Feedback Regulation of FLC by FLOWERING LOCUS T (FT) and FD through a 5' FLC Promoter Region in Arabidopsis

AtR8 lncRNA integrates WRKY46 into ABA signaling to regulate seed and seeding growth in Arabidopsis

Seed germination plays a vital role in ensuring plant survival under unfavorable conditions. Abscisic acid (ABA) signaling is important for integrating environmental information to regulate seed germination. Despite the identification of numerous regulatory factors in ABA signaling pathways during seed germination, the transcriptional regulatory mechanisms influencing ABA signaling remain largely uncharacterized. Long non-coding RNAs (lncRNAs) have many physiological functions in diverse organisms. To date, only a few seed germination-related lncRNAs have been reported. The AtR8 lncRNA (259 nt) in Arabidopsis is transcribed by the RNA polymerase III. We previously determined that the AtR8 lncRNA affects the innate immunity of seedlings as well as hypocotyl elongation. It is also highly expressed in the germinating seeds and induced by ABA. In this study, its loss-of-function mutant (atr8) had incompletely formed siliques and seeds and a relatively low germination rate. The germination efficiency and primary root elongation were strongly affected by the ABA level. In addition, ABA signaling and AtEM6 expression were significantly induced in the atr8 mutant. Moreover, the AtEM6-overexpressing Arabidopsis plants and the atr8 mutant had similar ABA-dependent phenotypes. Genetic analyses clarified the relationship between AtR8 and AtEM6 during ABA signaling. The stress-dependent transcription of WRKY46 in the germinating atr8 seeds was significantly upregulated by ABA. AtEM6 expression increased in a wrky46 background. WRKY46 promoted AtEM6 expression by binding to the gene promoter W-boxes in a yeast one-hybrid assay. These results suggest the AtR8 lncRNA integrates WRKY46 into the ABA signaling pathway to regulate AtEM6 expression and influences seed germination and silique development in Arabidopsis. The study elucidated the mechanism of AtR8 lncRNA in regulating seed germination and seedling growth through mediate ABA signaling.

Genome-wide characterization of PEBP genes in Mung bean (Vigna radiata L.) with functional analysis of VrFT1 in relation to photoperiod

Mung bean (Vigna radiata L.), a widely cultivated legume, belongs to the Fabaceae family's Papilionoideae subfamily. Although Phosphatidylethanolamine-binding protein (PEBP) genes have been identified in several plant species, their presence and function in mung bean remain largely unexplored. In this study, we identified seven VrPEBP genes from mung bean and classified them into four clades: FT, MFT, TFL and FT-like. Cis-regulatory element analysis revealed that VrPEBP genes may play a role in light, hormone, and stress responses. Quantitative real-time PCR (qRT-PCR) analysis indicated that VrPEBPs were constitutively expressed in various tissues. However, tissue-specific expression patterns were observed among VrPEBP genes. Under short-day (SD) conditions, VrFT1 and VrMFT1 exhibited significantly higher expression levels than under long-day (LD) conditions at 8 and 4 h, respectively. Conversely, VrTFL2 and VrTFL3 showed significantly higher expression levels under LD conditions compared to SD conditions at 8 and 12 h, respectively. The varied expression patterns of these genes under different photoperiod suggest their potential involvement in the photoperiodic regulation of flowering in mung bean. Additionally, phenotypic analysis of transgenic Arabidopsis plants overexpressing VrFT1 revealed higher expression levels under SD conditions and predicted its role in promoting flowering. These results provide valuable insights into the evolution and function of PEBP genes in mung bean and lay the foundation for further research on their regulatory mechanisms and potential applications in mung bean improvement.

Deciphering the Role of SVP-Like Genes and Their Key Regulation Networks During Reproductive Cone Development in Pinus tabuliformis

Reproductive development plays an essential role in the perpetuation of genetic material and environmental adaptation. In angiosperms, the Short Vegetative Phase (SVP) serves as a flowering repressor, influencing the development of floral organs. In this study, heterologous transformation of Arabidopsis thaliana with SVP-like genes (PtSVL1 and PtSVL2) derived from Pinus tabuliformis significantly impacted stamen formation and pollen fertility, without altering flowering time. Gene co-expression networks revealed that SVP-like and SOC1-like genes function as key coregulatory transcription factors during the initial stages of cone development in P. tabuliformis. Interestingly, the regulatory module of SOC1 regulated by SVP in angiosperms is absent in conifers and conifer SVP-like exercises its function in a form that is physically bound to SOC1-like. Furthermore, combining the yeast one-hybrid scanning with co-expression network analysis, revealed that SPLs and TPSs were the principal downstream target genes of PtSVL1. Notably, the PtSPL16 promoter is positively regulated by PtSVL1, and overexpression of PtSPL16 results in delayed flowering in Arabidopsis, suggesting that the PtSVL1-PtSPL16 module plays a crucial role in regulating reproductive development in conifers. Collectively, these findings enhance our understanding of the roles of SVP-like genes in conifers and the key regulatory networks centred on PtSVL1 during reproductive cone development.

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.

Phosphatidyl Ethanolamine Binding Protein FLOWERING LOCUS T-like 12 (OsFTL12) Regulates the Rice Heading Date under Different Day-Length Conditions

Plant FLOWERING LOCUS T-Like (FTL) genes often redundantly duplicate on chromosomes and functionally diverge to modulate reproductive traits. Rice harbors thirteen FTL genes, the functions of which are still not clear, except for the Hd3a and RFT genes. Here, we identified the molecular detail of OsFTL12 in rice reproductive stage. OsFTL12 encoding protein contained PEBP domain and localized into the nucleus, which transcripts specifically expressed in the shoot and leaf blade with high abundance. Further GUS-staining results show the OsFTL12 promoter activity highly expressed in the leaf and stem. OsFTL12 knock-out concurrently exhibited early flowering phenotype under the short- and long-day conditions as compared with wild-type and over-expression plants, which independently regulates flowering without an involved Hd1/Hd3a and Ehd1/RFT pathway. Further, an AT-hook protein OsATH1 was identified to act as upstream regulator of OsFTL12, as the knock-out OsATH1 elevated the OsFTL12 expression by modifying Histone H3 acetylation abundance. According to the dissection of OsFTL12 molecular functions, our study expanded the roles intellectual function of OsFTL12 in the mediating of a rice heading date.

COOLAIR and PRC2 function in parallel to silence FLC during vernalization

Noncoding transcription induces chromatin changes that can mediate environmental responsiveness, but the causes and consequences of these mechanisms are still unclear. Here, we investigate how antisense transcription (termed COOLAIR) interfaces with Polycomb Repressive Complex 2 (PRC2) silencing during winter-induced epigenetic regulation of Arabidopsis FLOWERING LOCUS C (FLC). We use genetic and chromatin analyses on lines ineffective or hyperactive for the antisense pathway in combination with computational modeling to define the mechanisms underlying FLC repression. Our results show that FLC is silenced through pathways that function with different dynamics: a COOLAIR transcription-mediated pathway capable of fast response and in parallel a slow PRC2 switching mechanism that maintains each allele in an epigenetically silenced state. Components of both the COOLAIR and PRC2 pathways are regulated by a common transcriptional regulator (NTL8), which accumulates by reduced dilution due to slow growth at low temperature. The parallel activities of the regulatory steps, and their control by temperature-dependent growth dynamics, create a flexible system for registering widely fluctuating natural temperature conditions that change year on year, and yet ensure robust epigenetic silencing of FLC.

Vernalization-triggered expression of the antisense transcript COOLAIR is mediated by CBF genes

To synchronize flowering time with spring, many plants undergo vernalization, a floral-promotion process triggered by exposure to long-term winter cold. In Arabidopsis thaliana, this is achieved through cold-mediated epigenetic silencing of the floral repressor, FLOWERING LOCUS C (FLC). COOLAIR, a cold-induced antisense RNA transcribed from the FLC locus, has been proposed to facilitate FLC silencing. Here, we show that C-repeat (CRT)/dehydration-responsive elements (DREs) at the 3'-end of FLC and CRT/DRE-binding factors (CBFs) are required for cold-mediated expression of COOLAIR. CBFs bind to CRT/DREs at the 3'-end of FLC, both in vitro and in vivo, and CBF levels increase gradually during vernalization. Cold-induced COOLAIR expression is severely impaired in cbfs mutants in which all CBF genes are knocked-out. Conversely, CBF-overexpressing plants show increased COOLAIR levels even at warm temperatures. We show that COOLAIR is induced by CBFs during early stages of vernalization but COOLAIR levels decrease in later phases as FLC chromatin transitions to an inactive state to which CBFs can no longer bind. We also demonstrate that cbfs and FLC_ΔCOOLAIR mutants exhibit a normal vernalization response despite their inability to activate COOLAIR expression during cold, revealing that COOLAIR is not required for the vernalization process.

Rice CENTRORADIALIS 2 regulates seed germination and salt tolerance via ABA-mediated pathway

A FT/TFL1 subfamily gene, rice CENTRORADIALIS 2, also known as RCN1, regulates seed germination and increase salt tolerance via ABA-mediated pathway. The ABA synthesis and metabolism related genes were changed relative expression levels. Seed germination is a complex biological process that is affected by many factors. Although a number of germination-related genes have been reported, the molecular mechanism of germination regulation has not yet been fully elucidated. Here, we reported that the rice OsCEN2 gene can negatively regulate seed germination. The germination speed of OsCEN2-RNAi seeds was significantly faster while that of OsCEN2-overexpression (OE) seeds was slower than that of the wild type (WT). The results of qRT-PCR showed that the OsCEN2 expression was increased in the early stage of seed germination. Exogenous application of abscisic acid (ABA) on seeds and seedlings showed that OsCEN2-OE seeds and seedlings were highly sensitive to ABA during germination and post-germination growth, respectively. The determination of endogenous ABA content in seeds also showed that the ABA content of OsCEN2-RNAi seeds was lower, while that of OsCEN2-OE seeds was higher. Moreover, the transgenic plants changed salt tolerance because of the altered ABA level. In addition, differences were also observed in the expression of genes related to ABA synthesis and metabolism in the seeds of OsCEN2-transgenic lines. This study reveals that OsCEN2 regulates the germination speed by affecting the content of ABA during seed germination and provides a theoretical basis for research on rice direct seeding.

Genome-wide characterization of PEBP gene family in Perilla frutescens and PfFT1 promotes flowering time in Arabidopsis thaliana

Phosphatidylethanolamine-binding proteins (PEBP) family plays important roles in regulating plant flowering time and morphogenesis. However, geneme-wide identification and functional analysis of PEBP genes in the rigorous short-day plant Perilla frutescens (PfPEBP) have not been studied. In this study, 10 PfPEBP were identified and divided into three subfamilies based on their phylogenetic relationships: FT-like, TFL1-like and MFT-like. Gene structure analysis showed that all PfPEBP genes contain 4 exons and 3 introns. Motifs DPDxP and GIHR essential for anion-binding activity are highly conserved in PfPEBP. A large number of light-responsive elements were detected in promoter regions of PfPEBP. Gene expression of PfFT1 exhibited a diurnal rhythm. It was highly expressed in leaves under the short-day photoperiod, but higher in flowers and seeds under the long-day photoperiod. Overexpression of PfFT1 in Arabidopsis thaliana not only promoted early flowering of Col-0 or Ler, but also rescued the late flowering phenotype of ft-1 mutant. We concluded that PfFT1 promotes early flowering by regulating the expression of flowering-related genes AtAP1, AtLFY, AtFUL and AtSOC1. In conclusion, our results provided valuable information for elucidating the functions of PfPEBP in P. frutescens and shed light on the promoting effect of PfFT1 on flowering.

Effects of low temperature on flowering and the expression of related genes in Loropetalum chinense var. rubrum

INTRODUCTION

Loropetalum chinense var. rubrum blooms 2-3 times a year, among which the autumn flowering period has great potential for exploitation, but the number of flowers in the autumn flowering period is much smaller than that in the spring flowering period.

METHODS

Using 'Hei Zhenzhu' and 'Xiangnong Xiangyun' as experimental materials, the winter growth environment of L. chinense var. rubrum in Changsha, Hunan Province was simulated by setting a low temperature of 6-10°C in an artificial climate chamber to investigate the effect of winter low temperature on the flowering traits and related gene expression of L. chinense var. rubrum.

RESULTS

The results showed that after 45 days of low temperature culture and a subsequent period of 25°C greenhouse culture, flower buds and flowers started to appear on days 24 and 33 of 25°C greenhouse culture for 'Hei Zhenzhu', and flower buds and flowers started to appear on days 21 and 33 of 25°C greenhouse culture for 'Xiangnong Xiangyun'. The absolute growth rate of buds showed a 'Up-Down' pattern during the 7-28 days of low temperature culture; the chlorophyll fluorescence decay rate (Rfd) of both materials showed a 'Down-Up-Down' pattern during this period. The non-photochemical quenching coefficient (NPQ) showed the same trend as Rfd, and the photochemical quenching coefficient (QP) fluctuated above and below 0.05. The expression of AP1 and FT similar genes of L. chinense var. rubrum gradually increased after the beginning of low temperature culture, reaching the highest expression on day 14 and day 28, respectively, and the expression of both in the experimental group was higher than that in the control group. The expressions of FLC, SVP and TFL1 similar genes all decreased gradually with low temperature culture, among which the expressions of FLC similar genes and TFL1 similar genes in the experimental group were extremely significantly lower than those in the control group; in the experimental group, the expressions of GA3 similar genes were all extremely significantly higher than those in the control group, and the expressions all increased with the increase of low temperature culture time.

DISCUSSION

We found that the high expression of gibberellin genes may play an important role in the process of low temperature promotion of L. chinense var. rubrum flowering, and in the future, it may be possible to regulate L. chinense var. rubrum flowering by simply spraying exogenous gibberellin instead of the promotion effect of low temperature.

Comparative Genomic and Expression Analysis Insight into Evolutionary Characteristics of PEBP Genes in Cultivated Peanuts and Their Roles in Floral Induction

Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in regulating flowering time and various developmental processes. Functions and expression patterns in cultivated peanuts (Arachis hypogaea L.) remain unknown. In this study, 33 PEBP genes in cultivated peanuts were identified and divided into four subgroups: FT, TFL, MFT and FT-like. Gene structure analysis showed that orthologs from A and B genomes in cultivated peanuts had highly similar structures, but some orthologous genes have subgenomic dominance. Gene collinearity and phylogenetic analysis explain that some PEBP genes play key roles in evolution. Cis-element analysis revealed that PEBP genes are mainly regulated by hormones, light signals and stress-related pathways. Multiple PEPB genes had different expression patterns between early and late-flowering genotypes. Further detection of its response to temperature and photoperiod revealed that PEBPs ArahyM2THPA, ArahyEM6VH3, Arahy4GAQ4U, ArahyIZ8FG5, ArahyG6F3P2, ArahyLUT2QN, ArahyDYRS20 and ArahyBBG51B were the key genes controlling the flowering response to different flowering time genotypes, photoperiods and temperature. This study laid the foundation for the functional study of the PEBP gene in cultivated peanuts and the adaptation of peanuts to different environments.

BnGF14-2c Positively Regulates Flowering via the Vernalization Pathway in Semi-Winter Rapeseed

14-3-3s are general regulatory factors (GF14s or GRFs) involved in a variety of physiological regulations in plants, including the control of flowering time. However, there are poorly relevant reports in rapeseed so far. In this study, we identified a homologous 14-3-3 gene BnGF14-2c (AtGRF2_Like in Brassica napus) in rapeseed based on bioinformatic analysis by using the sequences of the flowering-related 14-3-3s in other plant species. Then, we found that overexpression of BnGF14-2c in the semi-winter rapeseed “93275” promoted flowering without vernalization. Moreover, both yeast two-hybrid and bimolecular fluorescence complementation analysis indicated that BnGF14-2c may interact with two vernalization-related flowering regulators BnFT.A02 and BnFLC.A10., respectively. qPCR analysis showed that the expression of BnFT (AtFT_Like) was increased and the expression of two selected vernalization-related genes were reduced in the overexpression transgenic plants. Further investigation on subcellular localization demonstrated that BnGF14-2c localized in the nucleus and cytoplasm. The results of RNA-seq analysis and GUS staining indicated that BnGF14-2c is ubiquitously expressed except for mature seed coat. In general, the interaction of 14-3-3 and FLC was firstly documented in this study, indicating BnGF14-2c may act as a positive regulator of flowering in rapeseed, which is worthy for more in-depth exploration.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

A MADS-box gene with similarity to FLC is induced by cold and correlated with epigenetic changes to control budbreak in kiwifruit

Temperate perennials require exposure to chilling temperatures to resume growth in the following spring. Growth and dormancy cycles are controlled by complex genetic regulatory networks and are governed by epigenetic mechanisms, but the specific genes and mechanisms remain poorly understood. To understand how seasonal changes and chilling regulate dormancy and growth in the woody perennial vine kiwifruit (Ac, Actinidia chinensis), a transcriptome study of kiwifruit buds in the field and controlled conditions was performed. A MADS-box gene with homology to Arabidopsis FLOWERING LOCUS C (FLC) was identified and characterized. Elevated expression of AcFLC-like (AcFLCL) was detected during bud dormancy and chilling. A long noncoding (lnc) antisense transcript with an expression pattern opposite to AcFLCL and shorter sense noncoding RNAs were identified. Chilling induced an increase in trimethylation of lysine-4 of histone H3 (H3K4me3) in the 5' end of the gene, indicating multiple layers of epigenetic regulation in response to cold. Overexpression of AcFLCL in kiwifruit gave rise to plants with earlier budbreak, whilst gene editing using CRISPR-Cas9 resulted in transgenic lines with substantially delayed budbreak, suggesting a role in activation of growth. These results have implications for the future management and breeding of perennials for resilience to changing climate.

Germinating seed can sense low temperature for the floral transition and vernalization of winter rapeseed (Brassica rapa)

The hybrid production of winter rapeseed is limited by the difficult vernalization processes. Thus, floral regulation of winter rapeseed parental lines cannot be executed through selection of sowing time during hybrid production. Therefore, in this study, strong winter rapeseed was used as the material to analyse the floral transition mechanism of germinating seed vernalization. Results demonstrated that germinating seeds could sense low temperatures and complete vernalization following a low temperature treatment for 56.5 d with a 100 % vernalization rate. The regression equation between vernalization rate (y) and vernalization treatment days (x) was determined as y = 0.019x - 0.0765 (R² = 0.8529). When the vernalization treatment time was prolonged, the vernalization rate and fruiting ability increased rapidly, and variations were observed in the membrane lipid oxidation and physiological characteristics. Furthermore, at the prolonged treatment time of 10-50 d, the salicylic acid (SA) content continued to decrease, with values significantly lower than those of the control. SA content is significantly positively correlated with the level of BrFLC transcription and a significantly negatively correlated with the vernalization rate of germinating seeds. Moreover, the expressions of genes associated with SA biosynthesis, SA signal transduction, the flowering key negative regulators were suppressed and that of positive regulators were promoted during vernalization. These results suggest that SA as a floral repressor is involved in the regulation of the vernalization process of winter rapeseed germination seeds. In addition, SA may be related to the counting dosage of vernalization.

Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana

Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.

Natural temperature fluctuations promote COOLAIR regulation of FLC

In this study, Zhao et al. set out to characterize how plants respond to cold through regulation of FLC expression. Using genetics and genomics approaches, the authors reveal how natural temperature fluctuations promote COOLAIR regulation of FLC, with the first autumn frost acting as a key indicator of autumn/winter arrival.

Plants monitor many aspects of their fluctuating environments to help align their development with seasons. Molecular understanding of how noisy temperature cues are registered has emerged from dissection of vernalization in Arabidopsis, which involves a multiphase cold-dependent silencing of the floral repressor locus FLOWERING LOCUS C (FLC). Cold-induced transcriptional silencing precedes a low probability PRC2 epigenetic switching mechanism. The epigenetic switch requires the absence of warm temperatures as well as long-term cold exposure. However, the natural temperature inputs into the earlier transcriptional silencing phase are less well understood. Here, through investigation of Arabidopsis accessions in natural and climatically distinct field sites, we show that the first seasonal frost strongly induces expression of COOLAIR, the antisense transcripts at FLC. Chamber experiments delivering a constant mean temperature with different fluctuations showed the freezing induction of COOLAIR correlates with stronger repression of FLC mRNA. Identification of a mutant that ectopically activates COOLAIR revealed how COOLAIR up-regulation can directly reduce FLC expression. Consistent with this, transgenes designed to knockout COOLAIR perturbed the early phase of FLC silencing. However, all transgenes designed to remove COOLAIR resulted in increased production of novel convergent FLC antisense transcripts. Our study reveals how natural temperature fluctuations promote COOLAIR regulation of FLC, with the first autumn frost acting as a key indicator of autumn/winter arrival.

A light-regulated gene, TaLWD1L-A, affects flowering time in transgenic wheat (Triticum aestivum L.)

Flowering time is an important agronomic trait that greatly influences plant architecture and grain yield in cereal crops. The present study identified a light-regulated gene, TaLWD1L-A, from hexaploid wheat that encodes a WD40 domain-containing protein. TaLWD1L-A was localized in the nucleus. Phenotypic analysis demonstrated that TaLWD1L-A overexpression in transgenic wheat led to an obvious early flowering phenotype. Upregulation of the floral activator gene TaFT1 caused the early flowering phenotype in transgenic wheat plants. TaLWD1L-A also affected the expression of circadian clock genes, including TaTOC1, TaLHY, TaPRR59, TaPRR73 and TaPRR95, and indirectly regulated the expression of the TaFT1 in transgenic plants by affecting the expression of vernalization-related genes TaVRN1 and TaVRN2 and photoperiod-related genes TaPpd-1 and TaGI. The early flowering phenotype in TaLWD1L-A-overexpressing transgenic lines led to a relatively shorter phenotype and yield reduction. Our results revealed that TaLWD1L-A affected the expression of circadian clock-related genes and played an important role in wheat flowering regulation by influencing the expression of genes related to vernalization and photoperiod pathways.

Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana

Vernalization accelerates flowering after prolonged winter cold. Transcriptional and epigenetic changes are known to be involved in the regulation of the vernalization response. Despite intensive applications of next-generation sequencing in diverse aspects of plant research, genome-wide transcriptome and epigenome profiling during the vernalization response has not been conducted. In this work, to our knowledge, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in Arabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold exposure. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development-related transcription factors, which resulted in either inhibition of transcription or a bivalent status of the genes. Lastly, FLC-like and VIN3-like genes were identified that appear to be novel components of the vernalization pathway.

Molecular Regulation of Plant Responses to Environmental Temperatures

Temperature is a key factor governing the growth and development, distribution, and seasonal behavior of plants. The entire plant life cycle is affected by environmental temperatures. Plants grow rapidly and exhibit specific changes in morphology under mild average temperature conditions, a response termed thermomorphogenesis. When exposed to chilling or moist chilling low temperatures, flowering or seed germination is accelerated in some plant species; these processes are known as vernalization and cold stratification, respectively. Interestingly, once many temperate plants are exposed to chilling temperatures for some time, they can acquire the ability to resist freezing stress, a process termed cold acclimation. In the face of global climate change, heat stress has emerged as a frequent challenge, which adversely affects plant growth and development. In this review, we summarize and discuss recent progress in dissecting the molecular mechanisms regulating plant thermomorphogenesis, vernalization, and responses to extreme temperatures. We also discuss the remaining issues that are crucial for understanding the interactions between plants and temperature.

Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC

In Arabidopsis thaliana, the cold-induced epigenetic regulation of FLOWERING LOCUS C (FLC) involves distinct phases of Polycomb repressive complex 2 (PRC2) silencing. During cold, a PHD-PRC2 complex metastably and digitally nucleates H3K27me3 within FLC On return to warm, PHD-PRC2 spreads across the locus delivering H3K27me3 to maintain long-term silencing. Here, we studied natural variation in this process in Arabidopsis accessions, exploring Lov-1, which shows FLC reactivation on return to warm, a feature characteristic of FLC in perennial Brassicaceae This analysis identifies an additional phase in this Polycomb silencing mechanism downstream from H3K27me3 spreading. In this long-term silencing (perpetuated) phase, the PHD proteins are lost from the nucleation region and silencing is likely maintained by the read-write feedbacks associated with H3K27me3. A combination of noncoding SNPs in the nucleation region mediates instability in this long-term silencing phase with the result that Lov-1 FLC frequently digitally reactivates in individual cells, with a probability that diminishes with increasing cold duration. We propose that this decrease in reactivation probability is due to reduced DNA replication after flowering. Overall, this work defines an additional phase in the Polycomb mechanism instrumental in natural variation of silencing, and provides avenues to dissect broader evolutionary changes at FLC.

Genetic and Epigenetic Understanding of the Seasonal Timing of Flowering

The developmental transition to flowering in many plants is timed by changing seasons, which enables plants to flower at a season that is favorable for seed production. Many plants grown at high latitudes perceive the seasonal cues of changing day length and/or winter cold (prolonged cold exposure), to regulate the expression of flowering-regulatory genes through the photoperiod pathway and/or vernalization pathway, and thus align flowering with a particular season. Recent studies in the model flowering plant Arabidopsis thaliana have revealed that diverse transcription factors engage various chromatin modifiers to regulate several key flowering-regulatory genes including FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) in response to seasonal signals. Here, we summarize the current understanding of molecular and chromatin-regulatory or epigenetic mechanisms underlying the vernalization response and photoperiodic control of flowering in Arabidopsis. Moreover, the conservation and divergence of regulatory mechanisms for seasonal flowering in crops and other plants are briefly discussed.

The Role of FLOWERING LOCUS C Relatives in Cereals

FLOWERING LOCUS C (FLC) is one of the best characterized genes in plant research and is integral to vernalization-dependent flowering time regulation. Yet, despite the abundance of information on this gene and its relatives in Arabidopsis thaliana, the role FLC genes play in other species, in particular cereal crops and temperate grasses, remains elusive. This has been due in part to the comparative reduced availability of bioinformatic and mutant resources in cereals but also on the dominant effect in cereals of the VERNALIZATION (VRN) genes on the developmental process most associated with FLC in Arabidopsis. The strong effect of the VRN genes has led researchers to believe that the entire process of vernalization must have evolved separately in Arabidopsis and cereals. Yet, since the confirmation of the existence of FLC-like genes in monocots, new light has been shed on the roles these genes play in both vernalization and other mechanisms to fine tune development in response to specific environmental conditions. Comparisons of FLC gene function and their genetic and epigenetic regulation can now be made between Arabidopsis and cereals and how they overlap and diversify is coming into focus. With the advancement of genome editing techniques, further study on these genes is becoming increasingly easier, enabling us to investigate just how essential FLC-like genes are to modulating flowering time behavior in cereals.

RNA Splicing of FLC Modulates the Transition to Flowering

Flowering is a critical stage of plant development and is closely correlated with seed production and crop yield. Flowering transition is regulated by complex genetic networks in response to endogenous and environmental signals. FLOWERING LOCUS C (FLC) is a central repressor in the flowering transition of Arabidopsis thaliana. The regulation of FLC expression is well studied at transcriptional and post-transcriptional levels. A subset of antisense transcripts from FLC locus, collectively termed cold-induced long antisense intragenic RNAs (COOLAIR), repress FLC expression under cold exposure. Recent studies have provided important insights into the alternative splicing of COOLAIR and FLC sense transcripts in response to developmental and environmental cues. Herein, at the 20th anniversary of FLC functional identification, we summarise new research advances in the alternative splicing of FLC sense and antisense transcripts that regulates flowering.