Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene

The OsHAPL1-DTH8-Hd1 complex functions as the transcription regulator to repress heading date in rice

Heading date is an important agronomic trait related to crop yield. Many genes related to heading date have already been identified in rice (Oryza sativa), and a complicated, preliminary regulatory genetic network has also already been established, but the protein regulatory network is poorly understood. We have identified a novel heading date regulator, Heme Activator Protein like 1 (OsHAPL1), which inhibits flowering under long-day conditions. OsHAPL1 is a nuclear-localized protein that is highly expressed in leaves in a rhythmic manner. OsHAPL1 can physically interact with Days To Heading on chromosome 8 (DTH8), which physically interacts with Heading date 1 (Hd1) both in vitro and in vivo. OsHAPL1 forms a complex with DTH8 and Hd1 in Escherichia coli. OsHAPL1, DTH8, and Hd1 physically interact with the HAP complex, and also with general transcription factors in yeast (Saccharomyces cerevisiae). Further studies showed that OsHAPL1 represses the expression of the florigen genes and FLOWERING LOCUS T 1 (RFT1) and Hd3a through Early heading date 1 (Ehd1). We propose that OsHAPL1 functions as a transcriptional regulator and, together with DTH8, Hd1, the HAP complex, and general transcription factors, regulates the expression of target genes and then affects heading date by influencing the expression of Hd3a and RFT1 through Ehd1.

The Plant Circadian Clock: From a Simple Timekeeper to a Complex Developmental Manager

The plant circadian clock allows organisms to anticipate the predictable changes in the environment by adjusting their developmental and physiological traits. In the last few years, it was determined that responses known to be regulated by the oscillator are also able to modulate clock performance. These feedback loops and their multilayer communications create a complex web, and confer on the clock network a role that exceeds the measurement of time. In this article, we discuss the current knowledge of the wiring of the clock, including the interplay with metabolism, hormone, and stress pathways in the model species Arabidopsis thaliana We outline the importance of this system in crop agricultural traits, highlighting the identification of natural alleles that alter the pace of the timekeeper. We report evidence supporting the understanding of the circadian clock as a master regulator of plant life, and we hypothesize on its relevant role in the adaptability to the environment and the impact on the fitness of most organisms.

ABA-dependent control of GIGANTEA signalling enables drought escape via up-regulation of FLOWERING LOCUS T in Arabidopsis thaliana

One strategy deployed by plants to endure water scarcity is to accelerate the transition to flowering adaptively via the drought escape (DE) response. In Arabidopsis thaliana, activation of the DE response requires the photoperiodic response gene GIGANTEA (GI) and the florigen genes FLOWERING LOCUS T (FT) and TWIN SISTER OF FT (TSF). The phytohormone abscisic acid (ABA) is also required for the DE response, by promoting the transcriptional up-regulation of the florigen genes. The mode of interaction between ABA and the photoperiodic genes remains obscure. In this work we use a genetic approach to demonstrate that ABA modulates GI signalling and consequently its ability to activate the florigen genes. We also reveal that the ABA-dependent activation of FT, but not TSF, requires CONSTANS (CO) and that impairing ABA signalling dramatically reduces the expression of florigen genes with little effect on the CO transcript profile. ABA signalling thus has an impact on the core genes of photoperiodic signalling GI and CO by modulating their downstream function and/or activities rather than their transcript accumulation. In addition, we show that as well as promoting flowering, ABA simultaneously represses flowering, independent of the florigen genes. Genetic analysis indicates that the target of the repressive function of ABA is the flowering-promoting gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a transcription factor integrating floral cues in the shoot meristem. Our study suggests that variations in ABA signalling provide different developmental information that allows plants to co-ordinate the onset of the reproductive phase according to the available water resources.

Barley (Hordeum vulgare) circadian clock genes can respond rapidly to temperature in an EARLY FLOWERING 3-dependent manner

An increase in global temperatures will impact future crop yields. In the cereal crops wheat and barley, high temperatures accelerate reproductive development, reducing the number of grains per plant and final grain yield. Despite this relationship between temperature and cereal yield, it is not clear what genes and molecular pathways mediate the developmental response to increased temperatures. The plant circadian clock can respond to changes in temperature and is important for photoperiod-dependent flowering, and so is a potential mechanism controlling temperature responses in cereal crops. This study examines the relationship between temperature, the circadian clock, and the expression of flowering-time genes in barley (Hordeum vulgare), a crop model for temperate cereals. Transcript levels of barley core circadian clock genes were assayed over a range of temperatures. Transcript levels of core clock genes CCA1, GI, PRR59, PRR73, PRR95, and LUX are increased at higher temperatures. CCA1 and PRR73 respond rapidly to a decrease in temperature whereas GI and PRR59 respond rapidly to an increase in temperature. The response of GI and the PRR genes to changes in temperature is lost in the elf3 mutant indicating that their response to temperature may be dependent on a functional ELF3 gene.

Reduction of GIGANTEA expression in transgenic Brassica rapa enhances salt tolerance

Here we report the enhancement of tolerance to salt stress in Brassica rapa (Chinese cabbage) through the RNAi-mediated reduction of GIGANTEA ( GI ) expression. Circadian clocks integrate environmental signals with internal cues to coordinate diverse physiological outputs. The GIGANTEA (GI) gene was first discovered due to its important contribution to photoperiodic flowering and has since been shown to be a critical component of the plant circadian clock and to contribute to multiple environmental stress responses. We show that the GI gene in Brassica rapa (BrGI) is similar to Arabidopsis GI in terms of both expression pattern and function. BrGI functionally rescued the late-flowering phenotype of the Arabidopsis gi-201 loss-of-function mutant. RNAi-mediated suppression of GI expression in Arabidopsis Col-0 and in the Chinese cabbage, B. rapa DH03, increased tolerance to salt stress. Our results demonstrate that the molecular functions of GI described in Arabidopsis are conserved in B. rapa and suggest that manipulation of gene expression through RNAi and transgenic overexpression could enhance tolerance to abiotic stresses and thus improve agricultural crop production.

The wheat MYB-related transcription factor TaMYB72 promotes flowering in rice

Through large-scale transformation analyses, TaMYB72 was identified as a flowering time regulator in wheat. TaMYB72 is a MYB family transcription factor localized to the nucleus. Three TaMYB72 homologs, TaMYB72-A, TaMYB72-B and TaMYB72-D, cloned from hexaploid wheat were mapped to the short arm of the group 6 chromosomes. Under the long-day conditions, over-expression of the TaMYB72 in rice shortened the flowering time by approximately 12 d. Expression analyses suggest that TaMYB72 may function through up-regulation of florigen genes Hd3a and RFT1.

OsPhyA modulates rice flowering time mainly through OsGI under short days and Ghd7 under long days in the absence of phytochrome B

Phytochromes recognize light signals and control diverse developmental processes. In rice, all three phytochrome genes-OsphyA, OsphyB, and OsphyC-are involved in regulating flowering time. We investigated the role of OsPhyA by comparing the osphyA osphyB double mutant to an osphyB single mutant. Plants of the double mutant flowered later than the single under short days (SD) but bolted earlier under long days (LD). Under SD, this delayed-flowering phenotype was primarily due to the decreased expression of Oryza sativa GIGANTEA (OsGI), which controls three flowering activators: Heading date 1 (Hd1), OsMADS51, and Oryza sativa Indeterminate 1 (OsId1). Under LD, although the expression of several repressors, e.g., Hd1, Oryza sativa CONSTANS-like 4 (OsCOL4), and AP2 genes, was affected in the double mutant, that of Grain number, plant height and heading date 7 (Ghd7) was the most significantly reduced. These results indicated that OsPhyA influences flowering time mainly by affecting the expression of OsGI under SD and Ghd7 under LD when phytochrome B is absent. We also demonstrated that far-red light delays flowering time via both OsPhyA and OsPhyB.

A New Insight of Salt Stress Signaling in Plant

Many studies have been conducted to understand plant stress responses to salinity because irrigation-dependent salt accumulation compromises crop productivity and also to understand the mechanism through which some plants thrive under saline conditions. As mechanistic understanding has increased during the last decades, discovery-oriented approaches have begun to identify genetic determinants of salt tolerance. In addition to osmolytes, osmoprotectants, radical detoxification, ion transport systems, and changes in hormone levels and hormone-guided communications, the Salt Overly Sensitive (SOS) pathway has emerged to be a major defense mechanism. However, the mechanism by which the components of the SOS pathway are integrated to ultimately orchestrate plant-wide tolerance to salinity stress remains unclear. A higher-level control mechanism has recently emerged as a result of recognizing the involvement of GIGANTEA (GI), a protein involved in maintaining the plant circadian clock and control switch in flowering. The loss of GI function confers high tolerance to salt stress via its interaction with the components of the SOS pathway. The mechanism underlying this observation indicates the association between GI and the SOS pathway and thus, given the key influence of the circadian clock and the pathway on photoperiodic flowering, the association between GI and SOS can regulate growth and stress tolerance. In this review, we will analyze the components of the SOS pathways, with emphasis on the integration of components recognized as hallmarks of a halophytic lifestyle.

LATE ELONGATED HYPOCOTYL regulates photoperiodic flowering via the circadian clock in Arabidopsis

BACKGROUND

Plants constantly monitor changes in photoperiod or day length to trigger the flowering cycle at the most appropriate time of the year. It is well established that photoperiodic flowering is intimately associated with the circadian clock in Arabidopsis. In support of this notion, many clock-defective mutants exhibit altered photoperiodic sensitivity in inducing flowering. LATE ELONGATED HYPOCOTYL (LHY) and its functional paralogue CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) constitute the core of the circadian clock together with TIMING OF CAB EXPRSSION 1 (TOC1). While it is known that TOC1 contributes to the timing of flowering entirely by modulating the clock function, molecular mechanisms by which LHY and CCA1 regulate flowering time have not been explored.

RESULTS

We investigated how LHY and CCA1 regulate photoperiodic flowering through molecular genetic and biochemical studies. It was found that LHY-defective mutants (lhy-7 and lhy-20) exhibit accelerated flowering under both long days (LDs) and short days (SDs). Consistent with the accelerated flowering phenotypes, gene expression analysis revealed that expression of the floral integrator FLOWERING LOCUS T (FT) is up-regulated in the lhy mutants. In addition, the expression peaks of GIGANTEA (GI) and FLAVIN-BINDING, KELCH REPEAT, F-BOX PROTEIN 1 (FKF1) genes, which constitute the clock output pathway that is linked with photoperiodic flowering, were advanced by approximately 4 h in the mutants. Furthermore, the up-regulation of FT disappeared when the endogenous circadian period is matched to the external light/dark cycles in the lhy-7 mutant. Notably, whereas CCA1 binds strongly to FT gene promoter, LHY does not show such DNA-binding activity.

CONCLUSIONS

Our data indicate that the advanced expression phases of photoperiodic flowering genes are associated with the clock defects in the lhy mutants and responsible for the reduced photoperiodic sensitivity of the mutant flowering, demonstrating that LHY regulates photoperiodic flowering via the circadian clock, similar to what has been shown with TOC1. It is notable that while LHY regulates photoperiodic flowering in a similar manner as with TOC1, the underlying molecular mechanism would be somewhat distinct from that exerted by CCA1 in Arabidopsis.

Transcriptome analysis of sweet orange trees infected with 'Candidatus Liberibacter asiaticus' and two strains of Citrus Tristeza Virus

BACKGROUND

Huanglongbing (HLB) and tristeza, are diseases of citrus caused by a member of the α-proteobacteria, 'Candidatus Liberibacter asiaticus' (CaLas), and Citrus tristeza virus (CTV) respectively. HLB is a devastating disease, but CTV strains vary from very severe to very mild. Both CaLas and CTV are phloem-restricted. The CaLas-B232 strain and CTV-B6 cause a wide range of severe and similar symptoms. The mild strain CTV-B2 doesn't induce significant symptoms or damage to plants.

RESULTS

Transcriptome profiles obtained through RNA-seq revealed 611, 404 and 285 differentially expressed transcripts (DETs) after infection with CaLas-B232, CTV-B6 and CTV-B2. These DETs were components of a wide range of pathways involved in circadian rhythm, cell wall modification and cell organization, as well as transcription factors, transport, hormone response and secondary metabolism, signaling and stress response. The number of transcripts that responded to both CTV-B6 and CaLas-B232 was much larger than the number of transcripts that responded to both strains of CTV or to both CTV-B2 and CaLas-B232. A total of 38 genes were assayed by RT-qPCR and the correlation coefficients between Gfold and RT-qPCR were 0.82, 0.69, 0.81 for sweet orange plants infected with CTV-B2, CTV-B6 and CaLas-B232, respectively.

CONCLUSIONS

The number and composition of DETs reflected the complexity of symptoms caused by the pathogens in established infections, although the leaf tissues sampled were asymptomatic. There were greater similarities between the sweet orange in response to CTV-B6 and CaLas-B232 than between the two CTV strains, reflecting the similar physiological changes caused by both CTV-B6 and CaLas-B232. The circadian rhythm system of plants was perturbed by all three pathogens, especially by CTV-B6, and the ion balance was also disrupted by all three pathogens, especially by CaLas-B232. Defense responses related to cell wall modification, transcriptional regulation, hormones, secondary metabolites, kinases and stress were activated by all three pathogens but with different patterns. The transcriptome profiles of Citrus sinensis identified host genes whose expression is affected by the presence of a pathogen in the phloem without producing symptoms (CTV-B2), and host genes whose expression leads to induction of symptoms in the plant (CTV-B6, CaLas-B232).

MicroRNAs in Control of Plant Development

In the long evolutionary history, plant has evolved elaborate regulatory network to control functional gene expression for surviving and thriving, such as transcription factor-regulated transcriptional programming. However, plenty of evidences from the past decade studies demonstrate that the 21-24 nucleotides small RNA molecules, majorly microRNAs (miRNAs) play dominant roles in post-transcriptional gene regulation through base pairing with their complementary mRNA targets, especially prefer to target transcription factors in plants. Here, we review current progresses on miRNA-controlled plant development, from miRNA biogenesis dysregulation-caused pleiotropic developmental defects to specific developmental processes, such as SAM regulation, leaf and root system regulation, and plant floral transition. We also summarize some miRNAs that are experimentally proved to greatly affect crop plant productivity and quality. In addition, recent reports show that a single miRNA usually displays multiple regulatory roles, such as organ development, phase transition, and stresses responses. Thus, we infer that miRNA may act as a node molecule to coordinate the balance between plant development and environmental clues, which may shed the light on finding key regulator or regulatory pathway for uncovering the mysterious molecular network.

Mutation of OsGIGANTEA Leads to Enhanced Tolerance to Polyethylene Glycol-Generated Osmotic Stress in Rice

Water deficit is one of the most important environmental stresses limiting plant growth and crop yield. While the identification of many key factors involved in the plant water deficit response has greatly increased our knowledge about the regulation system, the mechanisms underlying dehydration tolerance in plants are still not well understood. In our current study, we investigated the roles of the key flowering time regulator, OsGIGANTEA (OsGI), in the osmotic stress tolerance in rice. Results showed that mutation of OsGI conferred tolerance to osmotic stress generated by polyethylene glycol (PEG), increased proline and sucrose contents, and accelerated stomata movement. In addition, qRT-PCR and microarray analysis revealed that the transcript abundance of some osmotic stress response genes, such as OsDREB1E, OsAP37, OsAP59, OsLIP9, OsLEA3, OsRAB16A, and OsSalT, was significantly higher in osgi than in WT plants, suggesting that OsGI might be a negative regulator in the osmotic stress response in rice.

Age-associated circadian period changes in Arabidopsis leaves

As most organisms age, their appearance, physiology, and behaviour alters as part of a life history strategy that maximizes their fitness over their lifetime. The passage of time is measured by organisms and is used to modulate these age-related changes. Organisms have an endogenous time measurement system called the circadian clock. This endogenous clock regulates many physiological responses throughout the life history of organisms to enhance their fitness. However, little is known about the relation between ageing and the circadian clock in plants. Here, we investigate the association of leaf ageing with circadian rhythm changes to better understand the regulation of life-history strategy in Arabidopsis. The circadian periods of clock output genes were approximately 1h shorter in older leaves than younger leaves. The periods of the core clock genes were also consistently shorter in older leaves, indicating an effect of ageing on regulation of the circadian period. Shortening of the circadian period with leaf age occurred faster in plants grown under a long photoperiod compared with a short photoperiod. We screened for a regulatory gene that links ageing and the circadian clock among multiple clock gene mutants. Only mutants for the clock oscillator TOC1 did not show a shortened circadian period during leaf ageing, suggesting that TOC1 may link age to changes in the circadian clock period. Our findings suggest that age-related information is incorporated into the regulation of the circadian period and that TOC1 is necessary for this integrative process.

OsCOL10, a CONSTANS-Like Gene, Functions as a Flowering Time Repressor Downstream of Ghd7 in Rice

Flowering time, or heading date, is a critical agronomic trait that determines the cropping season and regional adaptability, and ultimately grain yield in rice. A number of genes involved in photoperiodic flowering have been cloned and their roles in modulating expression of the flowering genes have been characterized to a certain extent. However, much less is known about the pathway in transmitting the day length response signal(s) to induce transition to reproductive growth. Here, we report a constitutive flowering repressor OsCOL10, which encodes a member of the CONSTANS-like (COL) family. Transgenic rice plants overexpressing OsCOL10 (driven by a strong promoter or by fusing it to the activation domain of VP64) showed delayed flowering time under both short and long days.OsCOL10 is affected by the circadian clock and is preferentially expressed in leaf mesophyll cells; it is localized to the nucleus and has transcriptional activation activity. Further studies show that OsCOL10 represses the expression of theFT-like genes RFT1 and Hd3a through Ehd1. Transcripts of OsCOL10 are more abundant in plants carrying a functional Ghd7 allele or overexpressing Ghd7 than in Ghd7-deficient plants, thus placing OsCOL10 downstream of Ghd7.Taking these findings together, we conclude that OsCOL10 functions as a flowering time repressor that links Ghd7 and Ehd1 in rice.

Homodimerization of Ehd1 Is Required to Induce Flowering in Rice

In plants, flowering time is elaborately controlled by various environment factors. Ultimately, florigens such as FLOWERING LOCUS T (FT) or FT-like molecules induce flowering. In rice (Oryza sativa), Early heading date 1 (Ehd1) is a major inducer of florigen gene expression. Although Ehd1 is highly homologous to the type-B response regulator (RR) family in the cytokinin signaling pathway, its precise molecular mechanism is not well understood. In this study, we showed that the C-terminal portion of the protein containing the GARP DNA-binding (G) domain can promote flowering when overexpressed. We also observed that the N-terminal portion of Ehd1, carrying the receiver (R) domain, delays flowering by inhibiting endogenous Ehd1 activity. Ehd1 protein forms a homomer via a 16-amino acid region in the inter domain between R and G. From the site-directed mutagenesis analyses, we demonstrated that phosphorylation of the Asp-63 residue within the R domain induces the homomerization of Ehd1, which is crucial for Ehd1 activity. A type-A RR, OsRR1, physically interacts with Ehd1 to form a heterodimer. In addition, OsRR1-overexpressing plants show a late-flowering phenotype. Based on these observations, we conclude that OsRR1 inhibits Ehd1 activity by binding to form an inactive complex.

Rice FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1) promotes flowering independent of photoperiod

In the facultative long-day (LD) plant Arabidopsis thaliana, FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) is activated by blue light and promotes flowering through the transcriptional and post-translational regulation of CONSTANS under inductive LD conditions. By contrast, the facultative short day (SD) plant rice (Oryza sativa) flowers early under inductive SD and late under non-inductive LD conditions; the regulatory function of OsFKF1 remains elusive. Here we show that osfkf1 mutants flower late under SD, LD and natural LD conditions. Transcriptional analysis revealed that OsFKF1 up-regulates the expression of the floral activator Ehd2 and down-regulates the expression of the floral repressor Ghd7; these regulators up- and down-regulate Ehd1 expression, respectively. Moreover, OsFKF1 can up-regulate Ehd1 expression under blue light treatment, without affecting the expression of Ehd2 and Ghd7. In contrast to the LD-specific floral activator Arabidopsis FKF1, OsFKF1 likely acts as an autonomous floral activator because it promotes flowering independent of photoperiod, probably via its distinct roles in controlling the expression of rice-specific genes including Ehd2, Ghd7 and Ehd1. Like Arabidopsis FKF1, which interacts with GI and CDF1, OsFKF1 also interacts with OsGI and OsCDF1 (also termed OsDOF12). Thus, we have identified similar and distinct roles of FKF1 in Arabidopsis and rice.

CONSTITUTIVE PHOTOMORPHOGENIC 10 (COP10) Contributes to Floral Repression under Non-Inductive Short Days in Arabidopsis

In Arabidopsis, CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETIOLATED/FUSCA (COP/DET/FUS) genes act in repression of photomorphogenesis in darkness, and recent reports revealed that some of these genes, such as COP1 and DET1, also have important roles in controlling flowering time and circadian rhythm. The COP/DET/FUS protein COP10 interacts with DET1 and DNA DAMAGE-BINDING PROTEIN 1 (DDB1) to form a CDD complex and represses photomorphogenesis in darkness. The cop10-4 mutants flower normally in inductive long days (LD) but early in non-inductive short days (SD) compared with wild type (WT); however, the role of COP10 remains unknown. Here, we investigate the role of COP10 in SD-dependent floral repression. Reverse transcription-quantitative PCR revealed that in SD, expression of the LD-dependent floral inducers GI, FKF1, and FT significantly increased in cop10-4 mutants, compared with WT. This suggests that COP10 mainly regulates FT expression in a CO-independent manner. We also show that COP10 interacts with GI in vitro and in vivo, suggesting that COP10 could also affect GI function at the posttranslational level. Moreover, FLC expression was repressed drastically in cop10-4 mutants and COP10 interacts with MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4)/FVE (MSI4/FVE), which epigenetically inhibits FLC expression. These data suggest that COP10 contributes to delaying flowering in the photoperiod and autonomous pathways by downregulating FT expression under SD.

Circadian Clock Genes Universally Control Key Agricultural Traits

Circadian clocks are endogenous timers that enable plants to synchronize biological processes with daily and seasonal environmental conditions in order to allocate resources during the most beneficial times of day and year. The circadian clock regulates a number of central plant activities, including growth, development, and reproduction, primarily through controlling a substantial proportion of transcriptional activity and protein function. This review examines the roles that alleles of circadian clock genes have played in domestication and improvement of crop plants. The focus here is on three groups of circadian clock genes essential to clock function in Arabidopsis thaliana: PSEUDO-RESPONSE REGULATORs, GIGANTEA, and the evening complex genes early flowering 3, early flowering 4, and lux arrhythmo. homologous genes from each group underlie quantitative trait loci that have beneficial influences on key agricultural traits, especially flowering time but also yield, biomass, and biennial growth habit. Emerging insights into circadian clock regulation of other fundamental plant processes, including responses to abiotic and biotic stresses, are discussed to highlight promising avenues for further crop improvement.

Circadian clock gene LATE ELONGATED HYPOCOTYL directly regulates the timing of floral scent emission in Petunia

Flowers present a complex display of signals to attract pollinators, including the emission of floral volatiles. Volatile emission is highly regulated, and many species restrict emissions to specific times of the day. This rhythmic emission of scent is regulated by the circadian clock; however, the mechanisms have remained unknown. In Petunia hybrida, volatile emissions are dominated by products of the floral volatile benzenoid/phenylpropanoid (FVBP) metabolic pathway. Here we demonstrate that the circadian clock gene P. hybrida LATE ELONGATED HYPOCOTYL (LHY; PhLHY) regulates the daily expression patterns of the FVBP pathway genes and floral volatile production. PhLHY expression peaks in the morning, antiphasic to the expression of P. hybrida GIGANTEA (PhGI), the master scent regulator ODORANT1 (ODO1), and many other evening-expressed FVBP genes. Overexpression phenotypes of PhLHY in Arabidopsis caused an arrhythmic clock phenotype, which resembles those of LHY overexpressors. In Petunia, constitutive expression of PhLHY depressed the expression levels of PhGI, ODO1, evening-expressed FVBP pathway genes, and FVBP emission in flowers. Additionally, in the Petunia lines in which PhLHY expression was reduced, the timing of peak expression of PhGI, ODO1, and the FVBP pathway genes advanced to the morning. Moreover, PhLHY protein binds to cis-regulatory elements called evening elements that exist in promoters of ODO1 and other FVBP genes. Thus, our results imply that PhLHY directly sets the timing of floral volatile emission by restricting the expression of ODO1 and other FVBP genes to the evening in Petunia.

Dawn and Dusk Set States of the Circadian Oscillator in Sprouting Barley (Hordeum vulgare) Seedlings

The plant circadian clock is an internal timekeeper that coordinates biological processes with daily changes in the external environment. The transcript levels of clock genes, which oscillate to control circadian outputs, were examined during early seedling development in barley (Hordeum vulgare), a model for temperate cereal crops. Oscillations of clock gene transcript levels do not occur in barley seedlings grown in darkness or constant light but were observed with day-night cycles. A dark-to-light transition influenced transcript levels of some clock genes but triggered only weak oscillations of gene expression, whereas a light-to-dark transition triggered robust oscillations. Single light pulses of 6, 12 or 18 hours induced robust oscillations. The light-to-dark transition was the primary determinant of the timing of subsequent peaks of clock gene expression. After the light-to-dark transition the timing of peak transcript levels of clock gene also varied depending on the length of the preceding light pulse. Thus, a single photoperiod can trigger initiation of photoperiod-dependent circadian rhythms in barley seedlings. Photoperiod-specific rhythms of clock gene expression were observed in two week old barley plants. Changing the timing of dusk altered clock gene expression patterns within a single day, showing that alteration of circadian oscillator behaviour is amongst the most rapid molecular responses to changing photoperiod in barley. A barley EARLY FLOWERING3 mutant, which exhibits rapid photoperiod-insensitive flowering behaviour, does not establish clock rhythms in response to a single photoperiod. The data presented show that dawn and dusk cues are important signals for setting the state of the circadian oscillator during early development of barley and that the circadian oscillator of barley exhibits photoperiod-dependent oscillation states.

Negative regulatory roles of DE-ETIOLATED1 in flowering time in Arabidopsis

Arabidopsis flowers early under long days (LD) and late under short days (SD). The repressor of photomorphogenesis DE-ETIOLATED1 (DET1) delays flowering; det1-1 mutants flower early, especially under SD, but the molecular mechanism of DET1 regulation remains unknown. Here we examine the regulatory function of DET1 in repression of flowering. Under SD, the det1-1 mutation causes daytime expression of FKF1 and CO; however, their altered expression has only a small effect on early flowering in det1-1 mutants. Notably, DET1 interacts with GI and binding of GI to the FT promoter increases in det1-1 mutants, suggesting that DET1 mainly restricts GI function, directly promoting FT expression independent of CO expression. Moreover, DET1 interacts with MSI4/FVE, which epigenetically inhibits FLC expression, indicating that the lack of FLC expression in det1-1 mutants likely involves altered histone modifications at the FLC locus. These data demonstrate that DET1 acts in both photoperiod and autonomous pathways to inhibit expression of FT and SOC1. Consistent with this, the early flowering of det1-1 mutants disappears completely in the ft-1 soc1-2 double mutant background. Thus, we propose that DET1 is a strong repressor of flowering and has a pivotal role in maintaining photoperiod sensitivity in the regulation of flowering time.

Repression of flowering under a noninductive photoperiod by the HDA9-AGL19-FT module in Arabidopsis

Posttranslational acetylation of histones is reversibly regulated by histone deacetylases (HDACs). Despite the evident significance of HDACs in Arabidopsis development, the biological roles and underlying molecular mechanisms of many HDACs are yet to be elucidated. By a reverse-genetic approach, we isolated an hda9 mutant and performed phenotypic analyses on it. In order to address the role of HDA9 in flowering, genetic, molecular, and biochemical approaches were employed. hda9 flowered early under noninductive short-day (SD) conditions and had increased expression of the floral integrator FLOWERING LOCUS T (FT) and the floral activator AGAMOUS-LIKE 19 (AGL19) compared with the wild-type. The hda9 mutation increased histone acetylation and RNA polymerase II occupancy at AGL19 but not at FT during active transcription, and the HDA9 protein directly targeted AGL19. AGL19 expression was higher under SD than under inductive long-day (LD) conditions, and an AGL19 overexpression caused a strong up-regulation of FT. A genetic analysis showed that an agl19 mutation is epistatic to the hda9 mutation, masking both the early flowering and the increased FT expression of hda9. Taken together, our data indicate that HDA9 prevents precocious flowering under SD conditions by curbing the hyperactivation of AGL19, an upstream activator of FT, through resetting the local chromatin environment.

Shade avoidance components and pathways in adult plants revealed by phenotypic profiling

Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.

Transcriptomic analysis of American ginseng seeds during the dormancy release process by RNA-Seq

American ginseng (Panax quinquefolius L.) is an important herb that is cultivated in China, North American, and South Korea. It is propagated from seed, but the seed has deep dormancy characteristics described as morphophysiological dormancy. Two-stage temperature stratification, a warm (15–20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release. However, little is known about the molecular mechanisms of seed dormancy release in the stratification process. In this study, seed development after pollination and seed development in the dormancy release process were investigated in American ginseng. The transcriptome during seed dormancy release was analyzed using RNA-Seq technology and 78,207 unigenes (mean length 531 bp) were generated. Based on similarity searches of public databases, 54,292 of the unigenes (69.4%) were functionally annotated. Further, three digital gene expression (DGE) libraries were sequenced and differences in gene expression at three stages during seed cold stratification were examined. The greatest number of differentially expressed genes occurred in the 90DCS versus 180DCS libraries, while the lowest number of differentially expressed genes occurred in the 135DCS verus 180DCS libraries. GO enrichment analysis revealed that 59, 29, and 39 GO terms were significantly enriched in the biological process, molecular function, and cell component GO categories, respectively. There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared. The gene expressions of 30 selected unigenes were validated using quantitative PCR. This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release. These data provide a basis for future researches of seed dormancy in morphophysiological dormancy seeds in non-model plants.

Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa

GIGANTEA (GI) was originally identified by a late-flowering mutant in Arabidopsis, but subsequently has been shown to act in circadian period determination, light inhibition of hypocotyl elongation, and responses to multiple abiotic stresses, including tolerance to high salt and cold (freezing) temperature. Genetic mapping and analysis of families of heterogeneous inbred lines showed that natural variation in GI is responsible for a major quantitative trait locus in circadian period in Brassica rapa. We confirmed this conclusion by transgenic rescue of an Arabidopsis gi-201 loss of function mutant. The two B. rapa GI alleles each fully rescued the delayed flowering of Arabidopsis gi-201 but showed differential rescue of perturbations in red light inhibition of hypocotyl elongation and altered cold and salt tolerance. The B. rapa R500 GI allele, which failed to rescue the hypocotyl and abiotic stress phenotypes, disrupted circadian period determination in Arabidopsis. Analysis of chimeric B. rapa GI alleles identified the causal nucleotide polymorphism, which results in an amino acid substitution (S264A) between the two GI proteins. This polymorphism underlies variation in circadian period, cold and salt tolerance, and red light inhibition of hypocotyl elongation. Loss-of-function mutations of B. rapa GI confer delayed flowering, perturbed circadian rhythms in leaf movement, and increased freezing and increased salt tolerance, consistent with effects of similar mutations in Arabidopsis. Collectively, these data suggest that allelic variation of GI-and possibly of clock genes in general-offers an attractive target for molecular breeding for enhanced stress tolerance and potentially for improved crop yield.

The GI-CDF module of Arabidopsis affects freezing tolerance and growth as well as flowering

Plants monitor and integrate temperature, photoperiod and light quality signals to respond to continuous changes in their environment. The GIGANTEA (GI) protein is central in diverse signaling pathways, including photoperiodic, sugar and light signaling pathways, stress responses and circadian clock regulation. Previously, GI was shown to activate expression of the key floral regulators CONSTANS (CO) and FLOWERING LOCUS T (FT) by facilitating degradation of a family of CYCLING DOF FACTOR (CDF) transcriptional repressors. However, whether CDFs are implicated in other processes affected by GI remains unclear. We investigated the contribution of the GI-CDF module to traits that depend on GI. Transcriptome profiling indicated that mutations in GI and the CDF genes have antagonistic effects on expression of a wider set of genes than CO and FT, whilst other genes are regulated by GI independently of the CDFs. Detailed expression studies followed by phenotypic assays showed that the CDFs function downstream of GI, influencing responses to freezing temperatures and growth, but are not necessary for proper clock function. Thus GI-mediated regulation of CDFs contributes to several processes in addition to flowering, but is not implicated in all of the traits influenced by GI.

Casein kinases I and 2α phosphorylate oryza sativa pseudo-response regulator 37 (OsPRR37) in photoperiodic flowering in rice

Flowering time (or heading date) is controlled by intrinsic genetic programs in response to environmental cues, such as photoperiod and temperature. Rice, a facultative short-day (SD) plant, flowers early in SD and late in long-day (LD) conditions. Casein kinases (CKs) generally act as positive regulators in many signaling pathways in plants. In rice, Heading date 6 (Hd6) and Hd16 encode CK2α and CKI, respectively, and mainly function to delay flowering time. Additionally, the major LD-dependent floral repressors Hd2/Oryza sativa Pseudo-Response Regulator 37 (OsPRR37; hereafter PRR37) and Ghd7 also confer strong photoperiod sensitivity. In floral induction, Hd16 acts upstream of Ghd7 and CKI interacts with and phosphorylates Ghd7. In addition, Hd6 and Hd16 also act upstream of Hd2. However, whether CKI and CK2α directly regulate the function of PRR37 remains unclear. Here, we use in vitro pull-down and in vivo bimolecular fluorescence complementation assays to show that CKI and CK2α interact with PRR37. We further use in vitro kinase assays to show that CKI and CK2α phosphorylate different regions of PRR37. Our results indicate that direct posttranslational modification of PRR37 mediates the genetic interactions between these two protein kinases and PRR37. The significance of CK-mediated phosphorylation for PRR37 and Ghd7 function is discussed.

Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice

CCT domain-containing genes generally control flowering in plants. Currently, only six of the 41 CCT family genes have been confirmed to control flowering in rice. To efficiently identify more heading date-related genes from the CCT family, we compared the positions of heading date QTLs and CCT genes and found that 25 CCT family genes were located in the QTL regions. Association mapping showed that a total of 19 CCT family genes were associated with the heading date. Five of the seven associated genes within QTL regions and two of four associated genes outside of the QTL regions were confirmed to regulate heading date by transformation. None of the seven non-associated genes outside of the QTL regions regulates heading date. Obviously, combination of candidate gene-based association mapping with linkage analysis could improve the identification of functional genes. Three novel CCT family genes, including one non-associated (OsCCT01) and two associated genes (OsCCT11 and OsCCT19) regulated the heading date. The overexpression of OsCCT01 delayed flowering through suppressing the expression of Ehd1, Hd3a and RFT1 under both long day and short day conditions. Potential functions in regulating heading date of some untested CCT family genes were discussed.

GIGANTEA - an emerging story

GIGANTEA (GI) is a plant specific nuclear protein and functions in diverse physiological processes such as flowering time regulation, light signaling, hypocotyl elongation, control of circadian rhythm, sucrose signaling, starch accumulation, chlorophyll accumulation, transpiration, herbicide tolerance, cold tolerance, drought tolerance, and miRNA processing. It has been five decades since its discovery but the biochemical function of GI and its different domains are still unclear. Although it is known that both GI transcript and GI protein are clock controlled, the regulation of its abundance and functions at the molecular level are still some of the unexplored areas of intensive research. Since GI has many important pleotropic functions as described above scattered through literature, it is worthwhile and about time to encapsulate the available information in a concise review. Therefore, in this review, we are making an attempt to summarize (i) the various interconnected roles that GI possibly plays in the fine-tuning of plant development, and (ii) the known mutations of GI that have been instrumental in understanding its role in distinct physiological processes.

Photoperiodic control of sugar release during the floral transition: What is the role of sugars in the florigenic signal?

Florigen is a mobile signal released by the leaves that reaching the shoot apical meristem (SAM), changes its developmental program from vegetative to reproductive. The protein FLOWERING LOCUS T (FT) constitutes an important element of the florigen, but other components such as sugars, have been also proposed to be part of this signal. (1-5) We have studied the accumulation and composition of starch during the floral transition in Arabidopsis thaliana in order to understand the role of carbon mobilization in this process. In A. thaliana and Antirrhinum majus the gene coding for the Granule-Bound Starch Synthase (GBSS) is regulated by the circadian clock (6,7) while in the green alga Chlamydomonas reinhardtii the homolog gene CrGBSS is controlled by photoperiod and circadian signals. (8,9) In a recent paper(10) we described the role of the central photoperiodic factor CONSTANS (CO) in the regulation of GBSS expression in Arabidopsis. This regulation is in the basis of the change in the balance between starch and free sugars observed during the floral transition. We propose that this regulation may contribute to the florigenic signal and to the increase in sugar transport required during the flowering process.

Interactions between circadian clocks and photosynthesis for the temporal and spatial coordination of metabolism

All plant productivity, including the food that we eat, arises from the capture of solar energy by plants. At most latitudes sunlight is available for only part of the 24 h day due to the rotation of the planet. This rhythmic and predictable alteration in the environment has driven the evolution of the circadian clock, which has an extremely pervasive influence upon plant molecular biology, physiology and phenology. A number of recent studies have demonstrated that the circadian clock is integrated very closely with photosynthesis and its metabolic products. We consider the coupling of the circadian oscillator with carbohydrate biochemistry and the connections between the nuclear-encoded circadian clock and processes within chloroplasts. We describe how this might provide adaptations to optimize plant performance in an environment that varies both predictably upon a daily and seasonal basis, and unpredictably due to the weather.

Photoperiodic Regulation of Florigen Function in Arabidopsis thaliana

One mechanism through which flowering in response to seasonal change is brought about is by sensing the fluctuation in day-length; the photoperiod. Flowering induction occurs through the production of the florigenic protein FLOWERING LOCUS T (FT) and its movement from the phloem companion cells in the leaf vasculature into the shoot apex, where meristematic reprogramming occurs. FT activation in response to photoperiod condition is accomplished largely through the activity of the transcription factor CONSTANS (CO). Regulation of CO expression and protein stability, as well as the timing of other components via the circadian clock, is a critical mechanism by which plants are able to respond to photoperiod to initiate the floral transition. Modulation of FT expression in response to external and internal stimuli via components of the flowering network is crucial to mediate a fluid flowering response to a variety of environmental parameters. In addition, the regulated movement of FT protein from the phloem to the shoot apex, and interactions that determine floral meristem cell fate, constitute novel mechanisms through which photoperiodic information is translated into flowering time.

Natural diversity in daily rhythms of gene expression contributes to phenotypic variation

Daily rhythms of gene expression provide a benefit to most organisms by ensuring that biological processes are activated at the optimal time of day. Although temporal patterns of expression control plant traits of agricultural importance, how natural genetic variation modifies these patterns during the day and how precisely these patterns influence phenotypes is poorly understood. The circadian clock regulates the timing of gene expression, and natural variation in circadian rhythms has been described, but circadian rhythms are measured in artificial continuous conditions that do not reflect the complexity of biologically relevant day/night cycles. By studying transcriptional rhythms of the evening-expressed gene gigantea (GI) at high temporal resolution and during day/night cycles, we show that natural variation in the timing of GI expression occurs mostly under long days in 77 Arabidopsis accessions. This variation is explained by natural alleles that alter light sensitivity of GI, specifically in the evening, and that act at least partly independent of circadian rhythms. Natural alleles induce precise changes in the temporal waveform of GI expression, and these changes have detectable effects on phytochrome interacting factor 4 expression and growth. Our findings provide a paradigm for how natural alleles act within day/night cycles to precisely modify temporal gene expression waveforms and cause phenotypic diversity. Such alleles could confer an advantage by adjusting the activity of temporally regulated processes without severely disrupting the circadian system.

Plant genetic archaeology: whole-genome sequencing reveals the pedigree of a classical trisomic line

The circadian oscillator is astonishingly robust to changes in the environment but also to genomic changes that alter the copy number of its components through genome duplication, gene duplication, and homeologous gene loss. While studying the potential effect of aneuploidy on the Arabidopsis thaliana circadian clock, we discovered that a line thought to be trisomic for chromosome 3 also bears the gi-1 mutation, resulting in a short period and late flowering. With the help of whole-genome sequencing, we uncovered the unexpected complexity of this trisomic stock’s history, as its genome shows evidence of past outcrossing with another A. thaliana accession. Our study indicates that although historical aneuploidy lines exist and are available, it might be safer to generate new individuals and confirm their genomes and karyotypes by sequencing.

gigantea suppresses immutans variegation by interactions with cytokinin and gibberellin signaling pathways

The immutans (im) variegation mutant of Arabidopsis (Arabidopsis thaliana) is an ideal model to gain insight into factors that control chloroplast biogenesis. im defines the gene for PTOX, a plastoquinol terminal oxidase that participates in the control of thylakoid redox. Here, we report that the im defect can be suppressed during the late stages of plant development by gigantea (gi2), which defines the gene for GI, a central component of the circadian clock that plays a poorly understood role in diverse plant developmental processes. imgi2 mutants are late flowering and display other well-known phenotypes associated with gi2, such as starch accumulation and resistance to oxidative stress. We show that the restoration of chloroplast biogenesis in imgi2 is caused by a development-specific derepression of cytokinin signaling that involves cross talk with signaling pathways mediated by gibberellin (GA) and SPINDLY (SPY), a GA response inhibitor. Suppression of the plastid defect in imgi2 is likely caused by a relaxation of excitation pressures in developing plastids by factors contributed by gi2, including enhanced rates of photosynthesis and increased resistance to oxidative stress. Interestingly, the suppression phenotype of imgi can be mimicked by crossing im with the starch accumulation mutant, starch excess1 (sex1), perhaps because sex1 utilizes pathways similar to gi. We conclude that our studies provide a direct genetic linkage between GI and chloroplast biogenesis, and we construct a model of interactions between signaling pathways mediated by gi, GA, SPY, cytokinins, and sex1 that are required for chloroplast biogenesis.

EF8 is involved in photoperiodic flowering pathway and chlorophyll biogenesis in rice

A DTH8/Ghd8 allele suppresses flowering by altering the expression patterns of the 'florigen' genes, but also negatively regulates chlorophyll biogenesis. Flowering time is a critical agronomic trait determining the growing season, regional adaptation and yield potential in rice (Oryza sativa L.). We characterized a mutant named early flowering 8 (ef8) selected from an ethyl methanesulfonate (EMS)-treated population of indica cultivar 93-11. It showed earlier flowering, less grains per main panicle and slightly darker green leaves than the wild-type 93-11 under natural long-day conditions, but was not significantly different from 93-11 under natural short-day conditions. We isolated the Early Flowering 8 (EF8) gene by map-based cloning. EF8 encodes a putative HAP3 subunit of the CCAAT-box-binding transcription factor, which is localized to the nucleus. EF8 was expressed in various tissues, especially in leaves, with a rhythmic expression pattern. Our data showed that EF8 delayed flowering time under long-day conditions by altering the rhythmic expression patterns of 'florigen' genes Hd3a and RFT1. We also found that EF8 negatively regulates the expression of chlorophyll biosynthetic genes to reduce the chlorophyll content. Our data indicate that EF8 plays an important role in rice photoperiodic flowering pathway as well as yield potential and chlorophyll biogenesis and will be an important target for rice breeding programs.

Analysis of the transcriptional responses in inflorescence buds of Jatropha curcas exposed to cytokinin treatment

BACKGROUND

Jatropha curcas L. is a potential biofuel plant. Application of exogenous cytokinin (6-benzyladenine, BA) on its inflorescence buds can significantly increase the number of female flowers, thereby improving seed yield. To investigate which genes and signal pathways are involved in the response to cytokinin in J. curcas inflorescence buds, we monitored transcriptional activity in inflorescences at 0, 3, 12, 24, and 48 h after BA treatment using a microarray.

RESULTS

We detected 5,555 differentially expressed transcripts over the course of the experiment, which could be grouped into 12 distinct temporal expression patterns. We also identified 31 and 131 transcripts in J. curcas whose homologs in model plants function in flowering and phytohormonal signaling pathways, respectively. According to the transcriptional analysis of genes involved in flower development, we hypothesized that BA treatment delays floral organ formation by inhibiting the transcription of the A, B and E classes of floral organ-identity genes, which would allow more time to generate more floral primordia in inflorescence meristems, thereby enhancing inflorescence branching and significantly increasing flower number per inflorescence. BA treatment might also play an important role in maintaining the flowering signals by activating the transcription of GIGANTEA (GI) and inactivating the transcription of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and TERMINAL FLOWER 1b (TFL1b). In addition, exogenous cytokinin treatment could regulate the expression of genes involved in the metabolism and signaling of other phytohormones, indicating that cytokinin and other phytohormones jointly regulate flower development in J. curcas inflorescence buds.

CONCLUSIONS

Our study provides a framework to better understand the molecular mechanisms underlying changes in flowering traits in response to cytokinin treatment in J. curcas inflorescence buds. The results provide valuable information related to the mechanisms of cross-talk among multiple phytohormone signaling pathways in woody plants.

RAV genes: regulation of floral induction and beyond

BACKGROUND

Transcription factors of the RAV (RELATED TO ABI3 AND VP1) family are plant-specific and possess two DNA-binding domains. In Arabidopsis thaliana, the family comprises six members, including TEMPRANILLO 1 (TEM1) and TEM2. Arabidopsis RAV1 and TEM1 have been shown to bind bipartite DNA sequences, with the consensus motif C(A/C/G)ACA(N)2-8(C/A/T)ACCTG. Through direct binding to DNA, RAV proteins act as transcriptional repressors, probably in complexes with other co-repressors.

SCOPE AND CONCLUSIONS

In this review, a summary is given of current knowledge of the regulation and function of RAV genes in diverse plant species, paying particular attention to their roles in the control of flowering in arabidopsis. TEM1 and TEM2 delay flowering by repressing the production of two florigenic molecules, FLOWERING LOCUS T (FT) and gibberellins. In this way, TEM1 and TEM2 prevent precocious flowering and postpone floral induction until the plant has accumulated enough reserves or has reached a growth stage that ensures survival of the progeny. Recent results indicate that TEM1 and TEM2 are regulated by genes acting in several flowering pathways, suggesting that TEMs may integrate information from diverse pathways. However, flowering is not the only process controlled by RAV proteins. Family members are involved in other aspects of plant development, such as bud outgrowth in trees and leaf senescence, and possibly in general growth regulation. In addition, they respond to pathogen infections and abiotic stresses, including cold, dehydration, high salinity and osmotic stress.

Regulation of flowering time by the miR156-mediated age pathway

Precise flowering time is critical to reproductive success. In response to diverse exogenous and endogenous cues including age, hormones, photoperiod, and temperature, the floral transition is controlled by a complex regulatory network, which involves extensive crosstalks, feedback, or feedforward loops between the components within flowering time pathways. The newly identified age pathway, which is controlled by microRNA156 (miR156) and its target SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors, ensures plants flower under non-inductive conditions. In this review, I summarize the recent advance in understanding of the age pathway, focusing on the regulatory basis of the developmental decline in miR156 level by age and the molecular mechanism by which the age pathway is integrated into other flowering time pathways.

PHYTOCHROME C is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon

We show that in the temperate grass, Brachypodium distachyon, PHYTOCHROME C (PHYC), is necessary for photoperiodic flowering. In loss-of-function phyC mutants, flowering is extremely delayed in inductive photoperiods. PHYC was identified as the causative locus by utilizing a mapping by sequencing pipeline (Cloudmap) optimized for identification of induced mutations in Brachypodium. In phyC mutants the expression of Brachypodium homologs of key flowering time genes in the photoperiod pathway such as GIGANTEA (GI), PHOTOPERIOD 1 (PPD1/PRR37), CONSTANS (CO), and florigen/FT are greatly attenuated. PHYC also controls the day-length dependence of leaf size as the effect of day length on leaf size is abolished in phyC mutants. The control of genes upstream of florigen production by PHYC was likely to have been a key feature of the evolution of a long-day flowering response in temperate pooid grasses.

Rethinking transcriptional activation in the Arabidopsis circadian clock

Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors. The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interactions, and mathematical modelling has been useful in guiding clock research in model organisms such as Arabidopsis thaliana.

We present a model of the circadian clock in Arabidopsis, based on a large corpus of published time course data. It appears from experimental evidence in the literature that most interactions in the clock are repressive. Hence, we remove all transcriptional activation found in previous models of this system, and instead extend the system by including two new components, the morning-expressed activator RVE8 and the nightly repressor/activator NOX.

Our modelling results demonstrate that the clock does not need a large number of activators in order to reproduce the observed gene expression patterns. For example, the sequential expression of the PRR genes does not require the genes to be connected as a series of activators. In the presented model, transcriptional activation is exclusively the task of RVE8. Predictions of how strongly RVE8 affects its targets are found to agree with earlier interpretations of the experimental data, but generally we find that the many negative feedbacks in the system should discourage intuitive interpretations of mutant phenotypes. The dynamics of the clock are difficult to predict without mathematical modelling, and the clock is better viewed as a tangled web than as a series of loops.

Like most living organisms, plants are dependent on sunlight, and evolution has endowed them with an internal clock by which they can predict sunrise and sunset. The clock consists of many genes that control each other in a complex network, leading to daily oscillations in protein levels. The interactions between genes can be positive or negative, causing target genes to be turned on or off. By constructing mathematical models that incorporate our knowledge of this network, we can interpret experimental data by comparing with results from the models. Any discrepancy between experimental data and model predictions will highlight where we are lacking in understanding. We compiled more than 800 sets of measured data from published articles about the clock in the model organism thale cress (Arabidopsis thaliana). Using these data, we constructed a mathematical model which compares favourably with previous models for simulating the clock. We used our model to investigate the role of positive interactions between genes, whether they are necessary for the function of the clock and if they can be identified in the model.

Salt stress and senescence: identification of cross-talk regulatory components

Leaf senescence is an active process with a pivotal impact on plant productivity. It results from extensive signalling cross-talk coordinating environmental factors with intrinsic age-related mechanisms. Although many studies have shown that leaf senescence is affected by a range of external parameters, knowledge about the regulatory systems that govern the interplay between developmental programmes and environmental stress is still vague. Salinity is one of the most important environmental stresses that promote leaf senescence and thus affect crop yield. Improving salt tolerance by avoiding or delaying senescence under stress will therefore play an important role in maintaining high agricultural productivity. Experimental evidence suggests that hydrogen peroxide (H2O2) functions as a common signalling molecule in both developmental and salt-induced leaf senescence. In this study, microarray-based gene expression profiling on Arabidopsis thaliana plants subjected to long-term salinity stress to induce leaf senescence was performed, together with co-expression network analysis for H2O2-responsive genes that are mutually up-regulated by salt induced- and developmental leaf senescence. Promoter analysis of tightly co-expressed genes led to the identification of seven cis-regulatory motifs, three of which were known previously, namely CACGTGT and AAGTCAA, which are associated with reactive oxygen species (ROS)-responsive genes, and CCGCGT, described as a stress-responsive regulatory motif, while the others, namely ACGCGGT, AGCMGNC, GMCACGT, and TCSTYGACG were not characterized previously. These motifs are proposed to be novel elements involved in the H2O2-mediated control of gene expression during salinity stress-triggered and developmental senescence, acting through upstream transcription factors that bind to these sites.

The impact of chromatin dynamics on plant light responses and circadian clock function

Research on the functional properties of nucleosome structure and composition dynamics has revealed that chromatin-level regulation is an essential component of light signalling and clock function in plants, two processes that rely extensively on transcriptional controls. In particular, several types of histone post-translational modifications and chromatin-bound factors act sequentially or in combination to establish transcriptional patterns and to fine-tune the transcript abundance of a large repertoire of light-responsive genes and clock components. Cytogenetic approaches have also identified light-induced higher-order chromatin changes that dynamically organize the condensation of chromosomal domains into sub-nuclear foci containing silenced repeat elements. In this review, we report recently identified molecular actors that establish chromatin state dynamics in response to light signals such as photoperiod, intensity, and spectral quality. We also highlight the chromatin-dependent mechanisms that contribute to the 24-h circadian gene expression and its impact on plant physiology and development. The commonalities and contrasts of light- and clock-associated chromatin-based mechanisms are discussed, with particular emphasis on their impact on the selective regulation and rapid modulation of responsive genes.

Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS

The onset of flowering, the change from vegetative to reproductive development, is a major life history transition in flowering plants. Recent work suggests that mutations in cis-regulatory mutations should play critical roles in the evolution of this (as well as other) important adaptive traits, but thus far there has been little evidence that directly links regulatory mutations to evolutionary change at the species level. While several genes have previously been shown to affect natural variation in flowering time in Arabidopsis thaliana, most either show protein-coding changes and/or are found at low frequency (<5%). Here we identify and characterize natural variation in the cis-regulatory sequence in the transcription factor CONSTANS that underlies flowering time diversity in Arabidopsis. Mutation in this regulatory motif evolved recently and has spread to high frequency in Arabidopsis natural accessions, suggesting a role for these cis-regulatory changes in adaptive variation of flowering time.

The transcription factor CONSTANS regulates the timing of flowering in Arabidopsis. Rosas et al. report that genetic variation in the cis-regulatory regions of this gene contributes to natural phenotypic variation in flowering time.

A major QTL located on chromosome V associates with in vitro tuberization in a tetraploid potato population

The cultivated potato (Solanum tuberosum L.) is an autotetraploid species. The complexity of tetrasomic inheritance and the lack of pure lines increase the difficulty of genetic analysis of the inherited characteristics. Tuberization is the determinant step for economic yield of potato. To understand the complex genetic basis of tuberization of the cultivated potato, we developed linkage maps for a tetraploid population (F1) of 237 genotypes and mapped QTLs for the percent of in vitro tuberized plantlets (% IVT). The paternal map for E108 (well tuberized) covered 948 cM and included 12 linkage groups, all of which contained all four homologous chromosomes. The maternal map for E20 (nontuberized) covered 1,286 cM and included 14 linkage groups, 12 of which contained all four homologous chromosomes. All 12 chromosomes of potato were tagged using the SSR markers. A major QTL (MT05) with additive effect was detected on chromosome V of E108 which explained 16.23 % of the variation for % IVT, and two minor QTLs (mt05 and mt09) displaying simplex dominant effects were located on chromosome V and chromosome IX of E20 which explained 5.33 and 4.59 % of the variation for % IVT, respectively. Based on the additive model of MT05, the segregation ratio of the gametic genotypes (Q-: qq = 5:1) matched the ratio of the tuberized genotypes to the nontuberized genotypes in the population suggesting that the segregation of in vitro tuberization in this population is controlled by a major-effect gene or genes. The mapping results of three important candidate genes indicated that the QTL causal genes detected in our study are new. In this study, we developed the almost complete linkage maps of a tetraploid population, identified a major QTL on chromosome V affecting in vitro tuberization, suggested a major-effect gene with minor modifiers model controlling this trait and found that the QTLs identified here correspond to new tuberization genes. Our work provides new and useful information about the genetic basis for tuberization of this autotetraploid crop.

No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst)

The identification and cloning of full-length homologs of circadian clock genes from Picea abies represent a first step to study the function and evolution of the circadian clock in gymnosperms. Phylogenetic analyses suggest that the sequences of key circadian clock genes are conserved between angiosperms and gymnosperms. though fewer homologous copies were found for most gene families in P. abies. We detected diurnal cycling of circadian clock genes in P. abies using quantitative real-time PCR; however, cycling appeared to be rapidly dampened under free-running conditions. Given the unexpected absence of transcriptional cycling during constant conditions, we employed a complementary method to assay circadian rhythmic outputs and measured delayed fluorescence in seedlings of Norway spruce. Neither of the two approaches to study circadian rhythms in Norway spruce could detect robust ∼24 h cycling behavior under constant conditions. These data suggest gene conservation but fundamental differences in clock function between gymnosperms and other plant taxa.

The putative PRC1 RING-finger protein AtRING1A regulates flowering through repressing MADS AFFECTING FLOWERING genes in Arabidopsis

Polycomb group proteins play essential roles in the epigenetic control of gene expression in plants and animals. Although some components of Polycomb repressive complex 1 (PRC1)-like complexes have recently been reported in the model plant Arabidopsis, how they contribute to gene repression remains largely unknown. Here we show that a putative PRC1 RING-finger protein, AtRING1A, plays a hitherto unknown role in mediating the transition from vegetative to reproductive development in Arabidopsis. Loss of function of AtRING1A results in the late-flowering phenotype, which is attributed to derepression of two floral repressors, MADS AFFECTING FLOWERING 4/5 (MAF4/5), which in turn downregulate two floral pathway integrators, FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1. Levels of the H3K27me3 repressive mark at MAF4 and MAF5 loci, which is deposited by CURLY LEAF (CLF)-containing PRC2-like complexes and bound by LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), are affected by AtRING1A, which interacts with both CLF and LHP1. Levels of the H3K4me3 activation mark correlate inversely with H3K27me3 levels at MAF4 and MAF5 loci. Our results suggest that AtRING1A suppresses the expression of MAF4 and MAF5 through affecting H3K27me3 levels at these loci to regulate the floral transition in Arabidopsis.