Photoperiodic flowering in Arabidopsis: Multilayered regulatory mechanisms of CONSTANS and the florigen FLOWERING LOCUS T

Genome-wide identification and characterization of CONSTANS-like transcription factors reveal that three CsCOLs regulate the cannabinoid biosynthesis in Cannabis

Cannabis (Cannabis sativa L.) has been cultivated as a versatile industrial crop for millennia, serving for food, fiber, and medicine. Cannabinoids are characteristic medicinal active compounds in cannabis, mainly being rich in female inflorescences. CONSTANS-like (COL) transcription factors are primarily involved in the photoperiod process of flowering plants. However, knowledge about their regulatory mechanism for secondary metabolites is limited. Eleven CsCOLs were identified from the cannabis genome based on the phylogenetic relationship and conserved domains in this study. The number of CsCOLs in cannabis showed apparent contraction and their functional divergence. CsCOL1, CsCOL5, and CsCOL7 exhibited high expression in flowers and bracts and their overexpression elevated the content of CBDA and CBGA by promoting the expression of related structural genes involved in cannabinoid biosynthesis. In addition, CsCOL7 was bound to the promoters of four structural genes, including CsAAE, CsOLS, CsPT4, and CsCBDAS, to regulate their gene expression in the manner of repressing the upstream and activating the downstream genes. CsCOL1 positively regulated the expression of CsPT4 and CsCBDAS. In addition, CsCOL5 positively regulated the expression of CsOLS and CsPT4 via binding of their promoters. Here, we explored the potential transcription regulation mechanism of CsCOLs in cannabinoid biosynthesis in C. sativa for the first time, even though a more profound investigation should be conducted in cannabis plants in the future. The findings expanded the knowledge of COLs in regulating secondary metabolites and provided insights into CsCOLs in cannabinoid biosynthesis.

The regulatory module consisting of KNOTTED1-like homeobox 6, Homeobox-leucine zipper 14, and BLADE-ON-PETIOLE 2 is involved in shoot development and lateral branching in citrus

KNOTTED1-like homeobox (KNOX) family transcription factors (TFs) are important regulatory factors in plant growth and development, participating in various aspects of developmental regulation. In this study, we demonstrate that the citrus KNOX gene 6 (CiKN6) regulates shoot branch development. Overexpression of CiKN6 in citrus plants resulted in a significant phenotype characterized by increased branching and shortened shoots. Expression analysis revealed that CiKN6 was predominantly expressed in the stems. Protein interaction studies showed that CiKN6 interacted with Homeobox-leucine zipper 14 (CiHOX14). Furthermore, we discovered that CiHOX14 specifically binds to the BLADE-ON-PETIOLE 2 (CiBOP2) promoter and enhances its expression. Overexpression of CiBOP2 led to increased branching and shortened shoots in Arabidopsis and citrus, while suppression of CiBOP2 expression resulted in increased plant height in citrus. Additionally, we identified a TEOSINTE BRANCHED1/CYCLOIDEA/PCF TF, CiTCP15, that promotes CiBOP2 expression by binding to its promoter. Lastly, qRT-PCR assays demonstrate that the expression of CiKN6 and CiHOX14 was upregulated by CiBOP2 through feedback regulation. These findings suggest that the CiKN6-CiHOX14 complex, along with CiBOP2, interact to regulate shoot development and branching in citrus, providing new insights into the roles of homeobox proteins in citrus.

Dancing molecules: group A bZIPs and PEBPs at the heart of plant development and stress responses

Group A basic leucine zipper (bZIP) transcription factors play critical roles in abscisic acid (ABA) signaling and plant development. In Arabidopsis thaliana, these factors are defined by a highly conserved core bZIP domain, and four conserved domains throughout their length: three at the N-terminus (C1-C3) and a phosphorylatable C-terminal SAP motif located at the C4 domain. Initially, members such as ABI5 and ABFs were studied for their roles in ABA signaling during seed germination or stress responses. Later, a sub-clade of group A bZIPs, including FD, was found to play important roles in floral induction by interacting with the florigen FLOWERING LOCUS T (FT) at the shoot apical meristem. Recent research has expanded our understanding of these transcription factors by identifying intriguing parallels between those involved in ABA signaling and those promoting floral induction, and revealing dynamic interactions with FT and other phosphatidylethanolamine-binding proteins (PEBPs) such as TERMINAL FLOWER 1. Studies in crop plants and non-model species demonstrate broader roles, functions, and molecular targets of group A bZIPs. This review highlights common features of group A bZIPs and their post-translational regulation in enabling the activation of gene regulatory networks with important functions in plant development and stress responses.

Complex Signaling Networks Underlying Blue-Light-Mediated Floral Transition in Plants

Blue light (BL) is important in regulating floral transition. In a controlled environment production system, BL can be manipulated easily and precisely in aspects like peak wavelength, intensity, duration, and co-action with other wavelengths. However, the results of previous studies about BL-mediated floral transition are inconsistent, which implies that an in-depth critical examination of the relevant physiological mechanisms is necessary. This review consolidates the recent findings on the role of BL in mediating floral transition not only in model plants, such as Arabidopsis thaliana, but also in crops, especially horticultural crops. The photoreceptors, floral integrator proteins, signal pathways, and key network components involved in BL-mediated floral transition are critically reviewed. This review provides possible explanations for the contrasting results of previous studies on BL-mediated flowering; it provides valuable information to explain and develop BL manipulation strategies for mediating flowering, especially in horticultural plants. The review also identifies the knowledge gaps and outlines future directions for research in related fields.

Phenotypic plasticity of flowering time and plant height related traits in wheat

BACKGROUND

Climate changes pose challenges to crop production. However, the causes of phenotypic differences across environments remain unclear.

RESULTS

Here, heading date (HD), flowering date (FD), and plant height (PH) were measured along with four environmental factors (day length (DL), growing degree days (GDD), precipitation (PRCP), and photothermal ratio (PTR)) to investigate the genetic basis of phenotypic plasticity of these traits in 616 wheat accessions using genome-wide association studies. Regarding quantitative trait locus-by-environment interactions (QEIs), five known and three candidate genes for HD, six known and seven candidate genes for FD, and four known and eighteen candidate genes for PH were identified. For the genes associated with phenotypic plasticity, 10 genes exhibited responsiveness to alterations in diverse environmental conditions according to transcriptome data; haplotype effects of 33 genes were identified as significantly correlated with the changes in environmental factors; six candidate genes were identified as hub genes in the gene network, possibly influencing other genes and causing the phenotypic plasticity. And over-dominant effects can explain over 50% the genetic variance of phenotypic plasticity. More importantly, one FD/HD candidate gene (TraesCS4A01G180700) and two PH candidate genes (TraesCS5B01G054800 and TraesCS2A01G539400) partly explain the phenotypic plasticity for the FD/HD and PH traits, respectively. In addition, the potential utilization of these genes in wheat breeding was discussed.

CONCLUSIONS

This study elucidated the genetic basis of phenotypic differences caused by environments and provided a foundation for addressing the impact of climate change on crop production.

Genome-wide identification of CONSTANS-like genes in Dimocarpus longan and functional characterization of DlCOL9 revealing its role in floral induction

Longan (Dimocarpus longan L.), an economically important tropical/subtropical fruit species, faces production constraints due to unreliable floral induction processes. CONSTANS-like (COL) genes play an important role in the photoperiodic flowering pathway. In this study, a total of 10, 15 and 15 DlCOL genes were identified in longan cultivars HHZ, SX and JDB, respectively. Phylogenetic analysis showed that DlCOL genes were divided into three subgroups, and the members of each subgroup had conserved B-box and CCT domains, indicating potential binding interactions between DlCOL genes and flowering-related genes. Analysis of tissue-specific expression showed that all DlCOL genes were widely expressed in various organs of longan, and were preferentially expressed in the leaves. Notably, DlCOL9 exhibited preferential expression in apical buds during the physiological differentiation stage of floral bud induction. Transgenic Arabidopsis plants overexpressing DlCOL9 displayed a significantly shortened flowering time accompanied by the increasing expression of flowering genes AtFT, AtSOC1 and AtCO, indicating that DlCOL9 has the function of promoting flowering. Furthermore, DlCOL9 was co-expressed with key flowering regulators in longan, DlFKF1, DlGI and DlSOC1. Yeast one-hybrid combined with dual-luciferase assays demonstrated that both DlGI and DlFKF1 could bind to the promoter of DlCOL9 to enhance its expression, whereas DlCOL9 transcriptionally regulated DlSOC1 directly. Our results reveal a conserved DlGI/DlFKF1-DlCOL9-DlSOC1 regulatory module governing floral induction in longan which advance the functional understanding of the DlCOL gene family and provide a molecular basis for optimizing flowering regulation in longan production.

CONSTANS-like 13 homologs MiCOL13 A and MiCOL13B orchestrate flowering time and salt-drought tolerance in mango

The CO/COL gene family serves as a central regulator of photoperiod-dependent floral transition and exhibits functional diversification in plant adaptation to abiotic stress conditions. Through comprehensive analysis of the genomic data from the mango cultivar Guire 82 (Mangifera indica L.), two COL13 homologs, designated MiCOL13 A and MiCOL13B, were successfully characterized. Phylogenetic categorization revealed that MiCOL13 A and MiCOL13B cluster within evolutionary clade III of the CONSTANS-like superfamily. These two homologous genes displayed a circadian rhythm and were strongly expressed in the leaves throughout the flowering induction phase. Under short-day (SD) conditions, the flowering time of Arabidopsis strains overexpressing MiCOL13 A and MiCOL13B was significantly delayed. However, overexpression of MiCOL13 A promoted early flowering in Arabidopsis, and MiCOL13B delayed flowering under long-day (LD) conditions. Subcellular localization demonstrated that the nucleus was the location of MiCOL13 A and MiCOL13B. The study also revealed that the overexpression of MiCOL13 A and MiCOL13B enhances Arabidopsis resistance to salt and drought stresses, resulting in overexpressing lines with longer roots and higher survival rates. Investigations of physiological and biochemical parameters revealed that elevated expression of MiCOL13 A/B significantly upregulated the expression of stress-responsive endogenous genes in A. thaliana under saline and drought conditions. Moreover, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) analyses revealed that the MiCOL13A and MiCOL13B proteins interact with two stress-related proteins, zinc finger protein 4 (MiZFP4) and MYB30-INTERACTING E3 LIGASE 1 (MiMIEL1). Together, our findings indicate that MiCOL13 A and MiCOL13B have dual functions in controlling flowering and responding to abiotic stress in plants.

QTL mapping of flowering time in Brassica napus: a study on the interplay between temperature and day length after vernalization

Flowering is a critical life stage for plants, and the regulation of flowering is heavily influenced by environmental factors and is genetically very complex. In oilseed rape (Brassica napus L.), a major oil crop, yield is heavily dependent on successful flowering. Until now, the influences of day length and temperature on flowering time have mostly been studied in spring-type rape, although they also affect flowering in winter oilseed rape after vernalization, and changing climate conditions alter springtime temperatures. In this study, a doubled haploid population derived from a cross between a winter and a spring-type oilseed rape was examined for the effect of cool and warm temperatures (11°C and 22°C) in combination with long and short days (8/16-h light) on flowering time after vernalization. Quantitative trait locus (QTL) analysis revealed major QTLs for flowering time in two homologous regions on chromosomes C06 and A07, which were found to interact epistatically. It was found that temperature can either delay or promote flowering depending on day length and genotype, highlighting the complex interplay between these factors. Our study provides new insights into the genetic basis of flowering time regulation in B. napus, especially after vernalization, and highlights the importance of considering the interplay between temperature and day length in breeding programs for this crop, particularly in the context of climate change.

Flowering time regulation through the lens of evolution

Flowering, the onset of reproductive development, marks a critical transition in the angiosperm life cycle. In the model plant Arabidopsis thaliana, the process is tightly regulated by a complex network of approximately 300 genes organized into distinct pathways. This mini-review examines the genetic and molecular mechanisms regulating flowering time from an evolutionary perspective. Our analysis reveals that genes involved in the age and photoperiod pathways are evolutionarily ancient and highly conserved across bryophytes and vascular plants. In contrast, other regulatory modules appear to have evolved more recently, likely through the repurposing of existing genes or adaptations to environmental changes. We propose that future research should shift away from studying flowering regulation mechanisms in individual model plants to exploring the evolution of flowering time pathways and their underlying drivers. Adopting an evolutionary perspective may ultimately illuminate the fundamental principles governing the timing of reproductive development in plants.

UV-B Irradiation Does Not Promote Flowering in Arabidopsis Despite Increased FT Expression

Various environmental factors control the plant flowering time. However, the specific effects of ultraviolet (UV)-B radiation on flowering remain unclear. UV-B irradiation delays flowering in Arabidopsis during short-day (SD) photoperiods. In contrast, UV-B irradiation causes a variety of flowering phenotypes during long-day (LD) photoperiods, including unchanged, delayed, and accelerated flowering. We hypothesized that variations in UV-B intensity are responsible for the phenotypic changes under LD photoperiods. Therefore, in this study, Arabidopsis plants were exposed to two distinct UV-B intensities: a low UV-B intensity that activates UVR8-dependent pathways and high UV-B intensity that activates both UVR8-dependent and -independent pathways. Under LD photoperiods, neither the wild-type (WT) nor the uvr8 mutant showed any change in flowering time at either UV-B irradiation intensity. Under the SD photoperiod, UV-B irradiation delayed WT flowering. The expression of flowering locus T (FT) increased after UV-B irradiation under the LD photoperiod in a UVR8-dependent manner. However, despite the increased expression of FT, expression levels of floral meristem identity genes in shoot apical meristem (SAM) were not increased by UV-B irradiation. As UV-B irradiation is known to suppress flowering in SAM in a UVR8-dependent manner, increase in FT expression induced by UV-B irradiation possibly antagonized the suppressive effect of UV-B irradiation. Overall, these results suggest that flowering phenotypes do not change with UV-B intensity but with the balance between the inhibitory and promotive effects of UVR8 activated by UV-B irradiation.

Arabidopsis RGLG1/2 regulate flowering time under different soil moisture conditions by affecting the protein stability of TOE1/2

Drought constitutes a significant environmental factor influencing the growth and development of plants. Consequently, terrestrial plants have evolved a range of strategies to mitigate the adverse effects of soil water deficit. One such strategy, known as drought escape, involves the acceleration of flowering under drought, thereby enabling plants to complete their life cycle rapidly. However, the molecular mechanisms underlying this adaptive response remain largely unclear. Using genetic, molecular, and biochemical techniques, we demonstrated that the AP2 family proteins TARGET OF EAT 1/2 (TOE1/2) are essential for the drought escape response in Arabidopsis, with a significant reduction in their protein stability observed during this process. Our findings indicate that the RING-type E3 ubiquitin ligases RING DOMAIN LIGASE 1/2 (RGLG1/2) interact with TOE1/2 and facilitate their degradation within the nucleus. Under water deficit conditions, there is increased expression of RGLG1/2, and their protein products translocate to the nucleus to ubiquitinate and degrade TOE1/2, thereby enhancing the drought escape response. Furthermore, the loss of TOE1/2 in drought conditions directly results in a reduction of drought resistance in plants, suggesting that drought escape is a high-risk behaviour for plants and that the RGLG1/2-TOE1/2 signalling cascade may serve as a central regulatory mechanism governing the trade-off between drought escape and drought tolerance in plants.

Linking phenology, harvest index, and genetics to improve chickpea grain yield

Understanding phenology and its regulation is central for the agronomic adaptation of chickpea. We grew 24 chickpea (Cicer arietinum) genotypes in 12 environments to analyse the environmental and genotypic drivers of phenology, associations between phenology and yield, and phenotypes associated with allelic variants of three flowering related candidate loci: CaELF3a, a cluster of three FT genes on chromosome 3, and an orthologue of the floral promoter GIGANTEA on chromosome 4. A simple model with three genotype-specific parameters explained the differences in flowering response to daylength. Environmental factors causing flower abortion, such as low temperature and radiation and high humidity, led to a longer flowering-to-podding interval. Late podding associated with poor partition to grain, limiting yield in favourable environments. The genotype Sonali, carrying the early allele of Caelf3a (elf3a), was generally the earliest to set pod and had low biomass but the highest harvest index. Genotypes combining the early variants of GIGANTEA and FT orthologues featured early reproduction and high harvest index, returning high yield in favourable environments. Our results emphasize the importance of pod set, rather than flowering, as a target for breeding, agronomic, and modelling applications.

The LUX-SWI3C module regulates photoperiod sensitivity in Arabidopsis thaliana

In plants, the photoperiod sensitivity directly influences flowering time, which in turn affects latitudinal adaptation and yield. However, research into the mechanisms underlying photoperiod sensitivity, particularly those mediated by epigenetic regulation, is still in its nascent stages. In this study, we analyzed the regulation of photoperiod sensitivity in Arabidopsis thaliana. We demonstrate that the evening complex LUX ARRYTHMO (LUX) and the chromatin remodeling factor SWITCH/SUCROSE NONFERMENTING 3C (SWI3C) regulate GI locus chromatin compaction and H3K4me3 modification levels at the GIGANTEA locus under different photoperiod conditions. This mechanism is one of the key factors that allow plants to distinguish between long-day and short-day photoperiods. Our study provides insight into how the LUX-SWI3C module regulates photoperiod sensitivity at the epigenetic level.

Study on the effect of the chiral herbicide imazethapyr on flowering initiation in Arabidopsis thaliana

Non-target plants play a key role in maintaining ecological balance and biodiversity. Here, we studied the effect of the chiral herbicide imazethapyr (IM) on the flowering initiation of the non-target plant Arabidopsis thaliana and its underlying mechanism. Plants treated with R-IM initiated flowering earlier than those treated with S-IM. The herbicidally active R-IM had a much greater effect on various phytohormones than S-IM, and this effect increased with the concentration of R-IM. Before flowering, R-IM had a significant effect on the internal levels of 1-aminocyclopropane-1-carboxylic acid (ACC), indole-3-acetic acid (IAA), abscisic acid (ABA), and gibberellic acid (GA3) in Arabidopsis plants, which indicated that it promoted the production of ACC, and high concentrations of R-IM also promoted IAA, ABA, and GA3. R-IM promoted ACC, IAA, and GA3 before and during flowering. High concentrations of R-IM strongly promoted IAA and inhibited GA3, and R-IM inhibited or promoted ACC depending on the concentrations applied. Thus, earlier flowering of Arabidopsis under R-IM treatment may be affected by phytohormone levels throughout the plant, and IAA, ACC, and GA3 likely have significant effects on flowering.

Research progress on delayed flowering under short-day condition in Arabidopsis thaliana

Flowering represents a pivotal phase in the reproductive and survival processes of plants, with the photoperiod serving as a pivotal regulator of plant-flowering timing. An investigation of the mechanism of flowering inhibition in the model plant Arabidopsis thaliana under short-day (SD) conditions will facilitate a comprehensive approach to crop breeding for flowering time, reducing or removing flowering inhibition, for example, can extend the range of adaptation of soybean to high-latitude environments. In A. thaliana, CONSTANS (CO) is the most important component for promoting flowering under long-day (LD) conditions. However, CO inhibited flowering under the SD conditions. Furthermore, the current studies revealed that A. thaliana delayed flowering through multiple pathways that inhibit the transcription and sensitivity of FLOWERING LOCUS T (FT) and suppresses the response to, or synthesis of, gibberellins (GA) at different times, for potential crop breeding resources that can be explored in both aspects. However, the underlying mechanism remains poorly understood. In this review, we summarized the current understanding of delayed flowering under SD conditions and discussed future directions for related topics.

The role of nuclear factor-Y (NF-Y) transcription factor in plant growth and development

The nuclear factor-Y (NF-Y) transcription factor, also known as heme-activator protein (HAP) or CCAAT-binding factor (CBF), is a critical transcription factor widely present in eukaryotes. The number of NF-Y subunits has significantly increased in higher plants compared to animals and fungi. The NF-Y complex is composed of three subunits: (1) NF-YA; (2) NF-YB; and (3) NF-YC. NF-YB and NF-YC contain histone fold domains (HFDs), which can interact with NF-YA or other transcription factors, or directly bind to the promoter CCAAT box to regulate the transcription of downstream genes. NF-Y plays a significant role in various plant processes, including growth and development. This review elucidates the structural and functional aspects of NF-Y subunits, identified NF-Y complexes, and their molecular regulatory mechanisms. Understanding these facets of NF-Y provides valuable insights into advancing crop genetic improvement and promoting sustainable agricultural practices.

More than flowering: CONSTANS plays multifaceted roles in plant development and stress responses

Plants have evolved a remarkable ability to sense and respond to changes in photoperiod, allowing adjustments to their growth and development based on seasonal and environmental cues. The floral transition is a pivotal stage in plant growth and development, signifying a shift from vegetative to reproductive growth. CONSTANS (CO), a central photoperiodic response factor conserved in various plants, mediates day-length signals to control the floral transition, although its mechanisms of action vary among plants with different day-length requirements. In addition, recent studies have uncovered roles for CO in organ development and stress responses. These pleiotropic roles in model plants and crops make CO a potentially fruitful target for molecular breeding aimed at modifying crop agronomic traits. This review systematically traces research on CO, from its discovery and functional studies to the exploration of its regulatory mechanisms and newly discovered functions, providing important insight into the roles of CO and laying a foundation for future research.

Florigen-producing cells express FPF1-LIKE PROTEIN 1 to accelerate flowering and stem growth in Arabidopsis

Plants induce the expression of the florigen FLOWERING LOCUS T (FT) in response to seasonal changes. FT is expressed in a distinct subset of phloem companion cells in Arabidopsis. Using tissue-specific translatome analysis, we discovered that the FT-expressing cells also express FLOWERING PROMOTING FACTOR 1 (FPF1)-LIKE PROTEIN 1 (FLP1), specifically under long-day conditions with the red/far-red ratio of natural sunlight. The master regulator of FT, CONSTANS (CO), is essential for FLP1 expression, suggesting that FLP1 is involved in the photoperiod pathway. We show that FLP1 promotes early flowering independently of FT, is active in the shoot apical meristem, and induces the expression of SEPALLATA3 (SEP3), a key E-class homeotic gene. Unlike FT, FLP1 also facilitates inflorescence stem elongation. Our cumulative evidence suggests that the small FLP1 protein acts as a mobile signal like FT. Taken together, FLP1 accelerates flowering in parallel with FT and orchestrates flowering and stem elongation during the reproductive transition.

Regulatory principles of photoperiod-driven clock function in plants

The circadian clock provides a fundamental timing mechanism for plant fitting to seasonal changes in the photoperiod. Although photoperiodic regulation of developmental transition has been studied in several species, our understanding of core circadian clock parallelisms across species is sparse. Here we present a comparative analysis of circadian clock networks by identifying common regulatory principles that govern key genes in photoperiodic developmental transition. Using time-course transcriptomic datasets from long-day plants and short-day plants taken in different photoperiods, we propose a model that integrates a minimal set of circadian clock components to predict the necessary conditions governing species-specific clock outputs. This study identifies regulatory patterns associated with circadian clock function across different plants, linking photoperiod interpretation with minimal clock architecture.

Interplay of light and abscisic acid signaling to modulate plant development

Exogenous light cues and the phytohormone abscisic acid (ABA) regulate several aspects of plant growth and development. In recent years, the role of crosstalk between the light and ABA signaling pathways in regulating different physiological processes has become increasingly evident. This includes regulation of germination and early seedling development, control of stomatal development and conductance, growth, and development of roots, buds, and branches, and regulation of flowering. Light and ABA signaling cascades have various convergence points at both DNA and protein levels. The molecular crosstalk involves several light signaling factors such as HY5, COP1, PIFs, and BBXs that integrate with ABA signaling components such as the PYL receptors and ABI5. In particular, ABI5 and PIF4 promoters are key 'hotspots' for integrating these two pathways. Plants acquired both light and ABA signaling pathways before they colonized land almost 500 million years ago. In this review, we discuss recent advances in the interplay of light and ABA signaling regulating plant development and provide an overview of the evolution of these two pathways.

Characterization of pecan PEBP family genes and the potential regulation role of CiPEBP-like1 in fatty acid synthesis

Phosphatidyl ethanolamine-binding protein (PEBP) plays important roles in plant growth and development. However, few studies have investigated the PEBP gene family in pecan (Carya illinoinensis), particularly the function of the PEBP-like subfamily. In this study, we identified 12 PEBP genes from the pecan genome and classified them into four subfamilies: MFT-like, FT-like, TFL1-like and PEBP-like. Multiple sequence alignment, gene structure, and conserved motif analyses indicated that pecan PEBP subfamily genes were highly conserved. Cis-element analysis revealed that many light responsive elements and plant hormone-responsive elements are found in CiPEBPs promoters. Additionally, RNA-seq and RT-qPCR showed that CiPEBP-like1 was highly expressed during kernel filling stage. GO and KEGG enrichment analysis further indicated that CiPEBP-like1 was involved in fatty acid biosynthesis and metabolism progress. Overexpression of CiPEBP-like1 led to earlier flowering and altered fatty acid composition in Arabidopsis seeds. RT-qPCR confirmed that CiPEBP-like1 promoted fatty acid synthesis by regulating the expression of key genes. Overall, this study contributes to a comprehensive understanding of the potential functions of the PEBP family genes and lay a foundation to modifying fatty acid composition in pecan kernel.

CRF12 specifically regulates the flowering time of Arabidopsis thaliana under non-inductive conditions

The flowering time of Arabidopsis thaliana, a model plant, is significantly accelerated when exposed to long-day (LD) conditions, as it is a typical LD plant. Consequently, the investigation of the flowering regulatory network in A. thaliana under LD conditions has garnered considerable attention in the study of flowering signals, resulting in a significant breakthrough. While many LD plants, including A. thaliana, exhibit delayed flowering under non-inductive short-day (SD) conditions, they are still capable of flowering. Nevertheless, research on the regulation of flowering induction in LD plants under non-inductive SD conditions has been limited. This study demonstrated the involvement of CYTOKININ RESPONSE FACTORS 12 (CRF12) in the regulation of flowering in A. thaliana under non-inductive conditions. Analysis of the expression patterns revealed that the activation of CRF12 expression and protein stability occurred exclusively in non-inductive environments. Molecular and genetic analyses revealed that under a non-inductive photoperiod of 12 h of light and 12 h of darkness, CRF12, CONSTANS (CO), and TARGET OF EAT 1/2 (TOE1/2) engage in competitive interactions to regulate flowering time, while in a SD photoperiod of 8 h of light and 16 h of darkness, CRF12 modulates flowering time by inhibiting the activity of TOE1/2.

The Mining for Flowering-Related Genes Based on De Novo Transcriptome Sequencing in the Endangered Plant Phoebe chekiangensis

Phoebe chekiangensis is an indigenous, endangered, and valuable timber and garden tree species in China, which is notable for having a short juvenile phase (early flowering), unique among the Phoebe genus. However, the molecular mechanisms regulating the flowering of P. chekiangensis remain unexplored, primarily due to the lack of transcriptomic or genomic data. In the present study, transcriptome sequencing yielded 53 million RNA reads, resulting in 111,250 unigenes after de novo assembly. Of these, 47,525 unigenes (42.72%) were successfully annotated in the non-redundant (Nr) database. Furthermore, 15,605 unigenes were assigned to Clusters of Orthologous Groups (KOGs), and 36,370 unigenes were classified into Gene Ontology (GO) categories. A total of 16,135 unigenes were mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, involving 298 pathways. Based on the expression levels, Gibberellin signaling pathway-related genes were the most predominant expression levels. Hormonal analysis showed that gibberellin (GA) levels varied across tissues and flowering stages, as GA20 levels in leaves were low during full bloom, while GA1 and GA5 levels peaked in flowers. Furthermore, several key genes involved in gibberellin biosynthesis, including CPS, GID1, GA20ox, GA3ox, and GA2ox, exhibited stage-specific expression patterns. Certain genes were highly expressed during the initial phases of flowering, while others, like GA3ox and GA2ox, reached peak expression at full bloom. These findings provide valuable insights into the molecular mechanisms underlying flowering in P. chekiangensis, laying the foundation for future breeding efforts. This transcriptome dataset will serve as an important public resource for molecular research on this species, facilitating the discovery of functional genes related to its growth, development, and flowering regulation.

Quantitative Trait Loci for Phenology, Yield, and Phosphorus Use Efficiency in Cowpea

BACKGROUND/OBJECTIVES

Cowpea is an important legume crop in sub-Saharan Africa (SSA) and beyond. However, access to phosphorus (P), a critical element for plant growth and development, is a significant constraint in SSA. Thus, it is essential to have high P-use efficiency varieties to achieve increased yields in environments where little-to- no phosphate fertilizers are applied.

METHODS

In this study, crop phenology, yield, and grain P efficiency traits were assessed in two recombinant inbred line (RIL) populations across ten environments under high- and low-P soil conditions to identify traits' response to different soil P levels and associated quantitative trait loci (QTLs). Single-environment (SEA) and multi-environment (MEA) QTL analyses were conducted for days to flowering (DTF), days to maturity (DTM), biomass yield (BYLD), grain yield (GYLD), grain P-use efficiency (gPUE) and grain P-uptake efficiency (gPUpE).

RESULTS

Phenotypic data indicated significant variation among the RILs, and inadequate soil P had a negative impact on flowering, maturity, and yield traits. A total of 40 QTLs were identified by SEA, with most explaining greater than 10% of the phenotypic variance, indicating that many major-effect QTLs contributed to the genetic component of these traits. Similarly, MEA identified 23 QTLs associated with DTF, DTM, GYLD, and gPUpE under high- and low-P environments. Thirty percent (12/40) of the QTLs identified by SEA were also found by MEA, and some of those were identified in more than one P environment, highlighting their potential in breeding programs targeting PUE. QTLs on chromosomes Vu03 and Vu08 exhibited consistent effects under both high- and low-P conditions. In addition, candidate genes underlying the QTL regions were identified.

CONCLUSIONS

This study lays the foundation for molecular breeding for PUE and contributes to understanding the genetic basis of cowpea response in different soil P conditions. Some of the identified genomic loci, many being novel QTLs, could be deployed in marker-aided selection and fine mapping of candidate genes.

Exploring the metabolic daylength measurement system: implications for photoperiodic growth

Photoperiod is an environmental signal that varies predictably across the year. Therefore, the duration of sunlight available for photosynthesis and in turn the ability of plants to accumulate carbon resources also fluctuates across the year. To adapt to these variations in photoperiod, the metabolic daylength measurement (MDLM) system measures the photosynthetic period rather than the absolute photoperiod, translating it into seasonal gene expression changes linked to photoperiodic growth. In this Tansley Insight, we briefly summarize the current understanding of the MDLM system and highlight gaps in our knowledge. Given the system's critical role in seasonal growth, understanding the MDLM system is essential for enhancing plant adaptation to different photoperiods and optimizing agricultural production.

Genomic identification of the NF-Y gene family in apple and functional analysis of MdNF-YB18 involved in flowering transition

Apple is a crucial economic product extensively cultivated worldwide. Its production and quality are closely related to the floral transition, which is regulated by intricate molecular and environmental factors. Nuclear factor Y (NF-Y) is a transcription factor that is involved in regulating plant growth and development, with certain NF-Ys play significant roles in regulating flowering. However, there is little information available regarding NF-Ys and their role in apple flowering development. In the present study, 51 NF-Y proteins were identified and classified into three subfamilies, including 11 MdNF-YAs, 26 MdNF-YBs, and 14 MdNF-YCs, according to their structural and phylogenetic features. Further functional analysis focused on MdNF-YB18. Overexpression of MdNF-YB18 in Arabidopsis resulted in earlier flowering compared to the wild-type plants. Subcellular localization confirmed MdNF-YB18 was located in the nuclear. Interaction between MdNFY-B18 and MdNF-YC3/7 was demonstrated through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Yeast one-hybrid (Y1H) and the dual-luciferase reporter assays showed MdNF-YB18 could bind the promoter of MdFT1 and activate its expression. Moreover, this activation was enhanced with the addition of MdNF-YC3 and MdNF-YC7. Additionally, MdNF-YB18 also could interact with MdCOLs (CONSTANS Like). This study lays the foundation for exploring the functional traits of MdNF-Y proteins, highlighting the crucial role of MdNF-YB18 in activating MdFT1 in Malus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01524-2.

The AGL6-ELF3-FT circuit controls flowering time in Arabidopsis

Adjusting the timing of floral transition is essential for reproductive success in plants. A number of flowering regulators integrate internal and external signals to precisely determine the time to flower. We here report that the AGAMOUS-LIKE 6 (AGL6) - EARLY FLOWERING 3 (ELF3) module regulates flowering in the FLOWERING LOCUS T (FT)-dependent pathway in Arabidopsis. The AGL6 transcriptional repressor promotes floral transition by directly suppressing ELF3, which in turn directly represses FT expression that acts as a floral integrator. Indeed, ELF3 is epistatic to AGL6 in the control of floral transition. Overall, our findings propose that the AGL6-ELF3 module contributes to fine-tuning flowering time in plants.

Modeling Floral Induction in the Narrow-Leafed Lupin Lupinus angustifolius Under Different Environmental Conditions

Flowering is initiated in response to environmental cues, with the photoperiod and ambient temperature being the main ones. The regulatory pathways underlying floral transition are well studied in Arabidopsis thaliana but remain largely unknown in legumes. Here, we first applied an in silico approach to infer the regulatory inputs of four FT-like genes of the narrow-leafed lupin Lupinus angustifolius. We studied the roles of FTc1, FTc2, FTa1, and FTa2 in the activation of meristem identity gene AGL8 in response to 8 h and 16 h photoperiods, vernalization, and the circadian rhythm. We developed a set of regression models of AGL8 regulation by the FT-like genes and fitted these models to the recently published gene expression data. The importance of the input from each FT-like gene or their combinations was estimated by comparing the performance of models with one or few FT-like genes turned off, thereby simulating loss-of-function mutations that were yet unavailable in L. angustifolius. Our results suggested that in the early flowering Ku line and intermediate Pal line, the FTc1 gene played a major role in floral transition; however, it acted through different mechanisms under short and long days. Turning off the regulatory input of FTc1 resulted in substantial changes in AGL8 expression associated with vernalization sensitivity and the circadian rhythm. In the wild ku line, we found that both FTc1 and FTa1 genes had an essential role under long days, which was associated with the vernalization response. These results could be applied both for setting up new experiments and for data analysis using the proposed modeling approach.

Transcriptome Profiling Reveals Key Regulatory Networks for Age-Dependent Vernalization in Welsh Onion (Allium fistulosum L.)

Plants exhibit diverse pathways to regulate the timing of flowering. Some plant species require a vegetative phase before being able to perceive cold stimuli for the acceleration of flowering through vernalization. This research confirms the correlation between the vernalization process and seedling age in Welsh onions. Findings from two vernalization experiments conducted at different time intervals demonstrate that seedlings must reach a vegetative phase of at least 8 weeks to consistently respond to vernalization. Notably, 8-week-old seedlings subjected to 6 weeks of vernalization displayed the shortest time to bolting, with an average duration of 138.1 days. Transcriptome analysis led to the identification of genes homologous to those in Arabidopsis thaliana that regulate flowering. Specifically, AfisC7G05578 (CO), AfisC2G05881 (AP1), AfisC1G07745 (FT), AfisC1G06473 (RAP2.7), and AfisC2G01843 (VIM1) were identified and suggested to have potential significance in age-dependent vernalization in Welsh onions. This study not only presents a rapid vernalization method for Welsh onions but also provides a molecular foundation for understanding the interplay between seedling age and vernalization.

The B-box protein BBX13/COL15 suppresses photoperiodic flowering by attenuating the action of CONSTANS in Arabidopsis

The optimal timing of transition from vegetative to floral reproductive phase is critical for plant productivity and agricultural yields. Light plays a decisive role in regulating this transition. The B-box (BBX) family of transcription factors regulates several light-mediated developmental processes in plants, including flowering. Here, we identify a previously uncharacterized group II BBX family member, BBX13/COL15, as a negative regulator of flowering under long-day conditions. BBX13 is primarily expressed in the leaf vasculature, buds, and flowers, showing a similar spatial expression pattern to the major flowering time regulators CO and FT. bbx13 mutants flower early, while BBX13-overexpressors exhibit delayed flowering under long days. Genetic analyses showed that BBX13 acts upstream to CO and FT and negatively regulates their expression. BBX13 physically interacts with CO and inhibits the CO-mediated transcriptional activation of FT. In addition, BBX13 directly binds to the CORE2 motif on the FT promoter, where CO also binds. Chromatin immunoprecipitation data indicates that BBX13 reduces the in vivo binding of CO on the FT promoter. Through luciferase assay, we found that BBX13 inhibits the CO-mediated transcriptional activation of FT. Together, these findings suggest that BBX13/COL15 represses flowering in Arabidopsis by attenuating the binding of CO on the FT promoter.

Florigen and antiflorigen gene expression correlates with reproductive state in a marine angiosperm, Zostera marina

• Florigen and antiflorigen genes within the phosphatidylethanolamine-binding protein (PEBP) family regulate flowering in angiosperms. In eelgrass (Zostera marina), a marine foundation species threatened by climate change, flowering and seed production are crucial for population resilience. Yet, the molecular mechanism underpinning flowering remains unknown. • Using phylogenetic analysis and functional assays in Arabidopsis, we identified thirteen PEBP genes in Z. marina (ZmaPEBP) and showed that four genes altered flowering phenotypes when overexpressed. We used quantitative RT-PCR on Z. marina shoots from perennial and annual populations in Willapa Bay, USA to assess expression of these four genes in different tissue and expression changes throughout the growth season. • We demonstrated that ZmaFT2 and ZmaFT4 promote flowering, and ZmaFT9 and ZmaTFL1a repress flowering in Arabidopsis. Across five natural sites exhibiting different degrees of population genetic structure, ZmaFT2 and ZmaFT4 were expressed in leaves of vegetative and reproductive shoots and in stems and rhizomes of reproductive shoots. ZmaFT9 was distinctively expressed in leaves of vegetative and juvenile shoots, while ZmaTFL1a levels increased after flowering shoots emerged. • Our results suggest that ZmaFT2 and ZmaFT4 may promote flowering, while ZmaFT9 may inhibit a floral transition in eelgrass. We speculate that ZmaTFL1a may be involved in flowering shoot architecture.

A molecular module connects abscisic acid with auxin signals to facilitate seasonal wood formation in Populus

Perennial trees have a recurring annual cycle of wood formation in response to environmental fluctuations. However, the precise molecular mechanisms that regulate the seasonal formation of wood remain poorly understood. Our prior study indicates that VCM1 and VCM2 play a vital role in regulating the activity of the vascular cambium by controlling the auxin homoeostasis of the cambium zone in Populus. This study indicates that abscisic acid (ABA) affects the expression of VCM1 and VCM2, which display seasonal fluctuations in relation to photoperiod changes. ABA-responsive transcription factors AREB4 and AREB13, which are predominantly expressed in stem secondary vascular tissue, bind to VCM1 and VCM2 promoters to induce their expression. Seasonal changes in the photoperiod affect the ABA amount, which is linked to auxin-regulated cambium activity via the functions of VCM1 and VCM2. Thus, the study reveals that AREB4/AREB13-VCM1/VCM2-PIN5b acts as a molecular module connecting ABA and auxin signals to control vascular cambium activity in seasonal wood formation.

Forward genetic approach identifies a phylogenetically conserved serine residue critical for the catalytic activity of UBIQUITIN-SPECIFIC PROTEASE 12 in Arabidopsis

Circadian clocks rely on transcriptional/translational feedback loops involving clock genes and their corresponding proteins. While the primary oscillations originate from gene expression, the precise control of clock protein stability plays a pivotal role in establishing the 24-hour circadian rhythms. Most clock proteins are degraded through the ubiquitin/26S proteasome pathway, yet the enzymes responsible for ubiquitination and deubiquitination remain poorly characterised. We identified a missense allele (ubp12-3, S327F) of the UBP12 gene/protein in Arabidopsis. Despite ubp12-3 exhibited a short period phenotype similar to that of a loss-of-function allele, molecular analysis indicated elevated protease activity in ubp12-3. We demonstrated that early flowering of ubp12 mutants is a result of the shortened circadian period rather than a direct alteration of UBP12 function. Analysis of protease activity of non-phosphorylatable (S327A, S327F) and phosphomimetic (S327D) derivatives in bacteria suggested that phosphorylation of serine 327 inhibits UBP12 enzymatic activity, which could explain the over-functioning of S327F in vivo. We showed that phosphomimetic mutations of the conserved serine in the Neurospora and human orthologues reduced ubiquitin cleavage activity suggesting that not only the primary structures of UBP12-like enzymes are phylogenetically conserved across a wide range of species, but also the molecular mechanisms governing their enzymatic activity.

Decoding histone 3 lysine methylation: Insights into seed germination and flowering

Histone lysine methylation is a highly conserved epigenetic modification across eukaryotes that contributes to creating different dynamic chromatin states, which may result in transcriptional changes. Over the years, an accumulated set of evidence has shown that histone methylation allows plants to align their development with their surroundings, enabling them to respond and memorize past events due to changes in the environment. In this review, we discuss the molecular mechanisms of histone methylation in plants. Writers, readers, and erasers of Arabidopsis histone methylation marks are described with an emphasis on their role in two of the most important developmental transition phases in plants, seed germination and flowering. Further, the crosstalk between different methylation marks is also discussed. An overview of the mechanisms of histone methylation modifications and their biological outcomes will shed light on existing research gaps and may provide novel perspectives to increase crop yield and resistance in the era of global climate change.

ZmARF16 Regulates ZCN12 to Promote the Accumulation of Florigen and Accelerate Flowering

Auxin response factors(ARFs) are a class of transcription factors that regulate the expression of auxin response genes and play a crucial role in plant growth and development. Florigen plays a crucial role in the process of flowering. However, the process by which auxin regulates the accumulation of florigen remains largely unclear. This study found that the expression of ZmARF16 in maize increases during flowering, and the genetic transformation of ZmARF16 accelerates the flowering process in Arabidopsis and maize. Furthermore, ZmARF16 was found to be positively correlated with the transcription of the ZCN12 gene. Similarly, the FT-like gene ZCN12 in maize rescues the late flowering phenotype of the FT mutation in Arabidopsis. Moreover, ZCN12 actively participates in the accumulation of florigen and the flowering process. Further research revealed that ZmARF16 positively responds to the auxin signal, and that the interaction between ZmARF16 and the ZCN12 promoter, as well as the subsequent promotion of ZCN12 gene expression, leads to early flowering. This was confirmed through a yeast one-hybrid and dual-luciferase assay. Therefore, the study provides evidence that the ZmARF16-ZCN12 module plays a crucial role in regulating the flowering process of maize.

A florigen-expressing subpopulation of companion cells expresses other small proteins and reveals a nitrogen-sensitive FT repressor

The precise onset of flowering is crucial to ensure successful plant reproduction. The gene FLOWERING LOCUS T (FT) encodes florigen, a mobile signal produced in leaves that initiates flowering at the shoot apical meristem. In response to seasonal changes, FT is induced in phloem companion cells located in distal leaf regions. Thus far, a detailed molecular characterization of the FT-expressing cells has been lacking. Here, we used bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate gene expression in FT-expressing cells and other phloem companion cells. Our bulk nuclei RNA-seq demonstrated that FT-expressing cells in cotyledons and in true leaves differed transcriptionally. Within the true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster in which many genes involved in ATP biosynthesis are highly upregulated. The cluster also expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). In addition, we found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the consensus binding motifs of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of the paralogous NIGT1.2 and NIGT1.4 repressed FT expression and significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependent FT repressors. Taken together, our results demonstrate that major FT-expressing cells show a distinct expression profile that suggests that these cells may produce multiple systemic signals to regulate plant growth and development.

CsMIKC1 regulates inflorescence development and grain production in Cannabis sativa plants

Female inflorescence is the primary output of medical Cannabis. It contains hundreds of cannabinoids that accumulate in the glandular trichomes. However, little is known about the genetic mechanisms governing Cannabis inflorescence development. In this study, we reported the map-based cloning of a gene determining the number of inflorescences per branch. We named this gene CsMIKC1 since it encodes a transcription factor that belongs to the MIKC-type MADS subfamily. Constitutive overexpression of CsMIKC1 increases inflorescence number per branch, thereby promoting flower production as well as grain yield in transgenic Cannabis plants. We further identified a plant-specific transcription factor, CsBPC2, promoting the expression of CsMIKC1. CsBPC2 mutants and CsMIKC1 mutants were successfully created using the CRISPR-Cas9 system; they exhibited similar inflorescence degeneration and grain reduction. We also validated the interaction of CsMIKC1 with CsVIP3, which suppressed expression of four inflorescence development-related genes in Cannabis. Our findings establish important roles for CsMIKC1 in Cannabis, which could represent a previously unrecognized mechanism of inflorescence development regulated by ethylene.

Genetic and epigenetic basis of phytohormonal control of floral transition in plants

The timing of the developmental transition from the vegetative to the reproductive stage is critical for angiosperms, and is fine-tuned by the integration of endogenous factors and external environmental cues to ensure successful reproduction. Plants have evolved sophisticated mechanisms to response to diverse environmental or stress signals, and these can be mediated by hormones to coordinate flowering time. Phytohormones such as gibberellin, auxin, cytokinin, jasmonate, abscisic acid, ethylene, and brassinosteroids and the cross-talk among them are critical for the precise regulation of flowering time. Recent studies of the model flowering plant Arabidopsis have revealed that diverse transcription factors and epigenetic regulators play key roles in relation to the phytohormones that regulate floral transition. This review aims to summarize our current knowledge of the genetic and epigenetic mechanisms that underlie the phytohormonal control of floral transition in Arabidopsis, offering insights into how these processes are regulated and their implications for plant biology.

Flowering-associated gene expression and metabolic characteristics in adzuki bean (Vigna angularis L.) with different short-day induction periods

Background

The adzuki bean is a typical short-day plant and an important grain crop that is widely used due to its high nutritional and medicinal value. The adzuki bean flowering time is affected by multiple environmental factors, particularly the photoperiod. Adjusting the day length can induce flower synchronization in adzuki bean and accelerate the breeding process. In this study, we used RNA sequencing analysis to determine the effects of different day lengths on gene expression and metabolic characteristics related to adzuki bean flowering time.

Methods

'Tangshan hong xiao dou' was used as the experimental material in this study and field experiments were conducted in 2022 using a randomized block design with three treatments: short-day induction periods of 5 d (SD-5d), 10 d (SD-10d), and 15 d (SD-15d).

Results

A total of 5,939 differentially expressed genes (DEGs) were identified, of which 38.09% were up-regulated and 23.81% were down-regulated. Gene ontology enrichment analysis was performed on the target genes to identify common functions related to photosystems I and II. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified two pathways involved in the antenna protein and circadian rhythm. Furthermore, florescence was promoted by down-regulating genes in the circadian rhythm pathway through the blue light metabolic pathway; whereas, antenna proteins promoted flowering by enhancing the reception of light signals and accelerating electron transport. In these two metabolic pathways, the number of DEGs was the greatest between the SD-5d VS SD-15d groups. Real-time reverse transcription‒quantitative polymerase chain reaction analysis results of eight DEGs were consistent with the sequencing results. Thus, the sequencing results were accurate and reliable and eight genes were identified as candidates for the regulation of short-day induction at the adzuki bean seedling stage.

Conclusions

Short-day induction was able to down-regulate the expression of genes related to flowering according to the circadian rhythm and up-regulate the expression of certain genes in the antenna protein pathway. The results provide a theoretical reference for the molecular mechanism of short-day induction and multi-level information for future functional studies to verify the key genes regulating adzuki bean flowering.

Functional divergence of FTL9 and FTL10 in flowering control in rice

BACKGROUND

Floral transition in cereals is a critical phenomenon influenced by exogenous and endogenous signals, determining crop yield and reproduction. Flowering Locus T-like (FT-like) genes encode a mobile florigen, the main signaling molecule for flowering.

RESULTS

In this study, we characterized two FT-like genes, FTL9 and FTL10, to study their functional diversity in flowering control in rice. We compared independent mutant lines of ftl10 with WT and observed negligible differences in the flowering phenotype, or agronomic traits implying potentially redundant roles of FTL10 loss-of-function in flowering control in rice. Nevertheless, we found that overexpression of FTL10, but not FTL9, substantially accelerated flowering, indicating the flowering-promoting role of FTL10 and the divergent functions between FTL9 and FTL10 in flowering. Besides flowering, additive agronomic roles were observed for FTL10-OE regulating the number of effective panicles per plant, the number of primary branches per panicle, and spikelets per panicle without regulating seed size. Mechanistically, our Y2H and BiFC analyses demonstrate that FTL10, in contrast to FTL9, can interact with FD1 and GF14c, forming a flowering activation complex and thereby regulating flowering.

CONCLUSION

Altogether, our results elucidate the regulatory roles of FTL9 and FTL10 in flowering control, unveiling the molecular basis of functional divergence between FTL10 and FTL9, which provides mechanistic insights into shaping the dynamics of flowering time regulation in rice.

Insight from expression profiles of FT orthologs in plants: conserved photoperiodic transcriptional regulatory mechanisms

Floral transition from the vegetative to the reproductive stages is precisely regulated by both environmental and endogenous signals. Among these signals, photoperiod is one of the most important environmental factors for onset of flowering. A florigen, FLOWERING LOCUS T (FT) in Arabidopsis, has thought to be a major hub in the photoperiod-dependent flowering time regulation. Expression levels of FT likely correlates with potence of flowering. Under long days (LD), FT is mainly synthesized in leaves, and FT protein moves to shoot apical meristem (SAM) where it functions and in turns induces flowering. Recently, it has been reported that Arabidopsis grown under natural LD condition flowers earlier than that grown under laboratory LD condition, in which a red (R)/far-red (FR) ratio of light sources determines FT expression levels. Additionally, FT expression profile changes in response to combinatorial effects of FR light and photoperiod. FT orthologs exist in most of plants and functions are thought to be conserved. Although molecular mechanisms underlying photoperiodic transcriptional regulation of FT orthologs have been studied in several plants, such as rice, however, dynamics in expression profiles of FT orthologs have been less spotlighted. This review aims to revisit previously reported but overlooked expression information of FT orthologs from various plant species and classify these genes depending on the expression profiles. Plants, in general, could be classified into three groups depending on their photoperiodic flowering responses. Thus, we discuss relationship between photoperiodic responsiveness and expression of FT orthologs. Additionally, we also highlight the expression profiles of FT orthologs depending on their activities in flowering. Comparative analyses of diverse plant species will help to gain insight into molecular mechanisms for flowering in nature, and this can be utilized in the future for crop engineering to improve yield by controlling flowering time.

Comparative and functional analysis unveils the contribution of photoperiod to DNA methylation, sRNA accumulation, and gene expression variations in short-day and long-day grasses

Photoperiod employs complicated networks to regulate various developmental processes in plants, including flowering transition. However, the specific mechanisms by which photoperiod affects epigenetic modifications and gene expression variations in plants remain elusive. In this study, we conducted a comprehensive analysis of DNA methylation, small RNA (sRNA) accumulation, and gene expressions under different daylengths in facultative long-day (LD) grass Brachypodium distachyon and short-day (SD) grass rice. Our results showed that while overall DNA methylation levels were minimally affected by different photoperiods, CHH methylation levels were repressed under their favorable light conditions, particularly in rice. We identified numerous differentially methylated regions (DMRs) that were influenced by photoperiod in both plant species. Apart from differential sRNA clusters, we observed alterations in the expression of key components of the RNA-directed DNA methylation pathway, DNA methyltransferases, and demethylases, which may contribute to the identified photoperiod-influenced CHH DMRs. Furthermore, we identified many differentially expressed genes in response to different daylengths, some of which were associated with the DMRs. Notably, we discovered a photoperiod-responsive gene MYB11 in the transcriptome of B. distachyon, and further demonstrated its role as a flowering inhibitor by repressing FT1 transcription. Together, our comparative and functional analysis sheds light on the effects of daylength on DNA methylation, sRNA accumulation, and gene expression variations in LD and SD plants, thereby facilitating better designing breeding programs aimed at developing high-yield crops that can adapt to local growing seasons.

Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain

The rhizobacterial strain BJ3 showed 16S rDNA sequence similarity to species within the Burkholderia genus. Its complete genome sequence revealed a 97% match with Burkholderia contaminans and uncovered gene clusters essential for plant-growth-promoting traits (PGPTs). These clusters include genes responsible for producing indole acetic acid (IAA), osmolytes, non-ribosomal peptides (NRPS), volatile organic compounds (VOCs), siderophores, lipopolysaccharides, hydrolytic enzymes, and spermidine. Additionally, the genome contains genes for nitrogen fixation and phosphate solubilization, as well as a gene encoding 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The treatment with BJ3 enhanced root architecture, boosted vegetative growth, and accelerated early flowering in Arabidopsis. Treated seedlings also showed increased lignin production and antioxidant capabilities, as well as notably increased tolerance to water deficit and high salinity. An RNA-seq transcriptome analysis indicated that BJ3 treatment significantly activated genes related to immunity induction, hormone signaling, and vegetative growth. It specifically activated genes involved in the production of auxin, ethylene, and salicylic acid (SA), as well as genes involved in the synthesis of defense compounds like glucosinolates, camalexin, and terpenoids. The expression of AP2/ERF transcription factors was markedly increased. These findings highlight BJ3's potential to produce various bioactive metabolites and its ability to activate auxin, ethylene, and SA signaling in Arabidopsis, positioning it as a new Burkholderia strain that could significantly improve plant growth, stress resilience, and immune function.

CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits

How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.

Florigen-producing cells express FPF1-LIKE PROTEIN 1 that accelerates flowering and stem growth in long days with sunlight red/far-red ratio in Arabidopsis

Seasonal changes in spring induce flowering by expressing the florigen, FLOWERING LOCUS T (FT), in Arabidopsis. FT is expressed in unique phloem companion cells with unknown characteristics. The question of which genes are co-expressed with FT and whether they have roles in flowering remains elusive. Through tissue-specific translatome analysis, we discovered that under long-day conditions with the natural sunlight red/far-red ratio, the FT-producing cells express a gene encoding FPF1-LIKE PROTEIN 1 (FLP1). The master FT regulator, CONSTANS (CO), controls FLP1 expression, suggesting FLP1's involvement in the photoperiod pathway. FLP1 promotes early flowering independently of FT, is active in the shoot apical meristem, and induces the expression of SEPALLATA 3 (SEP3), a key E-class homeotic gene. Unlike FT, FLP1 facilitates inflorescence stem elongation. Our cumulative evidence indicates that FLP1 may act as a mobile signal. Thus, FLP1 orchestrates floral initiation together with FT and promotes inflorescence stem elongation during reproductive transitions.

Disrupting FKF1 homodimerization increases FT transcript levels in the evening by enhancing CO stabilization

KEY MESSAGE

FKF1 dimerization is crucial for proper FT levels to fine-tune flowering time. Attenuating FKF1 homodimerization increased CO abundance by enhancing its COP1 binding, thereby accelerating flowering under long days. In Arabidopsis (Arabidopsis thaliana), the blue-light photoreceptor FKF1 (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1) plays a key role in inducing the expression of FLOWERING LOCUS T (FT), encoding the main florigenic signal in plants, in the late afternoon under long-day conditions (LDs) by forming dimers with FT regulators. Although structural studies have unveiled a variant of FKF1 (FKF1 I160R) that disrupts homodimer formation in vitro, the mechanism by which disrupted FKF1 homodimer formation regulates flowering time remains elusive. In this study, we determined that the attenuation of FKF1 homodimer formation enhances FT expression in the evening by promoting the increased stability of CONSTANS (CO), a primary activator of FT, in the afternoon, thereby contributing to early flowering. In contrast to wild-type FKF1, introducing the FKF1 I160R variant into the fkf1 mutant led to increased FT expression under LDs. In addition, the FKF1 I160R variant exhibited diminished dimerization with FKF1, while its interaction with GIGANTEA (GI), a modulator of FKF1 function, was enhanced under LDs. Furthermore, the FKF1 I160R variant increased the level of CO in the afternoon under LDs by enhancing its binding to COP1, an E3 ubiquitin ligase responsible for CO degradation. These findings suggest that the regulation of FKF1 homodimerization and heterodimerization allows plants to finely adjust FT expression levels around dusk by modulating its interactions with GI and COP1.

The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem

Plants undergo a series of developmental phases throughout their life-cycle, each characterized by specific processes. Three critical features distinguish these phases: the arrangement of primordia (phyllotaxis), the timing of their differentiation (plastochron) and the characteristics of the lateral organs and axillary meristems. Identifying the unique molecular features of each phase, determining the molecular triggers that cause transitions and understanding the molecular mechanisms underlying these transitions are keys to gleaning a complete understanding of plant development. During the vegetative phase, the shoot apical meristem (SAM) facilitates continuous leaf and stem formation, with leaf development as the hallmark. The transition to the reproductive phase induces significant changes in these processes, driven mainly by the protein FT (FLOWERING LOCUS T) in Arabidopsis and proteins encoded by FT orthologs, which are specified as 'florigen'. These proteins are synthesized in leaves and transported to the SAM, and act as the primary flowering signal, although its impact varies among species. Within the SAM, florigen integrates with other signals, culminating in developmental changes. This review explores the central question of how florigen induces developmental phase transition in the SAM. Future research may combine phase transition studies, potentially revealing the florigen-induced developmental phase transition in the SAM.

Phylogeny and expression patterns of ERF genes that are potential reproductive inducers in hybrid larch

BACKGROUND

Larch is an important component of northern forests and a major cultivated tree species in restoration of forest cover using improved seed material. In recent years, the continuous low seed production has severely affected the production of improved variety seedlings and natural regeneration. However, research on the reproductive growth of gymnosperms is extremely scarce.

RESULTS

In this study, based on differential transcriptome analysis of two asexual reproductive phases, namely high-yield and low-yield, we further screened 5 ERF family genes that may affect the reproductive development of larch. We analyzed their genetic relationships and predicted their physicochemical properties. The expression patterns of these genes were analyzed in different tissues, developmental stages, hormone treatments, and environmental conditions in hybrid larch.

CONCLUSION

The results showed that all 5 genes were induced by low temperature and ABA, and their expression patterns in different tissues suggested a suppressive role in the development of female cones in larch. Among them, LkoERF3-like1 and LkoERF071 may be involved in the flowering age pathway. This study enriches the scarce research on reproductive development in gymnosperms and provides a theoretical basis and research direction for regulating the reproductive development of larch in seed orchards.