

The flower is an astonishing innovation that arose during plant evolution allowing flowering plants — also known as angiosperms — to dominate life on earth in a relatively short period of geological time. Flowers are formed from secondary meristems by co-ordinated differentiation of flower organs, such as sepals, petals, stamens, and carpels. The position, number and morphology of these flower organs impose a geometrical pattern — or symmetry type — within the flower which is a trait tightly connected to successful reproduction.

During evolution, flower symmetry switched from the ancestral poly-symmetric (radial symmetry) to the mono-symmetric (bilateral symmetry) type multiple times, including numerous reversals, with these events linked to co-evolution with pollinators and reproductive strategies.

In this review, we introduce the diversity of flower symmetry, trace its evolution in angiosperms, and highlight the conserved genetic basis underpinning symmetry control in flowers. Finally, we discuss the importance of building upon the concept of flower symmetry by looking at the mechanisms orchestrating symmetry within individual flower organs and summarise the current scenario on symmetry patterning of the female reproductive organ, the gynoecium, the ultimate flower structure presiding over fertilisation and seed production.

Genome-wide characterization and expression analysis of bHLH gene family in physic nut (Jatropha curcas L.)

The basic helix loop helix (bHLH) transcription factor perform essential roles in plant development and abiotic stress. Here, a total of 122 bHLH family members were identified from the physic nut (Jatropha curcas L.) genomic database. Chromosomal localization results showed that 120 members were located on 11 chromosomes. The phylogenetic tree manifested that the JcbHLHs could be grouped into 28 subfamilies. Syntenic analysis showed that there were 10 bHLH collinear genes among the physic nut, Arabidopsis thaliana and Oryza sativa. These genes, except JcbHLH84, were highly expressed in various tissues of the physic nut, implying a key role in plant development. Gene expression profiles showed that ten genes (especially JcbHLH33, JcbHLH45 and JcbHLH55) correspond to both salinity and drought stresses; while eight genes only respond to salinity and another eight genes only respond to drought stress. Moreover, the protein interaction network revealed that the JcbHLHs are involved in growth, development and stress signal transduction pathways. These discoveries will help to excavate several key genes may involve in salt or drought stresses and seed development, elucidate the complex transcriptional regulation mechanism of JcbHLH genes and provide the theoretical basis for stress response and genetic improvement of physic nut.

Gynoecium and fruit development in Arabidopsis

Flowering plants produce flowers and one of the most complex floral structures is the pistil or the gynoecium. All the floral organs differentiate from the floral meristem. Various reviews exist on molecular mechanisms controlling reproductive development, but most focus on a short time window and there has been no recent review on the complete developmental time frame of gynoecium and fruit formation. Here, we highlight recent discoveries, including the players, interactions and mechanisms that govern gynoecium and fruit development in Arabidopsis. We also present the currently known gene regulatory networks from gynoecium initiation until fruit maturation.

Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola

Background

Members of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available.

Methods

In the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed.

Results

Eight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development.

A transcriptional complex of NGATHA and bHLH transcription factors directs stigma development in Arabidopsis

The stigma is an angiosperm-specific tissue that is essential for pollination. In the last two decades, several transcription factors with key roles in stigma development in Arabidopsis thaliana have been identified. However, genetic analyses have thus far been unable to unravel the precise regulatory interactions among these transcription factors or the molecular basis for their selective roles in different spatial and temporal domains. Here, we show that the NGATHA (NGA) and HECATE (HEC) transcription factors, which are involved in different developmental processes but are both essential for stigma development, require each other to perform this function. This relationship is likely mediated by their physical interaction in the apical gynoecium. NGA/HEC transcription factors subsequently upregulate INDEHISCENT (IND) and SPATULA and are indispensable for the binding of IND to some of its targets to allow stigma differentiation. Our findings support a nonhierarchical regulatory scenario in which the combinatorial action of different transcription factors provides exquisite temporal and spatial specificity of their developmental outputs.

HECATE2 acts with GLABROUS3 and Tu to boost cytokinin biosynthesis and regulate cucumber fruit wart formation

Warty fruit in cucumber (Cucumis sativus L.) is an important quality trait that greatly affects fruit appearance and market value. The cucumber wart consists of fruit trichomes (spines) and underlying tubercules, in which the existence of spines is prerequisite for tubercule formation. Although several regulators have been reported to mediate spine or tubercule formation, the direct link between spine and tubercule development remains unknown. Here, we found that the basic Helix-Loop-Helix (bHLH) gene HECATE2 (CsHEC2) was highly expressed in cucumber fruit peels including spines and tubercules. Knockout of CsHEC2 by the CRISPR/Cas9 system resulted in reduced wart density and decreased cytokinin (CTK) accumulation in the fruit peel, whereas overexpression of CsHEC2 led to elevated wart density and CTK level. CsHEC2 is directly bound to the promoter of the CTK hydroxylase-like1 gene (CsCHL1) that catalyzes CTK biosynthesis, and activated CsCHL1 expression. Moreover, CsHEC2 physically interacted with GLABROUS3 (CsGL3, a key spine regulator) and Tuberculate fruit (CsTu, a core tubercule formation factor), and such interactions further enhanced CsHEC2-mediated CsCHL1 expression. These data suggested that CsHEC2 promotes wart formation by acting as an important cofactor for CsGL3 and CsTu to directly stimulate CTK biosynthesis in cucumber. Thus, CsHEC2 can serve as a valuable target for molecular breeding of cucumber varieties with different wart density requirements.

Casting the Net-Connecting Auxin Signaling to the Plant Genome

Auxin represents one of the most potent and most versatile hormonal signals in the plant kingdom. Built on a simple core of only a few dedicated components, the auxin signaling system plays important roles for diverse aspects of plant development, physiology, and defense. Key to the diversity of context-dependent functional outputs generated by cells in response to this small molecule are gene duplication events and sub-functionalization of signaling components on the one hand, and a deep embedding of the auxin signaling system into complex regulatory networks on the other hand. Together, these evolutionary innovations provide the mechanisms to allow each cell to display a highly specific auxin response that suits its individual requirements. In this review, we discuss the regulatory networks connecting auxin with a large number of diverse pathways at all relevant levels of the signaling system ranging from biosynthesis to transcriptional response.

Comparative anatomy and genetic bases of fruit development in selected Rubiaceae (Gentianales)

PREMISE

The Rubiaceae are ideal for studying the diversity of fruits that develop from flowers with inferior ovary. We aimed to identify morpho-anatomical changes during fruit development that distinguish those derived from the carpel versus the extra-carpellary tissues. In addition, we present the fruit genetic core regulatory network in selected Rubiaceae species and compare it in terms of copy number and expression patterns to model core eudicots in the Brassicaceae and the Solanaceae.

METHODS

We used light microscopy to follow morphoanatomical changes in four selected species with different fruit types. We generated reference transcriptomes for seven selected Rubiaceae species and isolated homologs of major transcription factors involved in fruit development histogenesis, assessed their homology, identified conserved and new protein motifs, and evaluated their expression in three species with different fruit types.

RESULTS

Our studies revealed ovary-derived pericarp tissues versus floral-cup-derived epicarp tissues. Gene evolution analyses of FRUITFULL, SHATTERPROOF, ALCATRAZ, INDEHISCENT and REPLUMLESS homologs suggest that the gene complement in Rubiaceae is simpler compared to that in Brassicaceae or Solanaceae. Expression patterns of targeted genes vary in response to the fruit type and the developmental stage evaluated.

CONCLUSIONS

Morphologically similar fruits can have different anatomies as a result of convergent tissues developed from the epicarps covering the anatomical changes from the pericarps. Expression analyses suggest that the fruit patterning regulatory network established in model core eudicots cannot be extrapolated to asterids with inferior ovaries.

Promoter analysis of the SPATULA (FvSPT) and SPIRAL (FvSPR) genes in the woodland diploid strawberry (Fragaria vesca L.)

The aim of this study was to identify transcription factor (TF) binding sites and cis-regulatory elements (CREs) on the promoters of FvSPR1-like2 (SPIRAL) and FvSPT (SPATULA) genes in the woodland diploid strawberry (Fragaria vesca L.). We identified: (1) MYB59, WRKY25 and WRKY8 TFs which play a role in ethylene signaling; (2) ARF family of TFs which play a role in ARF-mediated auxin signaling on the promoter of FvSPR1-like2 gene; (3) ARR family of TFs which play a role in cytokinin signaling; (4) ERF family of TFs which play a role in ethylene signaling on the promoter of FvSPT. This bioinformatic analysis of TFs and CREs may provide a better understanding of the function of genes involved in, and the mechanism underlying, non-climateric ripening during strawberry fruit maturation.

Coordination of biradial-to-radial symmetry and tissue polarity by HD-ZIP II proteins

Symmetry establishment is a critical process in the development of multicellular organs and requires careful coordination of polarity axes while cells actively divide within tissues. Formation of the apical style in the Arabidopsis gynoecium involves a bilateral-to-radial symmetry transition, a stepwise process underpinned by the dynamic distribution of the plant morphogen auxin. Here we show that SPATULA (SPT) and the HECATE (HEC) bHLH proteins mediate the final step in the style radialisation process and synergistically control the expression of adaxial-identity genes, HOMEOBOX ARABIDOPSIS THALIANA 3 (HAT3) and ARABIDOPSIS THALIANA HOMEOBOX 4 (ATHB4). HAT3/ATHB4 module drives radialisation of the apical style by promoting basal-to-apical auxin flow and via a negative feedback mechanism that finetune auxin distribution through repression of SPT expression and cytokinin sensitivity. Thus, this work reveals the molecular basis of axes-coordination and hormonal cross-talk during the sequential steps of symmetry transition in the Arabidopsis style.

The apical style in Arabidopsis is formed following a bilateral-to-radial symmetry transition in the gynoecium. Here the authors show that the final step in style radialization is coordinated by the adaxial regulators HAT3 and ATHB4, which are induced by the SPT and HEC transcription factors.

Interaction of gibberellin and other hormones in almond anthers: phenotypic and physiological changes and transcriptomic reprogramming

Low temperature causes anther dysfunction, severe pollen sterility and, ultimately, major yield losses in crop plants. Previous studies have shown that the gibberellic acid (GA) metabolic pathway plays an important role in this process by regulating tapetum function and pollen development. However, the interaction mechanism of GA with other hormones mediating anther development is still unclear. Herein, we collected and analyzed almond (Amygdalus communis L.) anthers at the meiosis, tetrad, 1-nucleus, and mature 2-nucleus stages. The growth rate per 1000 anthers exhibited a significant positive correlation with the total bioactive GA compound content, and the levels of all bioactive GA compounds were highest in the 1-nucleus pollen stage. GA₃ treatment experiments indicated that exogenous GA₃ increased the levels of indole-3-acetic acid (IAA), trans-zeatin (tZ), and jasmonic acid (JA) and decreased the levels of salicylic acid (SA) and abscisic acid (ABA); moreover, GA₃ improved pollen viability and quantities under cold conditions, whereas PP₃₃₃ (paclobutrazol, an inhibitor of GA biosynthesis) was antagonistic with GA₃ in controlling anther development. RNA-seq and qRT-PCR results showed that GA played an important role in anther development by regulating the expression of other phytohormone pathway genes, dehydration-responsive element-binding/C-repeat binding factor (DREB1/CBF)-mediated signaling genes, and anther development pathway genes. Our results reveal the novel finding that GA interacts with other hormones to balance anther development under normal- and low-temperature conditions in almond.

The Relationship between AGAMOUS and Cytokinin Signaling in the Establishment of Carpeloid Features

Gynoecium development is dependent on gene regulation and hormonal pathway interactions. The phytohormones auxin and cytokinin are involved in many developmental programs, where cytokinin is normally important for cell division and meristem activity, while auxin induces cell differentiation and organ initiation in the shoot. The MADS-box transcription factor AGAMOUS (AG) is important for the development of the reproductive structures of the flower. Here, we focus on the relationship between AG and cytokinin in Arabidopsis thaliana, and use the weak ag-12 and the strong ag-1 allele. We found that cytokinin induces carpeloid features in an AG-dependent manner and the expression of the transcription factors CRC, SHP2, and SPT that are involved in carpel development. AG is important for gynoecium development, and contributes to regulating, or else directly regulates CRC, SHP2, and SPT. All four genes respond to either reduced or induced cytokinin signaling and have the potential to be regulated by cytokinin via the type-B ARR proteins. We generated a model of a gene regulatory network, where cytokinin signaling is mainly upstream and in parallel with AG activity.

Transcriptome analysis of gynoecium morphogenesis uncovers the chronology of gene regulatory network activity

The gynoecium is the most complex organ formed by the flowering plants. It encloses the ovules, provides a surface for pollen contact and self-incompatibility reactions, allows pollen tube growth, and, post fertilization, develops into the fruit. Consequently, the regulation of gynoecium morphogenesis is complex and appropriate timing of this process in part determines reproductive success. However, little is known about the global control of gynoecium development, even though many regulatory genes have been characterized. Here, we characterized dynamic gene expression changes using laser-microdissected gynoecium tissue from four developmental stages in Arabidopsis. We provide a high-resolution map of global expression dynamics during gynoecium morphogenesis and link these to the gynoecium interactome. We reveal groups of genes acting together early and others acting late in morphogenesis. Clustering of co-expressed genes enables comparisons between the leaf, shoot apex, and gynoecium transcriptomes, allowing the dissection of common and distinct regulators. Furthermore, our results lead to the discovery of genes with putative transcription factor activity (B3LF1, -2, DOFLF1), which, when mutated, lead to impaired gynoecium expansion, illustrating that global transcriptome analyses reveal yet unknown developmental regulators. Our data show that genes encoding highly interacting proteins, such as SEPALLATA3, AGAMOUS, and TOPLESS, are expressed evenly during development but switch interactors over time, whereas stage-specific proteins tend to have fewer interactors. Our analysis connects specific transcriptional regulator activities, protein interactions, and underlying metabolic processes, contributing toward a dynamic network model for gynoecium development.

Molecular Control of Carpel Development in the Grass Family

Carpel is the ovule-bearing female reproductive organ of flowering plants and is required to ensure its protection, an efficient fertilization, and the development of diversified types of fruits, thereby it is a vital element of most food crops. The origin and morphological changes of the carpel are key to the evolution and adaption of angiosperms. Progresses have been made in elucidating the developmental mechanisms of carpel establishment in the model eudicot plant Arabidopsis thaliana, while little and fragmentary information is known in grasses, a family that includes many important crops such as rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aestivum). Here, we highlight recent advances in understanding the mechanisms underlying potential pathways of carpel development in grasses, including carpel identity determination, morphogenesis, and floral meristem determinacy. The known role of transcription factors, hormones, and miRNAs during grass carpel formation is summarized and compared with the extensively studied eudicot model plant Arabidopsis. The genetic and molecular aspects of carpel development that are conserved or diverged between grasses and eudicots are therefore discussed.

A COP1-PIF-HEC regulatory module fine-tunes photomorphogenesis in Arabidopsis

Light responses mediated by the photoreceptors play crucial roles in regulating different aspects of plant growth and development. An E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)1/SUPPRESSOR OF PHYA (SPA), one of the central repressors of photomorphogenesis, is critical for maintaining skotomorphogenesis. It targets several positive regulators of photomorphogenesis for degradation in darkness. Recently, we revealed that basic helix-loop-helix factors, HECATEs (HECs), function as positive regulators of photomorphogenesis by directly interacting and antagonizing the activity of another group of repressors called PHYTOCHROME-INTERACTING FACTORs (PIFs). It was also shown that HECs are partially degraded in the dark through the ubiquitin/26S proteasome pathway. However, the underlying mechanism of HEC degradation in the dark is still unclear. Here, we show that HECs also interact with both COP1 and SPA proteins in darkness, and that HEC2 is directly targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway. Moreover, COP1-mediated polyubiquitylation and degradation of HEC2 are enhanced by PIF1. Therefore, the ubiquitylation and subsequent degradation of HECs are significantly reduced in both cop1 and pif mutants. Consistent with this, the hec mutants partially suppress photomorphogenic phenotypes of both cop1 and pifQ mutants. Collectively, our work reveals that the COP1/SPA-mediated ubiquitylation and degradation of HECs contributes to the coordination of skoto/photomorphogenic development in plants.

Gynoecium size and ovule number are interconnected traits that impact seed yield

Angiosperms form the largest group of land plants and display an astonishing diversity of floral structures. The development of flowers greatly contributed to the evolutionary success of the angiosperms as they guarantee efficient reproduction with the help of either biotic or abiotic vectors. The female reproductive part of the flower is the gynoecium (also called pistil). Ovules arise from meristematic tissue within the gynoecium. Upon fertilization, these ovules develop into seeds while the gynoecium turns into a fruit. Gene regulatory networks involving transcription factors and hormonal communication regulate ovule primordium initiation, spacing on the placenta, and development. Ovule number and gynoecium size are usually correlated and several genetic factors that impact these traits have been identified. Understanding and fine-tuning the gene regulatory networks influencing ovule number and pistil length open up strategies for crop yield improvement, which is pivotal in light of a rapidly growing world population. In this review, we present an overview of the current knowledge of the genes and hormones involved in determining ovule number and gynoecium size. We propose a model for the gene regulatory network that guides the developmental processes that determine seed yield.

Expression of gynoecium patterning transcription factors in Aristolochia fimbriata (Aristolochiaceae) and their contribution to gynostemium development

Background

In Aristolochia (Aristolochiaceae) flowers, the congenital fusion of the anthers and the commissural, stigmatic lobes forms a gynostemium. Although the molecular bases associated to the apical–basal gynoecium patterning have been described in eudicots, comparative expression studies of the style and stigma regulatory genes have never been performed in early divergent angiosperms possessing a gynostemium.

Results

In this study, we assess the expression of five genes typically involved in gynoecium development in Aristolochia fimbriata. We found that all five genes (AfimCRC, AfimSPT, AfimNGA, AfimHEC1 and AfimHEC3) are expressed in the ovary, the placenta, the ovules and the transmitting tract. In addition, only AfimHEC3, AfimNGA and AfimSPT are temporarily expressed during the initiation of the stigma, while none of the genes studied is maintained during the elaboration of the stigmatic surfaces in the gynostemium.

Conclusions

Expression patterns suggest that CRC, HEC, NGA and SPT homologs establish ovary and style identity in Aristolochia fimbriata. Only NGA,HEC3 and SPT genes may play a role in the early differentiation of the stigmatic lobes, but none of the genes studied seems to control late stigma differentiation in the gynostemium. The data gathered so far raises the possibility that such transient expression early on provides sufficient signal for late stigma differentiation or that unidentified late identity genes are controlling stigma development in the gynostemium. Our data does not rule out the possibility that stigmas could correspond to staminal filaments with convergent pollen-receptive surfaces.

A molecular update on the origin of the carpel

Carpels, the female reproductive organs of flowering plants, are of major economic importance since much of our food is ultimately derived from carpel tissue and they are a defining innovation for flowering plants. Amazingly, little is known about the origin and conservation of the developmental program of the carpel besides the knowledge generated by utilizing Arabidopsis thaliana. However, in the past few years advances in ancestral state reconstruction, developmental genetics, and phylogenetic analyses led to advances in the field of flower evodevo. Here, I summarize recent work on ancestral state reconstructions of carpels, and the functions of the major components of the genetic networks governing carpel development described for Arabidopsis. Then, I point out how the stepwise addition of genes during land plant evolution has generated the A. thaliana carpel's developmental toolkit. By merging these observations, I propose a basic version of the ancestral angiosperm carpel developmental network.

Advanced Cataloging of Lysine-63 Polyubiquitin Networks by Genomic, Interactome, and Sensor-Based Proteomic Analyses

The lack of resolution when studying the many different ubiquitin chain types found in eukaryotic cells has been a major hurdle to our understanding of their specific roles. We currently have very little insight into the cellular and physiological functions of Lys-63 (K63)-linked ubiquitin chains, although they are the second most abundant forms of ubiquitin in plant cells. To overcome this problem, we developed several large-scale approaches to characterize (1) the E2-E3 ubiquitination machinery driving K63-linked ubiquitin chain formation and (2) K63 polyubiquitination targets to provide a comprehensive picture of K63 polyubiquitin networks in Arabidopsis (Arabidopsis thaliana). Our work identified the ubiquitin-conjugating enzymes (E2s) UBC35/36 as the major drivers of K63 polyubiquitin chain formation and highlights the major role of these proteins in plant growth and development. Interactome approaches allowed us to identify many proteins that interact with the K63 polyubiquitination-dedicated E2s UBC35/36 and their cognate E2 variants, including more than a dozen E3 ligases and their putative targets. In parallel, we improved the in vivo detection of proteins decorated with K63-linked ubiquitin chains by sensor-based proteomics, yielding important insights into the roles of K63 polyubiquitination in plant cells. This work strongly increases our understanding of K63 polyubiquitination networks and functions in plants.

Basic helix-loop-helix (bHLH) gene family in Tartary buckwheat (Fagopyrum tataricum): Genome-wide identification, phylogeny, evolutionary expansion and expression analyses

Tartary buckwheat (Fagopyrum tataricum) a kind of edible and medicinal plant, is of great nutritional value. It is difficult to remove the hull of Tartary buckwheat fruit and breeding new easy-dehulled varieties has been one of the major breeding objectives. The bHLH gene family plays a vital role in plant growth and fruit dehiscence. In order to improve Tartary buckwheat breeding, we need to study the bHLH gene family for excavating genes with potential regulation of fruit development and dehiscence. Here, 164 Fagopyrum tataricum bHLH (FtbHLH) genes were identified. Analyses of gene structure and motif composition illustrate that the members of specific FtbHLH subfamily are relatively conserved. Synteny and phylogenetic analyses of bHLH genes in Tartary buckwheat and other plants lay a foundation for further exploring the evolutionary characteristic of the FtbHLH genes (FtbHLHs). qRT-PCR experiments showed that FtbHLHs expression patterns were different in plant organs, indicating that they may perform diverse functions. In addition, some genes that potentially regulate flower and fruit development and easy dehulling were screened out. Overall, this study will be helpful for further analyzing the biological function of FtbHLHs and provides clues for improving the genetic breeding and economic value of the Tartary buckwheat.

Two Auxin Response Elements Fine-Tune PINOID Expression During Gynoecium Development in Arabidopsis thaliana

The plant hormone auxin controls almost all aspects of plant development through the gene regulatory properties of auxin response factors (ARFs) which bind so-called auxin responsive elements (AuxREs) in regulatory regions of their target genes. It has been proposed that ARFs interact and cooperate with other transcription factors (TFs) to bind to complex DNA-binding sites harboring cis-elements for several TFs. Complex DNA-binding sites have not been studied systematically for ARF target genes. ETTIN (ETT; ARF3) is a key regulator of gynoecium development. Cooperatively with its interacting partner INDEHISCENT (IND), ETT regulates PINOID (PID), a gene involved in the regulation gynoecium apical development (style development). Here, we mutated two ETT-bound AuxREs within the PID promoter and observed increased style length in gynoecia of plants carrying mutated promoter variants. Furthermore, mutating the AuxREs led to ectopic repression of PID in one developmental context while leading to ectopically upregulated PID expression in another stage. Our data also show that IND associates with the PID promoter in an auxin-sensitive manner. In summary, we demonstrate that targeted mutations of cis-regulatory elements can be used to dissect the importance of single cis-regulatory elements within complex regulatory regions supporting the importance of the ETT-IND interaction for PID regulation. At the same time, our work also highlights the challenges of such studies, as gene regulation is highly robust, and mutations within gene regulatory regions may only display subtle phenotypes.

The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development

RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in the expression of pollen-differentiation genes, paps1 null-mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21- and particularly 24-nucleotide-long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double-mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.

How to build a fruit: Transcriptomics of a novel fruit type in the Brassiceae

Comparative gene expression studies are invaluable for predicting how existing genetic pathways may be modified or redeployed to produce novel and variable phenotypes. Fruits are ecologically important organs because of their impact on plant fitness and seed dispersal, modifications in which results in morphological variation across species. A novel fruit type in the Brassicaceae known as heteroarthrocarpy enables distinct dispersal methods in a single fruit through segmentation via a lateral joint and variable dehiscence at maturity. Given the close relationship to Arabidopsis, species that exhibit heteroarthrocarpy are powerful models to elucidate how differences in gene expression of a fruit patterning pathway may result in novel fruit types. Transcriptomes of distal, joint, and proximal regions from Erucaria erucarioides and Cakile lanceolata were analyzed to elucidate within fruit and between species differences in whole transcriptome, gene ontology, and fruit patterning expression profiles. Whole transcriptome expression profiles vary between fruit regions in patterns that are consistent with fruit anatomy. These transcriptomic variances do not correlate with changes in gene ontology, as they remain generally stable within and between both species. Upstream regulators in the fruit patterning pathway, FILAMENTOUS FLOWER and YABBY3, are expressed in the distal and proximal regions of E. erucarioides, but not in the joint, implicating alterations in the pathway in heteroarthrocarpic fruits. Downstream gene, INDEHISCENT, is significantly upregulated in the abscissing joint region of C. lanceolata, which suggests repurposing of valve margin genes for novel joint disarticulation in an otherwise indehiscent fruit. In summary, these data are consistent with modifications in fruit patterning genes producing heteroarthrocarpic fruits through different components of the pathway relative to other indehiscent, non-heteroarthrocarpic, species within the family. Our understanding of fruit development in Arabidopsis is now extended to atypical siliques within the Brassicaceae, facilitating future studies on seed shattering in important Brassicaceous crops and pernicious weeds.

Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube

Background

The bHLH (basic helix-loop-helix) transcription factor is one of the largest families of transcription factors in plants, containing a large number of members with diverse functions. Chinese jujube (Ziziphus jujuba Mill.) is the species with the highest economic value in the family Rhamnaceae. However, the characteristics of the bHLH family in the jujube genome are still unclear. Hence, ZjbHLHs were first searched at a genome-wide level, their expression levels under various conditions were investigated systematically, and their protein-protein interaction networks were predicted.

Results

We identified 92 ZjbHLHs in the jujube genome, and these genes were classified into 16 classes according to bHLH domains. Ten ZjbHLHs with atypical bHLH domains were found. Seventy ZjbHLHs were mapped to but not evenly distributed on 12 pseudo- chromosomes. The domain sequences among ZjbHLHs were highly conserved, and their conserved residues were also identified. The tissue-specific expression of 37 ZjbHLH genes in jujube and wild jujube showed diverse patterns, revealing that these genes likely perform multiple functions. Many ZjbHLH genes were screened and found to be involved in flower and fruit development, especially in earlier developmental stages. A few genes responsive to phytoplasma invasion were also verified. Based on protein-protein interaction prediction and homology comparison, protein-protein interaction networks composed of 92 ZjbHLHs were also established.

Conclusions

This study provides a comprehensive bioinformatics analysis of 92 identified ZjbHLH genes. We explored their expression patterns in various tissues, the flowering process, and fruit ripening and under phytoplasma stress. The protein-protein interaction networks of ZjbHLHs provide valuable clues toward further studies of their biological functions.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5936-2) contains supplementary material, which is available to authorized users.

OsPINOID Regulates Stigma and Ovule Initiation through Maintenance of the Floral Meristem by Auxin Signaling

Stigma and ovule initiation is essential for sexual reproduction in flowering plants. However, the mechanism underlying the initiation of stigma and ovule primordia remains elusive. We identified a stigma-less mutant of rice (Oryza sativa) and revealed that it was caused by the mutation in the PINOID (OsPID) gene. Unlike the pid mutant that shows typical pin-like inflorescences in maize (Zea mays) and Arabidopsis (Arabidopsis thaliana), the ospid mutant does not display any defects in inflorescence development and flower initiation, and fails to develop normal ovules in most spikelets. The auxin activity in the young pistil of ospid was lower than that in the wild-type pistil. Furthermore, the expression of most auxin response factor genes was down-regulated, and OsETTIN1, OsETTIN2, and OsMONOPTEROS lost their rearrangements of expression patterns during pistil and stamen primordia development in ospid Moreover, the transcription of the floral meristem marker gene, OSH1, was down-regulated and FLORAL ORGAN NUMBER4, the putative ortholog of Arabidopsis CLAVATA3, was up-regulated in the pistil primordium of ospid These results suggested that the meristem proliferation in the pistil primordium might be arrested prematurely in ospid Based on these results, we propose that the OsPID-mediated auxin signaling pathway plays a crucial role in the regulation of rice stigma and ovule initiation by maintaining the floral meristem.

Control of stem cell activity in the carpel margin meristem (CMM) in Arabidopsis

Overview of the current understanding of the molecular mechanisms that regulate meristem activity in the CMM compared to the SAM. Meristems are undifferentiated cells responsible for post-embryonic plant development. The meristems are able to form new organs continuously by carefully balancing between stem cell proliferation and cell differentiation. The plant stem cell niche in each meristem harbors the stem cells that are important to maintain each meristem. The shoot apical meristem (SAM) produces all above-parts of a plant and the molecular mechanisms active in the SAM are actively studied since many years, and models are available. During the reproductive phase of the plant, the inflorescence meristem gives rise to floral meristems, which give rise to the flowers. During floral development, the gynoecium forms that contains a new meristem inside, called the carpel margin meristem (CMM). In Arabidopsis, the gynoecium consists out of two fused carpels, where the CMM forms along the fused carpel margins. In this review, we focus on the molecular mechanisms taking place in the CMM, and we discuss similarities and differences found in the SAM.

An apical hypoxic niche sets the pace of shoot meristem activity

Complex multicellular organisms evolved on Earth in an oxygen-rich atmosphere¹; their tissues, including stem-cell niches, require continuous oxygen provision for efficient energy metabolism². Notably, the maintenance of the pluripotent state of animal stem cells requires hypoxic conditions, whereas higher oxygen tension promotes cell differentiation³. Here we demonstrate, using a combination of genetic reporters and in vivo oxygen measurements, that plant shoot meristems develop embedded in a low-oxygen niche, and that hypoxic conditions are required to regulate the production of new leaves. We show that hypoxia localized to the shoot meristem inhibits the proteolysis of an N-degron-pathway^4,5 substrate known as LITTLE ZIPPER 2 (ZPR2)-which evolved to control the activity of the class-III homeodomain-leucine zipper transcription factors^6-8-and thereby regulates the activity of shoot meristems. Our results reveal oxygen as a diffusible signal that is involved in the control of stem-cell activity in plants grown under aerobic conditions, which suggests that the spatially distinct distribution of oxygen affects plant development. In molecular terms, this signal is translated into transcriptional regulation by the N-degron pathway, thereby linking the control of metabolic activity to the regulation of development in plants.

Gynoecium development: networks in Arabidopsis and beyond

Life has always found a way to preserve itself. One strategy that has been developed for this purpose is sexual reproduction. In land plants, the gynoecium is considered to be at the top of evolutionary innovation, since it has been a key factor in the success of the angiosperms. The gynoecium is composed of carpels with different tissues that need to develop and differentiate in the correct way. In order to control and guide gynoecium development, plants have adapted elements of pre-existing gene regulatory networks (GRNs) but new ones have also evolved. The GRNs can interact with internal factors (e.g. hormones and other metabolites) and external factors (e.g. mechanical signals and temperature) at different levels, giving robustness and flexibility to gynoecium development. Here, we review recent findings regarding the role of cytokinin-auxin crosstalk and the genes that connect these hormonal pathways during early gynoecium development. We also discuss some examples of internal and external factors that can modify GRNs. Finally, we make a journey through the flowering plant lineage to determine how conserved are these GRNs that regulate gynoecium and fruit development.

Transcriptomic analysis reveals the regulatory module of apple (Malus × domestica) floral transition in response to 6-BA

BACKGROUND

Insufficient production of flower buds is an intractable problem in 'Fuji' apple orchards. Although cytokinin (CK) promotes flower bud formation in apple trees, little is known about the mechanisms regulating this phenomenon.

RESULTS

In the present study, high-throughput RNA sequencing (RNA-Seq) of 'Nagafu No. 2' buds was conducted to characterize the transcriptional response to 6-BA treatment during key period of floral transition. A weighted gene co-expression network analysis (WGCNA) of the differentially expressed genes identified hormone signal transduction pathways, totaling 84 genes were highly correlated with the expression pattern of flowering-time genes. The up-regulation of CK signal components and a gibberellin (GA) signal repressor were found to contribute to the promotion of floral transition. In relative comparison to non-treated buds, a series of sugar metabolism- and signal- related genes were associated with relatively high levels of sucrose, fructose, and glucose during floral induction in the 6-BA treated buds. Several transcription factors (i.e. SPLs, SOC1, FD, and COL) that are involved in GA, aging, and photoperiod-regulated flowering pathways were also upregulated by the 6-BA treatment. In addition, potential transcription factors integrating CK signaling to trigger floral induction in apple were also assessed; including PHYTO-CHROME-INTERACTING FACTOR (PIF1,3), WUSCHEL-related homeobox (WOX3,13), and CK response regulators (ARR2).

CONCLUSIONS

The present study provides insight into the response of flowering and development-related pathways and transcription factors to 6-BA during the period of floral transition in apple. It extends our knowledge of the fundamental mechanisms associated with CK-regulated floral transition in apple trees.

Cold stress signalling in female reproductive tissues

Cold stress is a significant threat for plant productivity and impacts on plant distribution and crop production, particularly so when it occurs during the growth phase. A developmental stage at risk is that of flowering, since a single stress event during sensitive stages, such as the full-bloom stage of fruit trees can be fatal for reproductive success. Although pollen development and fertilization are widely viewed as the most critical reproductive phases, the development and function of female reproductive tissues, which in Angiosperms are embedded in the gynoecium, are also affected by cold stress. Today however, we have essentially no understanding of the cold stress response pathways that act during floral organogenesis. In this review, we briefly summarize our current knowledge of cold stress signalling modules active in vegetative tissues that may provide a framework of general principles also transferable to female reproductive tissues. We then align these signalling cascades with those that govern gynoecium development to identify factors that may act in both processes and could thereby contribute to cold stress responses in female reproductive tissues.

How plants grow up

A plant's lateral structures, such as leaves, branches and flowers, literally hinge on the shoot axis, making its integrity and growth fundamental to plant form. In all plants, subapical proliferation within the shoot tip displaces cells downward to extrude the cylindrical stem. Following the transition to flowering, many plants show extensive axial elongation associated with increased subapical proliferation and expansion. However, the cereal grasses also elongate their stems, called culms, due to activity within detached intercalary meristems which displaces cells upward, elevating the grain-bearing inflorescence. Variation in culm length within species is especially relevant to cereal crops, as demonstrated by the high-yielding semi-dwarfed cereals of the Green Revolution. Although previously understudied, recent renewed interest the regulation of subapical and intercalary growth suggests that control of cell division planes, boundary formation and temporal dynamics of differentiation, are likely critical mechanisms coordinating axial growth and development in plants.

Female reproductive organ formation: A multitasking endeavor

Multicellular organisms, such as plants, fungi, and animals, develop organs with specialized functions. Major challenges in developing such structures include establishment of polarity along three axes (apical-basal, medio-lateral, and dorso-ventral/abaxial-adaxial), specification of tissue types and their coordinated growth, and maintenance of communication between the organ and the entire organism. The gynoecium of the model plant Arabidopsis thaliana embodies the female reproductive organ and has proven an excellent model system for studying organ establishment and development, given its division into different regions with distinct symmetries and highly diverse tissue types. Upon pollination, the gynoecium undergoes dramatic changes in morphology and developmental programming to form the seed-containing fruit. In this review, we wish to provide a detailed overview of the molecular and genetic mechanisms that are known to guide gynoecium and fruit development in A. thaliana. We describe networks of key genetic regulators and their interactions with hormonal dynamics in driving these developmental processes. The discoveries made to date clearly demonstrate that conclusions drawn from studying gynoecium and fruit development in flowering plants can be used to further our general understanding of organ formation across the plant kingdom. Importantly, this acquired knowledge is increasingly being used to improve fruit and seed crops, facilitated by the recent profound advances in genomics, cloning, and gene-editing technologies.

Synergistic action of GCN5 and CLAVATA1 in the regulation of gynoecium development in Arabidopsis thaliana

In Arabidopsis thaliana the CLAVATA1 (CLV1) receptor and GENERAL CONTROL NON DEREPRESSIBLE 5 (GCN5) histone acetyltransferase both regulate inflorescence meristem size and affect the expression of the meristem-promoting transcription factor WUSCHEL (WUS). Single and multiple mutants of GCN5 and CLAVATA members, were analysed for their gynoecium development, using morphological, physiological, genetic and molecular approaches. The clv1-1gcn5-1 double mutants exhibited novel phenotypes including elongated gynoecia with reduced valves and enlarged stigma and style, indicating a synergistic action of CLAVATA signaling and GCN5 action in the development of the gynoecium. Reporter line and gene expression analysis showed that clv1-1gcn5-1 plants have altered auxin and cytokinin response, distribution and ectopic overexpression of WUS. WUS expression was found in the style of wild-type gynoecia stage 10-13, suggesting a possible novel role for WUS in the development of the style. CLV1 and GCN5 are regulators of apical-basal and mediolateral polarity of the Arabidopsis gynoecium. They affect gynoecium morphogenesis through the negative regulation of auxin biosynthesis and promotion of polar auxin transport. They also promote cytokinin signaling in the carpel margin meristem and negatively regulate it at the stigma. Finally, they synergistically suppress WUS at the centre of the gynoecium.

Plant stem cells: what we know and what is anticipated

Plant stem cell research is of interest due to stem cells ability of unlimited division, therapeutic potential and steady supply to provide precursor cells. Their isolation and culture provides the important source for the production of homogenous lines of active constituents that allow large-scale production of various metabolites. The process of dedifferentiation and reversal to pluripotent cells involves the various pathways genes related to the stem cells and are associated to each other for maintaining a specific niche. Domains such as niche dynamics and maintenance signaling can be used for the identification of genes for stem cell niche. Significant findings have been achieved in the past on plant stem cells however our understanding towards mechanisms underlying some specific phenomenon like dedifferentiation, regulation, niche dynamics is still in infancy. The present review is based on the past research efforts and also pave a way forward for the future anticipation in the field of development of cell cultures for the production of active metabolites on large scale and undertanding transcriptional regulation of stem cell genes involved in niche signaling.

A molecular network for functional versatility of HECATE transcription factors

During the plant life cycle, diverse signaling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) basic helix-loop-helix transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dynamics and gynoecium patterning. However, the molecular mechanisms underlying their functional versatility and the deployment of specific HEC subprograms remain elusive. To address this issue, we systematically identified proteins with the capacity to interact with HEC1, the best-characterized member of the family, and integrated this information with our data set of direct HEC1 target genes. The resulting core genetic modules were consistent with specific developmental functions of HEC1, including its described activities in light signaling, gynoecium development and auxin homeostasis. Importantly, we found that HEC genes also play a role in the modulation of flowering time, and uncovered that their role in gynoecium development may involve the direct transcriptional regulation of NGATHA1 (NGA1) and NGA2 genes. NGA factors were previously shown to contribute to fruit development, but our data now show that they also modulate stem cell homeostasis in the shoot apical meristem. Taken together, our results delineate a molecular network underlying the functional versatility of HEC transcription factors. Our analyses have not only allowed us to identify relevant target genes controlling shoot stem cell activity and a so far undescribed biological function of HEC1, but also provide a rich resource for the mechanistic elucidation of further context-dependent HEC activities.

Comparative transcriptome analysis reveals the regulatory networks of cytokinin in promoting the floral feminization in the oil plant Sapium sebiferum

BACKGROUND

Sapium sebiferum, whose seeds contain high level of fatty acids, has been considered as one of the most important oil plants. However, the high male to female flower ratio limited the seed yield improvement and its industrial potentials. Thus, the study of the sex determination in S. sebiferum is of significant importance in increasing the seed yield.

RESULTS

In this study, we demonstrated that in S. sebiferum, cytokinin (CK) had strong feminization effects on the floral development. Exogenous application with 6-benzylaminopurine (6-BA) or thidiazuron (TDZ) significantly induced the development of female flowers and increased the fruit number. Interestingly, the feminization effects of cytokinin were also detected on the androecious genotype of S. sebiferum which only produce male flowers. To further investigate the mechanism underlying the role of cytokinin in the flower development and sex differentiation, we performed the comparative transcriptome analysis of the floral buds of the androecious plants subjected to 6-BA. The results showed that there were separately 129, 352 and 642 genes differentially expressed at 6 h, 12 h and 24 h after 6-BA treatment. Functional analysis of the differentially expressed genes (DEGs) showed that many genes are related to the hormonal biosynthesis and signaling, nutrients translocation and cell cycle. Moreover, there were twenty one flowering-related genes identified to be differentially regulated by 6-BA treatment. Specifically, the gynoecium development-related genes SPATULA (SPT), KANADI 2 (KAN2), JAGGED (JAG) and Cytochrome P450 78A9 (CYP79A9) were significantly up-regulated, whereas the expression of PISTILLATA (PI), TATA Box Associated Factor II 59 (TAFII59) and MYB Domain Protein 108 (MYB108) that were important for male organ development was down-regulated in response to 6-BA treatment, demonstrating that cytokinin could directly target the floral organ identity genes to regulate the flower sex.

CONCLUSIONS

Our work demonstrated that cytokinin is a potential regulator in female flower development in S. sebiferum. The transcriptome analysis of the floral sex transition from androecious to monoecious in response to cytokinin treatment on the androecious S. sebiferum provided valuable information related to the mechanism of sex determination in the perennial woody plants.

Evolution of genes associated with gynoecium patterning and fruit development in Solanaceae

BACKGROUND AND AIMS

The genetic basis of fruit development has been extensively studied in Arabidopsis, where major transcription factors controlling valve identity (i.e. FRUITFULL), replum development (i.e. REPLUMLESS) and the differentiation of the dehiscence zones (i.e. SHATTERPROOF, INDEHISCENT and ALCATRAZ) have been identified. This gene regulatory network in other flowering plants is influenced by duplication events during angiosperm diversification. Here we aim to characterize candidate fruit development genes in the Solanaceae and compare them with those of Brassicaceae.

METHODS

ALC/SPT, HEC/IND, RPL and AG/SHP homologues were isolated from publicly available databases and from our own transcriptomes of Brunfelsia australis and Streptosolen jamesonii. Maximum likelihood phylogenetic analyses were performed for each of the gene lineages. Shifts in protein motifs, as well as expression patterns of all identified homologues, are shown in dissected floral organs and fruits in different developmental stages of four Solanaceae species exhibiting different fruit types.

KEY RESULTS

Each gene lineage has undergone different duplication time-points, resulting in very different genetic complements in the Solanaceae when compared with the Brassicaceae. In general, Solanaceae species have more copies of HEC1/2 and RPL than Brassicaceae, have fewer copies of SHP and the same number of copies of AG, ALC and SPT. Solanaceae lack IND orthologues, but have pre-duplication HEC3 homologues. The expression analyses showed opposite expression of SPT and ALC orthologues between dry- and fleshy-fruited species during fruit maturation. Fleshy-fruited species turn off RPL and SPT orthologues during maturation.

CONCLUSIONS

The gynoecium patterning and fruit developmental genetic network in the Brassicaceae cannot be directly extrapolated to the Solanaceae. In Solanaceae ALC, SPT and RPL contribute differently to maturation of dry dehiscent and fleshy fruits, whereas HEC genes are not generally expressed in the gynoecium. RPL genes have broader expression patterns than expected.

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.