Regulation Of Flowering Time Research Articles

Comprehensive identification of major flowering time genes and their combinations, which determined rice distribution in Northeast China

Flowering time of rice (Oryza sativa L.) is among the most important agronomic traits for regional adaptation and grain yield. To date, a number of genes or quantitative trait loci (QTLs) controlling flowering time have been identified in rice, and diverse natural allelic variations for these flowering genes have been revealed, which suggested that the underlying regulation mechanism of flowering time in rice is very complicated. Northeast China is a major cultivation region for temperate japonica rice, where the temperature is cooler and the day length is longer. The regional adaptability of local rice cultivar is substantially different from that of other regions. Recently, some flowering genes have been proved to play roles in regulating flowering time of local cultivars. However, a comprehensive analysis of the effectiveness of these flowering genes has not been performed. In the present study, 395 cultivars collected from Northeast China is re-sequenced, SNP and InDel markers were called for 23 selected flowering-related genes. The heading date of these cultivars was also investigated for three consecutive years. Through association analysis, we found that Hd2, Hd4, and Hd5 are major flowering repressors, whereas Dth2 and Hd18 are major flowering promoters. Furthermore, Hd6 and Hd16 were identified as minor flowering repressors, and Hd17 was minor flowering promoter, in that their effectiveness can exclusively be detected when both Hd2 and Hd4 are functional. Collectively, we comprehensively identified the major and minor flowering genes which determine flowering time of temperate japonica rice grown in Northeast China.

Florigen and anti-florigen: flowering regulation in horticultural crops.

Flowering time regulation has significant effects on the agricultural and horticultural industries. Plants respond to changing environments and produce appropriate floral inducers (florigens) or inhibitors (anti-florigens) that determine flowering time. Recent studies have demonstrated that members of two homologous proteins, FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1), act as florigen and anti-florigen, respectively. Studies in diverse plant species have revealed universal but diverse roles of the FT/TFL1 gene family in many developmental processes. Recent studies in several crop species have revealed that modification of flowering responses, either due to mutations in the florigen/anti-florigen gene itself, or by modulation of the regulatory pathway, is crucial for crop domestication. The FT/TFL1 gene family could be an important potential breeding target in many crop species.

The autonomous flowering-time pathway pleiotropically regulates seed germination in Arabidopsis thaliana.

Two critical developmental transitions in plants are seed germination and flowering, and the timing of these transitions has strong fitness consequences. How genetically independent the regulation of these transitions is can influence the expression of life cycles. This study tested whether genes in the autonomous flowering-time pathway pleiotropically regulate flowering time and seed germination in the genetic model Arabidopsis thaliana, and tested whether the interactions among those genes are concordant between flowering and germination stages. Several autonomous-pathway genes promote flowering and impede germination. Moreover, the interactions among those genes were highly concordant between the regulation of flowering and germination. Despite some degree of functional divergence between the regulation of flowering and germination by autonomous-pathway genes, the autonomous pathway is highly functionally conserved across life stages. Therefore, genes in the autonomous flowering-time pathway are likely to contribute to genetic correlations between flowering and seed germination, possibly contributing to the winter-annual life history.

Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple

Ethylene has long been used to promote flowering in pineapple production. Ethylene-induced flowering is dose dependent, with a critical threshold level of ethylene response factors needed to trigger flowering. The mechanism of ethylene-induced flowering is still unclear. Here, we integrated isoform sequencing (iso-seq), Illumina short-reads sequencing and whole-genome bisulfite sequencing (WGBS) to explore the early changes of transcriptomic and DNA methylation in pineapple following high-concentration ethylene (HE) and low-concentration ethylene (LE) treatment. Iso-seq produced 122,338 transcripts, including 26,893 alternative splicing isoforms, 8,090 novel transcripts and 12,536 candidate long non-coding RNAs. The WGBS results suggested a decrease in CG methylation and increase in CHH methylation following HE treatment. The LE and HE treatments induced drastic changes in transcriptome and DNA methylome, with LE inducing the initial response to flower induction and HE inducing the subsequent response. The dose-dependent induction of FLOWERING LOCUS T-like genes (FTLs) may have contributed to dose-dependent flowering induction in pineapple by ethylene. Alterations in DNA methylation, lncRNAs and multiple genes may be involved in the regulation of FTLs. Our data provided a landscape of the transcriptome and DNA methylome and revealed a candidate network that regulates flowering time in pineapple, which may promote further studies.

Epitranscriptomics and Flowering: mRNA Methylation/Demethylation Regulates Flowering Time

DNA modifications such as methylation serve as epigenetic markers that influence gene expression and function. The importance of similar modifications in RNA is gaining appreciation, leading to the emergence of epitranscriptomic analyses. RNA modifications appear to be a general feature of

The F-box protein FKF1 inhibits dimerization of COP1 in the control of photoperiodic flowering

In Arabidopsis thaliana, CONSTANS (CO) plays an essential role in the regulation of photoperiodic flowering under long-day conditions. CO protein is stable only in the afternoon of long days, when it induces the expression of FLOWERING LOCUS T (FT), which promotes flowering. The blue-light photoreceptor FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (FKF1) interacts with CO and stabilizes it by an unknown mechanism. Here, we provide genetic and biochemical evidence that FKF1 inhibits CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1)-dependent CO degradation. Light-activated FKF1 has no apparent effect on COP1 stability but can interact with and negatively regulate COP1. We show that FKF1 can inhibit COP1 homo-dimerization. Mutation of the coiled-coil domain in COP1, which prevents dimer formation, impairs COP1 function in coordinating flowering time. Based on these results, we propose a model whereby the light- and day length-dependent interaction between FKF1 and COP1 controls CO stability to regulate flowering time.

Production and characterization of polyclonal antibody against Arabidopsis GIGANTEA, a circadian clock controlled flowering time regulator

Arabidopsis GIGANTEA (GI) is encoded by a single gene and highly conserved among vascular plants and its mutants display pleiotropic phenotypes involved in diverse biological processes such as light signaling, circadian clock, and sucrose metabolism as well as abiotic stress responses. However, molecular mechanisms of GI are largely unknown due to the lack of useful antibody. To date, the epitope tags have been widely used to detect GI in plants, but it needs to generate the transgenic plants which take a few months. Here, we produced polyclonal α-GI antibody using truncated variants of GI having amino-terminal (1–858 aa) and carboxyl-terminal (920–1173) regions as antigens. Both recombinant His-GI1-858 and His-GI920–1173 proteins were individually and successfully expressed in E. coli and immunized into rabbit. Anti-serum was purified by antigenspecific affinity purification method using both recombinant His-GI1–858 and His-GI920–1173 proteins. Purified polyclonal α-GI antibody not only detected endogenous GI proteins in wild-type Arabidopsis plants, but also reenacted its diel oscillations. Furthermore, the antibody showed cross-reactivity with the GI orthologs in other plants such as Chinese cabbage, rape and tomato. Our polyclonal GI antibody could help to determine the molecular mechanisms of GI involved in largely unknown pleiotropic responses in plants.

The Transcription Factor COL12 Is a Substrate of the COP1/SPA E3 Ligase and Regulates Flowering Time and Plant Architecture.

The ambient light environment controls many aspects of plant development throughout a plant's life cycle. Such complex control is achieved because a key repressor of light signaling, the Arabidopsis (Arabidopsis thaliana) COP1/SPA E3 ubiquitin ligase causes the degradation of multiple regulators of endogenous developmental pathways. This includes the CONSTANS (CO) transcription factor that is responsible for photoperiodic control of flowering time. There are 16 CO-like proteins whose functions are only partly understood. Here, we show that 14 CO-like (COL) proteins bind CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and SUPPRESSOR OF PHYTOCHROME A-105 (SPA)1 in vitro. We subsequently focused on COL12 and show that COL12 binds COP1 and SPA proteins in vivo. The COL12 protein is degraded in darkness in a COP1-dependent fashion, indicating that COL12 is a substrate of the COP1/SPA ubiquitin ligase. Overexpression of COL12 causes late flowering specifically in long day conditions by decreasing the expression of FLOWERING LOCUS T This phenotype is genetically dependent on CO. Consistent with this finding, COL12 physically interacts with CO in vivo, suggesting that COL12 represses flowering by inhibiting CO protein function. We show that COL12 overexpression did not alter CO protein stability. It is therefore likely that COL12 represses the activity of CO rather than CO levels. Overexpression of COL12 also affects plant architecture by increasing the number of rosette branches and reducing inflorescence height. These phenotypes are CO independent. Hence, we suggest that COL12 affects plant development through CO-dependent and CO-independent mechanisms.

RETRACTED ARTICLE: SOC1 and AGL24 interact with AGL18-1, not the other family members AGL18-2 and AGL18-3 in Brassica juncea

Many MCM1-AGAMOUS-DEFICIENS-SRF (MADS) genes have been proved to play an important role in the flowering time regulation of plants. The flowering-inhibiting factor AGAMOUS-LIKE 18 (AGL18) integrates into the two flowering-activating factors SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and AGAMOUS-LIKE 24 (AGL24), which play an important role during the plant developmental stages of the flowering pathway. However, it remains unknown whether and how the AGL18 protein directly interacts with SOC1 and/or AGL24 genes to regulate flowering time in Brassica juncea. In this study, three members (AGL18-1 in florescence, AGL18-2 and AGL18-3 in young seedlings) of the AGL18 family, and SOC1 and AGL24 in florescence were cloned in Brassica juncea. Yeast One-Hybrid assays and Dual-Glo® Luciferase assays showed that the SOC1 and AGL24 promoters interacted only with AGL18-1 protein, not AGL18-2 and AGL18-3. The typical conserved structure of the M-domain of AGL18-1 was the key region that mediated the interaction between the AGL18-1 protein and SOC1 promoter, and the I-domain, K-domain and C-domain did not regulate the interaction of AGL18-1/SOC1. In contrast, the K-domain and M-domain in AGL18-1 could mediate the interaction between the AGL18-1 protein and AGL24 promoter. This indicated that the AGL18-1 protein must have its unique functions that differed from AGL18-2 and AGL18-3. This work provides valuable information for in-depth studies into the molecular mechanisms of the AGL18 protein with SOC1 and AGL24 for flowering time control of Brassica juncea.

Pleiotropic effect of the Flowering Locus C on plant resistance and defence against insect herbivores

Abstract Plants vary widely in the extent to which they defend themselves against herbivores. Because the resources available to plants are often site‐specific, variation among sites dictates investment into defence and may reveal a growth–defence trade‐off. Moreover, plants that have evolved different life‐history strategies in different environments may situate themselves on this trade‐off curve differently. For instance, plants that flower later have a longer vegetative life span and may accordingly defend themselves differently than those that flower earlier. Here, we tested whether late‐flowering plants, with a longer vegetative life span, invest more in defence than early‐flowering plants, using recombinant genotypes of the annual herb Cardamine hirsuta that differ in flowering time as a result of differences in the activity of the major floral repressor Flowering Locus C (FLC). We found that variation at FLC was mainly responsible for regulating flowering time and allocation to reproduction, but this partially depended on where the plants grew. We also found that variation at FLC mediated plant allocation to defence, with late‐flowering plants producing higher levels of total glucosinolates and stress‐related phytohormones. Nonetheless, plant growth and the qualitative values of plant defence and plant resistance against specialist herbivores were mainly independent from FLC. Synthesis. Our results highlight pleiotropic effects associated with flowering‐time genes that might influence plant defence and plant–herbivore interactions.

Arabidopsis inositol polyphosphate multikinase delays flowering time through mediating transcriptional activation of FLOWERING LOCUS C.

Timely flowering is critical for successful reproduction and seed yield in plants. A diverse range of regulators have been found to control flowering time in response to environmental and endogenous signals. Among these regulators, FLOWERING LOCUS C (FLC) acts as a central repressor of floral transition by blocking the expression of flowering integrator genes. Here, we report that Arabidopsis inositol polyphosphate multikinase (AtIPK2β) functions in flowering time control by mediating transcriptional regulation of FLC at the chromatin level. The atipk2β mutant flowers earlier, and AtIPK2β overexpressing plants exhibit late-flowering phenotypes. Quantitative reverse transcription-PCR (qRT-PCR) revealed that AtIPK2β promotes FLC expression. We performed chromatin immunoprecipitation-qPCR (ChIP-qPCR) assays and found that AtIPK2β binds to FLC chromatin. Further analysis showed that AtIPK2β interacts with FVE, a key repressor required for epigenetic silencing of FLC. qRT-PCR, ChIP-qPCR, and genetic analysis demonstrated that AtIPK2β is involved in FVE-mediated transcriptional regulation of FLC by repressing the accumulation of FVE on FLC. Moreover, we found that AtIPK2β associates with HDA6, an interaction partner of FVE mediating FLC chromatin silencing, and attenuates HDA6 accumulation at the FLC locus. Taken together, these findings suggest that AtIPK2β negatively regulates flowering time by blocking chromatin silencing of FLC.

Regulation of flowering time: a splicy business.

This article comments on: Capovilla G, Symeonidi E, Wu R, Schmid M. 2017. Contribution of major FLM isoforms to temperature-dependent mediated flowering in Arabidopsis thaliana. Journal of Experimental Botany 68, 5117–5127 .

CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and the Circadian Control of Stomatal Aperture.

The endogenous circadian (∼24 h) system allows plants to anticipate and adapt to daily environmental changes. Stomatal aperture is one of the many processes under circadian control; stomatal opening and closing occurs under constant conditions, even in the absence of environmental cues. To understand the significance of circadian-mediated anticipation in stomatal opening, we have generated SGC (specifically guard cell) Arabidopsis (Arabidopsis thaliana) plants in which the oscillator gene CIRCADIAN CLOCK ASSOCIATED1 (CCA1) was overexpressed under the control of the guard-cell-specific promoter, GC1. The SGC plants showed a loss of ability to open stomata in anticipation of daily dark-to-light changes and of circadian-mediated stomatal opening in constant light. We observed that under fully watered and mild drought conditions, SGC plants outperform wild type with larger leaf area and biomass. To investigate the molecular basis for circadian control of guard cell aperture, we used large-scale qRT-PCR to compare circadian oscillator gene expression in guard cells compared with the "average" whole-leaf oscillator and examined gene expression and stomatal aperture in several lines of plants with misexpressed CCA1 Our results show that the guard cell oscillator is different from the average plant oscillator. Moreover, the differences in guard cell oscillator function may be important for the correct regulation of photoperiod pathway genes that have previously been reported to control stomatal aperture. We conclude by showing that CONSTANS and FLOWERING LOCUS T, components of the photoperiod pathway that regulate flowering time, also control stomatal aperture in a daylength-dependent manner.

PbCOL8 is a clock-regulated flowering time repressor in pear

The floral transition is controlled by diverse endogenous and exogenous cues. In many species, COL (CONSTANS-like) genes integrate light and circadian clock signals to regulate flowering time. However, little is known about COLs in perennial woody plants. Here, we identified 15 PbCOLs in pear (Pyrus bretschneideri). PbCOLs were classified into three groups by phylogenetic tree analysis using protein sequences. Multiple sequence alignment analysis revealed conserved B-box and CCT (CO, CO-like, and TOC1) domains in all PbCOL members. This result suggested that PbCOLs might possess conserved functions as other species. Six PbCOLs were found to be regulated by both circadian clock and photoperiod. Here, we showed that PbCOL8, a member of group 2, suppressed the flowering signal integrators FT and SOC1 and could repress flowering time. These findings will contribute to elucidation of the mechanism of floral initiation in pear.

SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis

BackgroundSimilar to other eukaryotes, splicing is emerging as an important process affecting development and stress tolerance in plants. Ski-interacting protein (SKIP), a splicing factor, is essential for circadian clock function and abiotic stress tolerance; however, the mechanisms whereby it regulates flowering time are unknown.ResultsIn this study, we found that SKIP is required for the splicing of serratedleaves and early flowering (SEF) pre-messenger RNA (mRNA), which encodes a component of the ATP-dependent SWR1 chromatin remodeling complex (SWR1-C). Defects in the splicing of SEF pre-mRNA reduced H2A.Z enrichment at FLC, MAF4, and MAF5, suppressed the expression of these genes, and produced an early flowering phenotype in skip-1 plants.ConclusionsOur findings indicate that SKIP regulates SWR1-C function via alternative splicing to control the floral transition in Arabidopsis thaliana.

QTL effects and epistatic interaction for flowering time and branch number in a soybean mapping population of Japanese×Chinese cultivars

Flowering time and branching type are important agronomic traits related to the adaptability and yield of soybean. Molecular bases for major flowering time or maturity loci, E1 to E4, have been identified. However, more flowering time genes in cultivars with different genetic backgrounds are needed to be mapped and cloned for a better understanding of flowering time regulation in soybean. In this study, we developed a population of Japanese cultivar (Toyomusume)×Chinese cultivar (Suinong 10) to map novel quantitative trait locus (QTL) for flowering time and branch number. A genetic linkage map of a F2 population was constructed using 1 306 polymorphic single nucleotide polymorphism (SNP) markers using Illumina SoySNP8k iSelect BeadChip containing 7 189 (SNPs). Two major QTLs at E1 and E9, and two minor QTLs at a novel locus, qFT2_1 and at E3 region were mapped. Using other sets of F2 populations and their derived progenies, the existence of a novel QTL of qFT2_1 was verified. qBR6_1, the major QTL for branch number was mapped to the proximate to the E1 gene, inferring that E1 gene or neighboring genetic factor is significantly contributing to the branch number.

Seasonal Regulation of Petal Number.

Four petals characterize the flowers of most species in the Brassicaceae family, and this phenotype is generally robust to genetic and environmental variation. A variable petal number distinguishes the flowers of Cardamine hirsuta from those of its close relative Arabidopsis (Arabidopsis thaliana), and allelic variation at many loci contribute to this trait. However, it is less clear whether C. hirsuta petal number varies in response to seasonal changes in environment. To address this question, we assessed whether petal number responds to a suite of environmental and endogenous cues that regulate flowering time in C. hirsuta We found that petal number showed seasonal variation in C. hirsuta, such that spring flowering plants developed more petals than those flowering in summer. Conditions associated with spring flowering, including cool ambient temperature, short photoperiod, and vernalization, all increased petal number in C. hirsuta Cool temperature caused the strongest increase in petal number and lengthened the time interval over which floral meristems matured. We performed live imaging of early flower development and showed that floral buds developed more slowly at 15°C versus 20°C. This extended phase of floral meristem formation, coupled with slower growth of sepals at 15°C, produced larger intersepal regions with more space available for petal initiation. In summary, the growth and maturation of floral buds is associated with variable petal number in C. hirsuta and responds to seasonal changes in ambient temperature.

Phosphorylation of Histone H2A at Serine 95: A Plant-Specific Mark Involved in Flowering Time Regulation and H2A.Z Deposition.

Phosphorylation of histone H3 affects transcription, chromatin condensation, and chromosome segregation. However, the role of phosphorylation of histone H2A remains unclear. Here, we found that Arabidopsis thaliana MUT9P-LIKE-KINASE (MLK4) phosphorylates histone H2A on serine 95, a plant-specific modification in the histone core domain. Mutations in MLK4 caused late flowering under long-day conditions but no notable phenotype under short days. MLK4 interacts with CIRCADIAN CLOCK ASSOCIATED1 (CCA1), which allows MLK4 to bind to the GIGANTEA (GI) promoter. CCA1 interacts with YAF9a, a co-subunit of the Swi2/Snf2-related ATPase (SWR1) and NuA4 complexes, which are responsible for incorporating the histone variant H2A.Z into chromatin and histone H4 acetylase activity, respectively. Importantly, loss of MLK4 function led to delayed flowering by decreasing phosphorylation of H2A serine 95, along with attenuated accumulation of H2A.Z and the acetylation of H4 at GI, thus reducing GI expression. Together, our results provide insight into how phosphorylation of H2A serine 95 promotes flowering time and suggest that phosphorylation of H2A serine 95 modulated by MLK4 is required for the regulation of flowering time and is involved in deposition of the histone variant H2A.Z and H4 acetylation in Arabidopsis.

Hyperactivity of the Arabidopsis cryptochrome (cry1) L407F mutant is caused by a structural alteration close to the cry1 ATP-binding site

Plant cryptochromes (cry) act as UV-A/blue light receptors. The prototype, Arabidopsis thaliana cry1, regulates several light responses during the life cycle, including de-etiolation, and is also involved in regulating flowering time. The cry1 photocycle is initiated by light absorption by its FAD chromophore, which is most likely fully oxidized (FADox) in the dark state and photoreduced to the neutral flavin semiquinone (FADH°) in its lit state. Cryptochromes lack the DNA-repair activity of the closely related DNA photolyases, but they retain the ability to bind nucleotides such as ATP. The previously characterized L407F mutant allele of Arabidopsis cry1 is biologically hyperactive and seems to mimic the ATP-bound state of cry1, but the reason for this phenotypic change is unclear. Here, we show that cry1L407F can still bind ATP, has less pronounced photoreduction and formation of FADH° than wild-type cry1, and has a dark reversion rate 1.7 times lower than that of the wild type. The hyperactivity of cry1L407F is not related to a higher FADH° occupancy of the photoreceptor but is caused by a structural alteration close to the ATP-binding site. Moreover, we show that ATP binds to cry1 in both the dark and the lit states. This binding was not affected by cry1's C-terminal extension, which is important for signal transduction. Finally, we show that a recently discovered chemical inhibitor of cry1, 3-bromo-7-nitroindazole, competes for ATP binding and thereby diminishes FADH° formation, which demonstrates that both processes are important for cry1 function.

Construction and application of functional gene modules to regulatory pathways in rice

Signal transduction and transcriptional regulation pathways are key elements in the control of diverse physiological responses and agronomic traits in plants. The regulatory roles of more than 1,000 known genes have been functionally characterized in rice, a model crop plant, and many of them are associated with transcriptional regulation and signal transduction pathways. In this study, we collected and analyzed 417 known genes associated with regulatory pathways, about 40% of the known genes, using the regulation overview installed in the MapMan toolkit. Connecting novel genes to current knowledge about regulatory pathways can elucidate their molecular functions and inspire ideas for further applications. We have summarized the functions of known regulatory genes in the areas of transcriptional regulation, epigenetic regulation, protein modification, protein degradation, signaling and hormone metabolism, also we have emphasized the unique features of several gene families in these classes, including MADS box families, which are strongly associated with the regulation of floral organ identity and flowering time. In addition, our construction of functional modules in four agronomic categories, morphological, physiological, biotic stress and abiotic stress, suggests a basic framework for expanding current knowledge about regulatory pathways to enhance agronomic traits in rice. We also provide a quick illustration of the positive and negative regulatory relationships of the target gene to manipulate agronomic trait by using genome-wide transcriptome data of knockout or overexpression mutations of genes of interest in each functional module.