When to switch to flowering

Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage

Rice yield is most sensitive to salinity stress imposed during the panicle initiation (PI) stage. In this study, we have focused on physiological and transcriptional responses of four rice genotypes exposed to salinity stress during PI. The genotypes selected included a pair of indicas (IR63731 and IR29) and a pair of japonica (Agami and M103) rice subspecies with contrasting salt tolerance. Physiological characterization showed that tolerant genotypes maintained a much lower shoot Na+ concentration relative to sensitive genotypes under salinity stress. Global gene expression analysis revealed a strikingly large number of genes which are induced by salinity stress in sensitive genotypes, IR29 and M103 relative to tolerant lines. We found 19 probe sets to be commonly induced in all four genotypes. We found several salinity modulated, ion homeostasis related genes from our analysis. We also studied the expression of SKC1, a cation transporter reported by others as a major source of variation in salt tolerance in rice. The transcript abundance of SKC1 did not change in response to salinity stress at PI stage in the shoot tissue of all four genotypes. However, we found the transcript abundance of SKC1 to be significantly higher in tolerant japonica Agami relative to sensitive japonica M103 under control and stressed conditions during PI stage.

Delayed flowering time in Arabidopsis and Brassica rapa by the overexpression of FLOWERING LOCUS C (FLC) homologs isolated from Chinese cabbage (Brassica rapa L.: ssp. pekinensis)

Chinese cabbage plants remain in the vegetative growth phase until they have experienced prolonged exposure to cold temperature, known as vernalization. This inhibition of flowering is caused by the high levels of FLOWERING LOCUS C (FLC) expression. To increase the product value of Chinese cabbage by inhibiting the floral transition, three genes (BrFLC1, BrFLC2, and BrFLC3) homologous to the AtFLC gene, which encodes a floral repressor, were isolated from the Chinese cabbage 'Chiifu'. These genes showed high similarity to AtFLC, although the putative BrFLC1 protein contained ten more residues than AtFLC. The BrFLC genes were expressed ubiquitously, except that BrFLC3 was not expressed in roots. BrFLC1 and BrFLC2 showed stronger expression than BrFLC3 in unvernalized and vernalized Chinese cabbage. The expression levels of the three BrFLC genes were lower in an early-flowering Chinese cabbage, suggesting that the BrFLC transcript level was associated with flowering time. Constitutive expression of the BrFLC genes in Arabidopsis significantly delayed flowering, which was also observed in transgenic Chinese cabbage overexpressing BrFLC3. These results suggest that the BrFLC genes act similarly to AtFLC. Our results provide a technique for controlling flowering time in Chinese cabbage and other crops to produce high yields of vegetative tissues.

Flowering time and elevated atmospheric CO2

Flowering is a critical milestone in the life cycle of plants, and changes in the timing of flowering may alter processes at the species, community and ecosystem levels. Therefore understanding flowering-time responses to global change drivers, such as elevated atmospheric carbon dioxide concentrations, [CO(2)], is necessary to predict the impacts of global change on natural and agricultural ecosystems. Here we summarize the results of 60 studies reporting flowering-time responses (defined as the time to first visible flower) of both crop and wild species at elevated [CO(2)]. These studies suggest that elevated [CO(2)] will influence flowering time in the future. In addition, interactions between elevated [CO(2)] and other global change factors may further complicate our ability to predict changes in flowering time. One approach to overcoming this problem is to elucidate the primary mechanisms that control flowering-time responses to elevated [CO(2)]. Unfortunately, the mechanisms controlling these responses are not known. However, past work has indicated that carbon metabolism exerts partial control on flowering time, and therefore may be involved in elevated [CO(2)]-induced changes in flowering time. This review also indicates the need for more studies addressing the effects of global change drivers on developmental processes in plants.

PDX1 is essential for vitamin B6 biosynthesis, development and stress tolerance in Arabidopsis

Vitamin B6 is an essential coenzyme for numerous metabolic enzymes and is a potent antioxidant. In plants, very little is known about its contribution to viability, growth and development. The de novo pathway of vitamin B6 biosynthesis has only been described recently and involves the protein PDX1 (pyridoxal phosphate synthase protein). Arabidopsis thaliana has three homologs of PDX1, two of which, PDX1.1 and PDX1.3, have been demonstrated as functional in vitamin B6 biosynthesis in vitro and by yeast complementation. In this study, we show that the spatial and temporal expression patterns of PDX1.1 and PDX1.3, investigated at the transcript and protein level, largely overlap, but PDX1.3 is more abundant than PDX1.1. Development of single pdx1.1 and pdx1.3 mutants is partially affected, whereas disruption of both genes causes embryo lethality at the globular stage. Detailed examination of the single mutants, in addition to those that only have a single functional copy of either gene, indicates that although these genes are partially redundant in vitamin B6 synthesis, PDX1.3 is more requisite than PDX1.1. Developmental distinctions correlate with the vitamin B6 content. Furthermore, we provide evidence that in addition to being essential for plant growth and development, vitamin B6 also plays a role in stress tolerance and photoprotection of plants.

C2H2 zinc finger-SET histone methyltransferase is a plant-specific chromatin modifier

Histone modification represents a universal mechanism for regulation of eukaryotic gene expression underlying diverse biological processes from neuronal gene expression in mammals to control of flowering in plants. In animal cells, these chromatin modifications are effected by well-defined multiprotein complexes containing specific histone-modifying activities. In plants, information about the composition of such co-repressor complexes is just beginning to emerge. Here, we report that two Arabidopsis thaliana factors, a SWIRM domain polyamine oxidase protein, AtSWP1, and a plant-specific C2H2 zinc finger-SET domain protein, AtCZS, interact with each other in plant cells and repress expression of a negative regulator of flowering, FLOWERING LOCUS C (FLC) via an autonomous, vernalization-independent pathway. Loss-of-function of either AtSWP1 or AtCZS results in reduced dimethylation of lysine 9 and lysine 27 of histone H3 and hyperacetylation of histone H4 within the FLC locus, in elevated FLC mRNA levels, and in moderately delayed flowering. Thus, AtSWP1 and AtCZS represent two main components of a co-repressor complex that fine tunes flowering and is unique to plants.

Rapid differentiation of experimental populations of wheat for heading time in response to local climatic conditions

BACKGROUND AND AIMS

Dynamic management (DM) of genetic resources aims at maintaining genetic variability between different populations evolving under natural selection in contrasting environments. In 1984, this strategy was applied in a pilot experiment on wheat (Triticum aestivum). Spatio-temporal evolution of earliness and its components (partial vernalization sensitivity, daylength sensitivity and earliness per se that determines flowering time independently of environmental stimuli) was investigated in this multisite and long-term experiment.

METHODS

Heading time of six populations from the tenth generation was evaluated under different vernalization and photoperiodic conditions.

KEY RESULTS

Although temporal evolution during ten generations was not significant, populations of generation 10 were genetically differentiated according to a north-south latitudinal trend for two components out of three: partial vernalization sensitivity and narrow-sense earliness.

CONCLUSIONS

It is concluded that local climatic conditions greatly influenced the evolution of population earliness, thus being a major factor of differentiation in the DM system. Accordingly, a substantial proportion (approximately 25 %) of genetic variance was distributed among populations, suggesting that diversity was on average conserved during evolution but was differently distributed by natural selection (and possibly drift). Earliness is a complex trait and each genetic factor is controlled by multiple homeoalleles; the next step will be to look for spatial divergence in allele frequencies.

VvMADS9, a class B MADS-box gene involved in grapevine flowering, shows different expression patterns in mutants with abnormal petal and stamen structures

VvMADS9, a MADS-box gene, from grapevine (Vitis vinifera L.) cultivar Cabernet Sauvignon has been isolated and its expression pattern studied in wild type Cabernet Sauvignon, Mourvèdre, and Bouchalès cultivars and mutants of the latter two genotypes showing abnormal petal / stamen structures. Sequence analysis showed that VvMADS9 was highly similar to PISTILLATA (PI), the class B gene that specifies the identity of petals and stamens in Arabidopsis. The temporal expression pattern of VvMADS9 studied through real-time PCR revealed that its expression was specific to flower development. The low levels of expression in the Mourvèdre mutant and the skewed expression pattern in the Bouchalès mutant as compared to their wild type counterparts suggested that VvMADS9 is involved in normal formation of petals and stamens. Through in situ hybridisation, expression of VvMADS9 was detected in stamens and weak expression on the basal regions of the petals. This suggested a possible role for VvMADS9 in specifying stamen and petal organ identity in grapevine similar to Class B genes in other species. All evidence thus pointed to the conclusion that VvMADS9 is an orthologue of PISTILLATA in grapevine.

Alternative splicing and expression analysis of OsFCA (FCA in Oryza sativa L.), a gene homologous to FCA in Arabidopsis

A subtracted cDNAs library was constructed using rice (Oryza sativa L.) calli cDNA as driver and differentiating calli cDNA as tester. A novel gene homologous with FCA in Arabidopsis was cloned from rice by screening the SSH (suppression subtractive hybridization) library followed by RACE. Four alternative transcripts of OsFCA were cloned from the leaves of rice, and designated as OsFCA-1, OsFCA-2, OsFCA-3 and OsFCA-4 respectively. OsFCA-1 was homologous to FCA-gamma of Arabidopsis and contained several conserved domains (two RNA Recognition Motifs and one WW-domain). OsFCA-2 was 102 bp shorter than OsFCA-1 which caused the WW-domain deletion. The proteins encoded by OsFCA-3 and OsFCA-4 were 101 amino acids shorter than OsFCA-1 at the N-terminal which is a glycine-rich region. The fluorescence quantitative PCR analysis showed that the mRNA of OsFCA-1 is the most abundant in the four splicing variants of rice FCA, and its expression level is much higher in differentiating calli than in calli. The expression of OsFCA-1 is steady in the leaves of three different stage, but up-regulated in young spikelet of primary branch-differentiating stage and down-regulated in young spikelet of pistil and stamen-differentiating stage.

Potent induction of Arabidopsis thaliana flowering by elevated growth temperature

The transition to flowering is an important event in the plant life cycle and is modulated by several environmental factors including photoperiod, light quality, vernalization, and growth temperature, as well as biotic and abiotic stresses. In contrast to light and vernalization, little is known about the pathways that mediate the responses to other environmental variables. A mild increase in growth temperature, from 23 degrees C to 27 degrees C, is equally efficient in inducing flowering of Arabidopsis plants grown in 8-h short days as is transfer to 16-h long days. There is extensive natural variation in this response, and we identify strains with contrasting thermal reaction norms. Exploiting this natural variation, we show that FLOWERING LOCUS C potently suppresses thermal induction, and that the closely related floral repressor FLOWERING LOCUS M is a major-effect quantitative trait locus modulating thermosensitivity. Thermal induction does not require the photoperiod effector CONSTANS, acts upstream of the floral integrator FLOWERING LOCUS T, and depends on the hormone gibberellin. Analysis of mutants defective in salicylic acid biosynthesis suggests that thermal induction is independent of previously identified stress-signaling pathways. Microarray analyses confirm that the genomic responses to floral induction by photoperiod and temperature differ. Furthermore, we report that gene products that participate in RNA splicing are specifically affected by thermal induction. Above a critical threshold, even small changes in temperature can act as cues for the induction of flowering. This response has a genetic basis that is distinct from the known genetic pathways of floral transition, and appears to correlate with changes in RNA processing.

The tropical cedar tree (Cedrela fissilis Vell., Meliaceae) homolog of the Arabidopsis LEAFY gene is expressed in reproductive tissues and can complement Arabidopsis leafy mutants

A homolog of FLORICAULA/LEAFY, CfLFY (for Cedrela fissilis LFY), was isolated from tropical cedar. The main stages of the reproductive development in C. fissilis were documented by scanning electron microscopy and the expression patterns of CfLFY were studied during the differentiation of the floral meristems. Furthermore, the biological role of the CfLFY gene was assessed using transgenic Arabidopsis plants. CfLFY showed a high degree of similarity to other plant homologs of FLO/LFY. Southern analysis showed that CfLFY is a single-copy gene in the tropical cedar genome. Northern blot analysis and in situ hybridization results showed that CfLFY was expressed in the reproductive buds during the transition from vegetative to reproductive growth, as well as in floral meristems and floral organs but was excluded from the vegetative apex and leaves. Transgenic Arabidopsis lfy26 mutant lines expressing the CfLFY coding region, under the control of the LFY promoter, showed restored wild-type phenotype. Taken together, our results suggest that CfLFY is a FLO/LFY homolog probably involved in the control of tropical cedar reproductive development.

Microarray Analysis Reveals Vegetative Molecular Phenotypes of Arabidopsis Flowering-time Mutants

The transition to flowering occurs at the shoot apex; however, most of the characterized genes that affect the timing of floral induction are expressed throughout the plant. To further our understanding of these genes and the flowering process, the vegetative molecular phenotypes of 16 Arabidopsis mutants associated with the major flowering initiation pathways were assayed using a 13,000 clone microarray under two different conditions that affect flowering. All mutants showed at least one change in gene expression other than the mutant flowering gene. Metabolism- and defence-related pathways were the areas with the most frequent gene expression changes detected in the mutants. Several genes such as EARLI1 were differentially expressed in a number of flowering mutants from different flowering pathways. Analysis of the promoter regions of genes differentially expressed identified common promoter elements, indicating some form of common regulation.

The rubber tree (Hevea brasiliensis Muell. Arg.) homologue of the LEAFY/FLORICAULA gene is preferentially expressed in both male and female floral meristems

The rubber tree (Hevea brasiliensis Muell. Arg.) is an important source of natural rubber in tropical regions and, as with many woody species, shows a long juvenile phase. To understand the genetic and molecular mechanisms underlying the reproductive process in rubber trees, H. brasiliensis RRIM600 flower and inflorescence development have been characterized, the rubber tree FLORICAULA/LEAFY (FLO/LFY) orthologue, HbLFY, cloned, and its expression patterns were analysed during vegetative and reproductive development. The rubber tree, similar to other Euphorbiaceae species, produces lateral inflorescences containing male, female, and bisexual flowers. HbLFY is expressed in lateral meristems that give rise to inflorescences and in all flower meristems, consistent with a role in reproductive development. Complementation studies using Arabidopsis lfy mutants indicated that the biological function of LFY might be conserved among Brassicaceae and Euphorbiaceae species.

Simple heuristics and rules of thumb: Where psychologists and behavioural biologists might meet

The Centre for Adaptive Behaviour and Cognition (ABC) has hypothesised that much human decision-making can be described by simple algorithmic process models (heuristics). This paper explains this approach and relates it to research in biology on rules of thumb, which we also review. As an example of a simple heuristic, consider the lexicographic strategy of Take The Best for choosing between two alternatives: cues are searched in turn until one discriminates, then search stops and all other cues are ignored. Heuristics consist of building blocks, and building blocks exploit evolved or learned abilities such as recognition memory; it is the complexity of these abilities that allows the heuristics to be simple. Simple heuristics have an advantage in making decisions fast and with little information, and in avoiding overfitting. Furthermore, humans are observed to use simple heuristics. Simulations show that the statistical structures of different environments affect which heuristics perform better, a relationship referred to as ecological rationality. We contrast ecological rationality with the stronger claim of adaptation. Rules of thumb from biology provide clearer examples of adaptation because animals can be studied in the environments in which they evolved. The range of examples is also much more diverse. To investigate them, biologists have sometimes used similar simulation techniques to ABC, but many examples depend on empirically driven approaches. ABC's theoretical framework can be useful in connecting some of these examples, particularly the scattered literature on how information from different cues is integrated. Optimality modelling is usually used to explain less detailed aspects of behaviour but might more often be redirected to investigate rules of thumb.

Silencing the nuclear actin-related protein AtARP4 in Arabidopsis has multiple effects on plant development, including early flowering and delayed floral senescence

Actin-related proteins (ARPs) share moderate sequence homology and basal structure with conventional actins and are found in all eukaryotes. While the functions of most of the divergent ARPs are not clear, several of them are localized to the nucleus and have been identified as components of various chromatin-modifying complexes. Using an antibody to Arabidopsis AtARP4, we found this conserved homolog of human BAF53 and yeast Arp4 is concentrated in the nucleoplasm of Arabidopsis, Brassica, and tobacco cells. To gain further insight into the role of ARP4, we have examined Arabidopsis plants that are defective in AtARP4 expression. Phenotypic analysis of the arp4-1 mutant allele, which has a T-DNA insertion in the promoter region and a moderate reduction in the level of AtARP4 protein expression, revealed partial sterility due to defects in anther development. Targeting the distinct, 3' UTR of AtARP4 transcripts with RNA interference caused a drastic reduction in the level of AtARP4 protein expression in several independent transgenic lines, and resulted in strong pleiotropic phenotypes such as altered organization of plant organs, early flowering, delayed flower senescence and high levels of sterility. Western blot analysis and immunolabeling demonstrated a clear correlation between reductions in the level of AtARP4 expression and severity of the phenotypes. Based on our results and data on the orthologs of AtARP4 in yeast and other organisms, we suggest that AtARP4 is likely to exert its effects on plant development through the modulation of chromatin structure and subsequent changes in gene regulation.

Differential regulation of FLOWERING LOCUS C expression by vernalization in cabbage and Arabidopsis

Vernalization is required to induce flowering in cabbage (Brassica oleracea var Capitata L.). Since FLOWERING LOCUS C (FLC) was identified as a major repressor of flowering in the vernalization pathway in Arabidopsis (Arabidopsis thaliana), two homologs of AtFLC, BoFLC3-2 and BoFLC4-1, were isolated from cabbage to investigate the molecular mechanism of vernalization in cabbage flowering. In addition to the sequence homology, the genomic organization of cabbage FLC is similar to that of AtFLC, except that BoFLC has a relatively smaller intron 1 compared to that of AtFLC. A vernalization-mediated decrease in FLC transcript level was correlated with an increase in FT transcript level in the apex of cabbage. This observation is in agreement with the down-regulation of FT by FLC in Arabidopsis. Yet, unlike that in Arabidopsis, the accumulation of cabbage FLC transcript decreased after cold treatment of leafy plants but not imbibed seeds, which is consistent with the promotion of cabbage flowering by vernalizing adult plants rather than seeds. To further dissect the different regulation of FLC expression between seed-vernalization-responsive species (e.g. Arabidopsis) and plant-vernalization-responsive species (e.g. cabbage), the pBoFLC4-1BoFLC4-1GUS construct was introduced into Arabidopsis to examine its vernalization response. Down-regulation of the BoFLC4-1GUS construct by seed vernalization was unstable and incomplete; in addition, the expression of BoFLC4-1GUS was not suppressed by vernalization of transgenic rosette-stage Arabidopsis plants. We propose a hypothesis to illustrate the distinct mechanism by which vernalization regulates the expression of FLC in cabbage and Arabidopsis.

Flowering time control: gene network modelling and the link to quantitative genetics

Flowering is a key stage in plant development that initiates grain production and is vulnerable to stress. The genes controlling flowering time in the model plant Arabidopsis thaliana are reviewed. Interactions between these genes have been described previously by qualitative network diagrams. We mathematically relate environmentally dependent transcription, RNA processing, translation, and protein–protein interaction rates to resultant phenotypes. We have developed models (reported elsewhere) based on these concepts that simulate flowering times for novel A. thaliana genotype–environment combinations. Here we draw 12 contrasts between genetic network (GN) models of this type and quantitative genetics (QG), showing that both have equal contributions to make to an ideal theory. Physiological dominance and additivity are examined as emergent properties in the context of feed-forwards networks, an instance of which is the signal-integration portion of the A. thaliana flowering time network. Additivity is seen to be a complex, multi-gene property with contributions from mass balance in transcript production, the feed-forwards structure itself, and downstream promoter reaction thermodynamics. Higher level emergent properties are exemplified by critical short daylength (CSDL), which we relate to gene expression dynamics in rice (Oryza sativa). Next to be discussed are synergies between QG and GN relating to the quantitative trait locus (QTL) mapping of model coefficients. This suggests a new verification test useful in GN model development and in identifying needed updates to existing crop models. Finally, the utility of simple models is evinced by 80 years of QG theory and mathematical ecology.

A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles

Flowers are icons in developmental studies of complex structures. The vast majority of 250,000 angiosperm plant species have flowers with a conserved organ plan bearing sepals, petals, stamens, and carpels in the center. The combinatorial model for the activity of the so-called ABC homeotic floral genes has guided extensive experimental studies in Arabidopsis thaliana and many other plant species. However, a mechanistic and dynamical explanation for the ABC model and prevalence among flowering plants is lacking. Here, we put forward a simple discrete model that postulates logical rules that formally summarize published ABC and non-ABC gene interaction data for Arabidopsis floral organ cell fate determination and integrates this data into a dynamic network model. This model shows that all possible initial conditions converge to few steady gene activity states that match gene expression profiles observed experimentally in primordial floral organ cells of wild-type and mutant plants. Therefore, the network proposed here provides a dynamical explanation for the ABC model and shows that precise signaling pathways are not required to restrain cell types to those found in Arabidopsis, but these are rather determined by the overall gene network dynamics. Furthermore, we performed robustness analyses that clearly show that the cell types recovered depend on the network architecture rather than on specific values of the model's gene interaction parameters. These results support the hypothesis that such a network constitutes a developmental module, and hence provide a possible explanation for the overall conservation of the ABC model and overall floral plan among angiosperms. In addition, we have been able to predict the effects of differences in network architecture between Arabidopsis and Petunia hybrida.

A cluster of Arabidopsis genes with a coordinate response to an environmental stimulus

Vernalization, the promotion of flowering after prolonged exposure to low temperatures, is an adaptive response of plants ensuring that flowering occurs at a propitious time in the annual seasonal cycle. In Arabidopsis, FLOWERING LOCUS C (FLC), which encodes a repressor of flowering, is a key gene in the vernalization response; plants with high-FLC expression respond to vernalization by downregulating FLC and thereby flowering at an earlier time. Vernalization has the hallmarks of an epigenetically regulated process. The downregulation of FLC by low temperatures is maintained throughout vegetative development but is reset at each generation. During our study of vernalization, we have found that a small gene cluster, including FLC and its two flanking genes, is coordinately regulated in response to genetic modifiers, to the environmental stimulus of vernalization, and in plants with low levels of DNA methylation. Genes encoded on foreign DNA inserted into the cluster also acquire the low-temperature response. At other chromosomal locations, FLC maintains its response to vernalization and imposes a parallel response on a flanking gene. This suggests that FLC contains sequences that confer changes in gene expression extending beyond FLC itself, perhaps through chromatin modification.

Cell wall invertase expression at the apical meristem alters floral, architectural, and reproductive traits in Arabidopsis thaliana

Resource allocation is a major determinant of plant fitness and is influenced by external as well as internal stimuli. We have investigated the effect of cell wall invertase activity on the transition from vegetative to reproductive growth, inflorescence architecture, and reproductive output, i.e. seed production, in the model plant Arabidopsis thaliana by expressing a cell wall invertase under a meristem-specific promoter. Increased cell wall invertase activity causes accelerated flowering and an increase in seed yield by nearly 30%. This increase is caused by an elevation of the number of siliques, which results from enhanced branching of the inflorescence. On the contrary, as cytosolic enzyme, the invertase causes delayed flowering, reduced seed yield, and branching. This demonstrates that invertases not only are important in determining sink strength of storage organs but also play a role in regulating developmental processes.

Floral meristem identity genes are expressed during tendril development in grapevine

To study the early steps of flower initiation and development in grapevine (Vitis vinifera), we have isolated two MADS-box genes, VFUL-L and VAP1, the putative FUL-like and AP1 grapevine orthologs, and analyzed their expression patterns during vegetative and reproductive development. Both genes are expressed in lateral meristems that, in grapevine, can give rise to either inflorescences or tendrils. They are also coexpressed in inflorescence and flower meristems. During flower development, VFUL-L transcripts are restricted to the central part of young flower meristems and, later, to the prospective carpel-forming region, which is consistent with a role of this gene in floral transition and carpel and fruit development. Expression pattern of VAP1 suggests that it may play a role in flowering transition and flower development. However, its lack of expression in sepal primordia, does not support its role as an A-function gene in grapevine. Neither VFUL-L nor VAP1 expression was detected in vegetative organs such as leaves or roots. In contrast, they are expressed throughout tendril development. Transcription of both genes in tendrils of very young plants that have not undergone flowering transition indicates that this expression is independent of the flowering process. These unique expression patterns of genes typically involved in reproductive development have implications on our understanding of flower induction and initiation in grapevine, on the origin of grapevine tendrils and on the functional roles of AP1-and FUL-like genes in plant development. These results also provide molecular support to the hypothesis that Vitis tendrils are modified reproductive organs adapted to climb.

Environmental and genetic effects on flowering differences between northern and southern populations of Arabidopsis lyrata (Brassicaceae)

Arabidopsis lyrata (Brassicaceae) is a close outcrossing relative of A. thaliana. We examine flowering time variation of northern and southern A. lyrata populations in controlled environmental conditions, in a common garden experiment with A. thaliana, and in the field. Southern populations of A. lyrata flowered earlier than northern ones in all environmental conditions. Individuals from southern populations were more likely to flower in short days (14 h light) than northern ones, and all populations had a higher probability of flowering and flowered more rapidly in long days (20 h). The interaction of population and day length significantly affected flowering probability, and flowering time in one of two comparisons. The common garden experiment demonstrated differences between populations in the response to seed cold treatment, but growth chamber experiments showed no vernalization effect after 4 wk of rosette cold treatment. In a field population in Norway, a high proportion of the plants flowered in each year of the study. The plants progressed to flowering more rapidly in the field and common garden than in the growth chamber. The genetic basis of these flowering time differences here can be further studied using A. thaliana genetic tools.

Altered expression of GFLO, the Gesneriaceae homologue of FLORICAULA/LEAFY, is associated with the transition to bulbil formation in Titanotrichum oldhamii

Titanotrichum oldhamii inflorescences switch from flower to bulbil production at the end of the flowering season. The structure of the bulbiliferous shoots resembles the abnormal meristematic organization of the Antirrhinum mutant, floricaula. Gesneriaceae- FLORICAULA (GFLO) is thus a candidate gene in the regulation of bulbil formation. To investigate this hypothesis, part of the GFLO gene (between the second and third exon) was isolated using degenerate primers designed in regions conserved between Antirrhinum, Nicotiana and Arabidopsis, followed by genome walking to obtain the complete gene and flanking sequences. RT-PCR results showed that the GFLO homologue is strongly expressed in inflorescence apical meristems and young flowers. However, in meristems that had switched to bulbil formation, GFLO transcription was greatly reduced. The down-regulation of GFLO in bulbil primordia indicates that this gene is connected to, or part of, the bulbil-flower regulatory pathway. Phylogenetic analysis confirms the orthology of GFLO and FLO, and indicates that the gene may be useful for phylogenetic reconstruction at the genus or family level.

Salicylic acid regulates flowering time and links defence responses and reproductive development

Flowering relies on signaling networks that integrate endogenous and external cues. Normally, plants flower at a particular season, reflecting day length and/or temperature cues. However, plants can surpass this seasonal regulation and show precocious flowering under stress environmental conditions. Here, we show that UV-C light stress activates the transition to flowering in Arabidopsis thaliana through salicylic acid (SA). Moreover, SA also regulates flowering time in non-stressed plants, as SA-deficient plants are late flowering. The regulation of flowering time by SA seems to involve the photoperiod and autonomous pathways, but it does not require the function of the flowering time genes CONSTANS (CO), FCA, or FLOWERING LOCUS C (FLC).

Regulation of Flowering Time by Histone Acetylation in Arabidopsis

The Arabidopsis autonomous floral-promotion pathway promotes flowering independently of the photoperiod and vernalization pathways by repressing FLOWERING LOCUS C (FLC), a MADS-box transcription factor that blocks the transition from vegetative to reproductive development. Here, we report that FLOWERING LOCUS D (FLD), one of six genes in the autonomous pathway, encodes a plant homolog of a protein found in histone deacetylase complexes in mammals. Lesions in FLD result in hyperacetylation of histones in FLC chromatin, up-regulation of FLC expression, and extremely delayed flowering. Thus, the autonomous pathway regulates flowering in part by histone deacetylation. However, not all autonomous-pathway mutants exhibit FLC hyperacetylation, indicating that multiple means exist by which this pathway represses FLC expression.

The role of cryptochrome 2 in flowering in Arabidopsis

We have investigated the genetic interactions between cry2 and the various flowering pathways in relation to the regulation of flowering by photoperiod and vernalization. For this, we combined three alleles of CRY2, the wild-type CRY2-Landsberg erecta (Ler), a cry2 loss-of-function null allele, and the gain-of-function CRY2-Cape Verde Islands (Cvi), with mutants representing the various photoreceptors and flowering pathways. The analysis of CRY2 alleles combined with photoreceptor mutants showed that CRY2-Cvi could compensate the loss of phyA and cry1, also indicating that cry2 does not require functional phyA or cry1. The analysis of mutants of the photoperiod pathway showed epistasis of co and gi to the CRY2 alleles, indicating that cry2 needs the product of CO and GI genes to promote flowering. All double mutants of this pathway showed a photoperiod response very much reduced compared with Ler. In contrast, mutations in the autonomous pathway genes were additive to the CRY2 alleles, partially overcoming the effects of CRY2-Cvi and restoring day length responsiveness. The three CRY2 alleles were day length sensitive when combined with FRI-Sf2 and/or FLC-Sf2 genes, which could be reverted when the delay of flowering caused by FRI-Sf2 and FLC-Sf2 alleles was removed by vernalization. In addition, we looked at the expression of FLC and CRY2 genes and showed that CRY2 is negatively regulated by FLC. These results indicate an interaction between the photoperiod and the FLC-dependent pathways upstream to the common downstream targets of both pathways, SOC1 and FT.

EARLY FLOWERING 4 functions in phytochrome B-regulated seedling de-etiolation

To define the functions of genes previously identified by expression profiling as being rapidly light induced under phytochrome (phy) control, we are investigating the seedling de-etiolation phenotypes of mutants carrying T-DNA insertional disruptions at these loci. Mutants at one such locus displayed reduced responsiveness to continuous red, but not continuous far-red light, suggesting a role in phyB signaling but not phyA signaling. Consistent with such a role, expression of this gene is induced by continuous red light in wild-type seedlings, but the level of induction is strongly reduced in phyB-null mutants. The locus encodes a novel protein that we show localizes to the nucleus, thus suggesting a function in light-regulated gene expression. Recently, this locus was identified as EARLY FLOWERING 4, a gene implicated in floral induction and regulating the expression of the gene CIRCADIAN CLOCK-ASSOCIATED 1. Together with these previous data, our findings suggest that EARLY FLOWERING 4 functions as a signaling intermediate in phy-regulated gene expression involved in promotion of seedling de-etiolation, circadian clock function, and photoperiod perception.

Characterization and functional analysis of three wheat genes with homology to the CONSTANS flowering time gene in transgenic rice

The CONSTANS (CO) gene of Arabidopsis plays a key role in the photoperiodic flowering pathway. To investigate photoperiod responses in cereals in more detail, we isolated three kinds of CO/Hd1 (rice ortholog of CO) homolog from hexaploid wheat, derived from the A, B, and D genomes and designated as wheat ortholog of CO from A genome (TaHd1-1), TaHd1-2, and TaHd1-3, respectively. They were highly similar to each other and to Hd1, and in addition harbored two conserved regions: two zinc finger motifs and CONSTANS, CONSTANS-LIKE and TIMING OF CAB EXPRESSION 1 (CCT) domain like CO/Hd1. They were located on the long arm of the homoeologous chromosome 6. TaHd1-2 harbored a 63-bp deletion at the promoter region containing the GATA-1 box, and consequently, we detected no subsequent transcript. The TaHd1-1 genomic clone was introduced to a rice line deficient in Hd1 function. Transgenic plants complemented the functions of rice Hd1: they promoted heading under short-day (SD) conditions and delayed it under long-day (LD)/natural conditions, indicating that Hd1 proteins from SD and LD plants share common structures and functions.

Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L)

BACKGROUND

The genetics of spikelet formation, a feature unique to grasses such as rice and maize, is yet to be fully understood, although a number of meristem and organ identity mutants have been isolated and investigated in Arabidopsis and maize. Using a two-element Ac/Ds transposon tagging system we have isolated a rice mutant, designated branched floretless 1 (bfl1) which is defective in the transition from spikelet meristem to floret meristem.

RESULTS

The bfl1 mutant shows normal differentiation of the primary rachis-branches leading to initial spikelet meristem (bract-like structure equivalent to rudimentary glumes) formation but fails to develop empty glumes and florets. Instead, axillary meristems in the bract-like structure produce sequential alternate branching, thus resulting in a coral shaped morphology of the branches in the developing panicle. The bfl1 mutant harbours a single Ds insertion in the upstream region of the BFL1 gene on chromosome 7 corresponding to PAC clone P0625E02 (GenBank Acc No. message URL http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=34395191&dopt=GenBank&term=ap004570AP004570). RT-PCR analyses revealed a drastic reduction of BFL1 transcript levels in the bfl1 mutant compared to that in the wild-type. In each of the normal panicle-bearing progeny plants, from occasional revertant seeds of the vegetatively-propagated mutant plant, Ds was shown to be excised from the bfl1 locus. BFL1 contains an EREBP/AP2 domain and is most likely an ortholog of the maize transcription factor gene BRANCHED SILKLESS1 (BD1).

CONCLUSIONS

bfl1 is a Ds-tagged rice mutant defective in the transition from spikelet meristem (SM) to floret meristem (FM). BFL1 is most probably a rice ortholog of the maize ERF (EREBP/AP2) transcription factor gene BD1. Based on the similarities in mutant phenotypes bfl1 is likely to be an allele of the previously reported frizzy panicle locus.

Flowering time: a pathway that begins at the 3' end

Flowering time control in plants involves integration of multiple signals. One of the signalling pathways in Arabidopsis involves a negative autoregulatory loop, in which the FCA protein together with FY promotes the choice of an alternative polyadenylation site within the FCA pre-mRNA to produce a transcript that does not encode a functional protein.

Genotype-Environment Interactions at Quantitative Trait Loci Affecting Inflorescence Development in Arabidopsis thaliana

Phenotypic plasticity and genotype-environment interactions (GEI) play a prominent role in plant morphological diversity and in the potential functional capacities of plant life-history traits. The genetic basis of plasticity and GEI, however, is poorly understood in most organisms. In this report, inflorescence development patterns in Arabidopsis thaliana were examined under different, ecologically relevant photoperiod environments for two recombinant inbred mapping populations (Ler × Col and Cvi × Ler) using a combination of quantitative genetics and quantitative trait locus (QTL) mapping. Plasticity and GEI were regularly observed for the majority of 13 inflorescence traits. These observations can be attributable (at least partly) to variable effects of specific QTL. Pooled across traits, 12/44 (27.3%) and 32/62 (51.6%) of QTL exhibited significant QTL × environment interactions in the Ler × Col and Cvi × Ler lines, respectively. These interactions were attributable to changes in magnitude of effect of QTL more often than to changes in rank order (sign) of effect. Multiple QTL × environment interactions (in Cvi × Ler) clustered in two genomic regions on chromosomes 1 and 5, indicating a disproportionate contribution of these regions to the phenotypic patterns observed. High-resolution mapping will be necessary to distinguish between the alternative explanations of pleiotropy and tight linkage among multiple genes.

The SOC1 MADS-box gene integrates vernalization and gibberellin signals for flowering in Arabidopsis

The floral transition in Arabidopsis is regulated by at least four flowering pathways: the long-day, autonomous, vernalization, and gibberellin (GA)-dependent pathways. Previously, we reported that the MADS-box transcription factor SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) integrates the long-day and vernalization/autonomous pathways. Here, we present evidences that SOC1 also integrates signaling from the GA-dependent pathway, a major flowering pathway under non-inductive short days. Under short days, the flowering time of GA-biosynthetic and -signaling mutants was well correlated with the level of SOC1 expression; overexpression of SOC1 rescued the non-flowering phenotype of ga1-3, and the soc1 null mutant showed reduced sensitivity to GA for flowering. In addition, we show that vernalization-induced repression of FLOWERING LOCUS C (FLC), an upstream negative regulator of SOC1, is not sufficient to activate SOC1; positive factors are also required. Under short days, the GA pathway provides a positive factor for SOC1 activation. In contrast to SOC1, the GA pathway does not regulate expression of other flowering integrators FLC and FT. Our results explain why the GA pathway has a strong effect on flowering under short days and how vernalization and GA interact at the molecular level.

TaVRT-1, a putative transcription factor associated with vegetative to reproductive transition in cereals

The molecular genetics of vernalization, defined as the promotion of flowering by cold treatment, is still poorly understood in cereals. To better understand this mechanism, we cloned and characterized a gene that we named TaVRT-1 (wheat [Triticum aestivum] vegetative to reproductive transition-1). Molecular and sequence analyses indicated that this gene encodes a protein homologous to the MADS-box family of transcription factors that comprises certain flowering control proteins in Arabidopsis. Mapping studies have localized this gene to the Vrn-1 regions on the long arms of homeologous group 5 chromosomes, regions that are associated with vernalization and freezing tolerance (FT) in wheat. The level of expression of TaVRT-1 is positively associated with the vernalization response and transition from vegetative to reproductive phase and is negatively associated with the accumulation of COR genes and degree of FT. Comparisons among different wheat genotypes, near-isogenic lines, and cereal species, which differ in their vernalization response and FT, indicated that the gene is inducible only in those species that require vernalization, whereas it is constitutively expressed in spring habit genotypes. In addition, experiments using both the photoperiod-sensitive barley (Hordeum vulgare cv Dicktoo) and short or long day de-acclimated wheat revealed that the expression of TaVRT-1 is also regulated by photoperiod. These expression studies indicate that photoperiod and vernalization may regulate this gene through separate pathways. We suggest that TaVRT-1 is a key developmental gene in the regulatory pathway that controls the transition from the vegetative to reproductive phase in cereals.

Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes

Floral transition should be strictly regulated because it is one of the most critical developmental processes in plants. Arabidopsis terminal flower 2 (tfl2) mutants show an early-flowering phenotype that is relatively insensitive to photoperiod, as well as several other pleiotropic phenotypes. We found that the early flowering of tfl2 is caused mainly by ectopic expression of the FLOWERING LOCUS T (FT) gene, a floral pathway integrator. Molecular cloning of TFL2 showed that it encodes a protein with homology to heterochromatin protein 1 (HP1) of animals and Swi6 of fission yeast. TFL2 protein localizes in subnuclear foci and expression of the TFL2 gene complemented yeast swi6(-) mutants. These results suggested that TFL2 might function as an HP1 in Arabidopsis: Gene expression analyses using DNA microarrays, however, did not show an increase in the expression of heterochromatin genes in tfl2 mutants but instead showed the upregulation of the floral homeotic genes APETALA3, PISTILLATA, AGAMOUS and SEPALLATA3. The pleiotropic phenotype of the tfl2 mutant could reflect the fact that TFL2 represses the expression of multiple genes. Our results demonstrate that despite its homology to HP1, TFL2 is involved in the repression of specific euchromatin genes and not heterochromatin genes in Arabidopsis.

Forestry's fertile crescent: the application of biotechnology to forest trees

Relative to crop plants, the domestication of forest trees is still in its infancy. For example, the domestication of many crop plants was initiated some 10,000 years ago in the so-called 'Fertile Crescent' of the Middle East. By contrast, the domestication of forest trees for the purposes of producing more fibre began in earnest in the last half century. The application of biotechnology to forest trees offers a great potential to hasten the pace of tree improvement for desirable end uses. This review outlines some of the progress that has been made in the application of biotechnology to forest trees, and considers the prospects for biotechnologically based tree improvement in the future.

Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold

The Arabidopsis FLOWERING LOCUS C (FLC) gene is a key floral repressor in the maintenance of a vernalization response. In vernalization-sensitive genetic backgrounds, FLC levels are high, and they decline after exposure to long cold periods. Four FLC paralogs (MAF2 [MADS AFFECTING FLOWERING2] to MAF5) are arranged in a tandem array on the bottom of Arabidopsis chromosome V. We used a reverse genetics approach to analyze their functions. Loss-of-function and gain-of-function studies indicate that MAF2 acts as a floral repressor. In particular, maf2 mutant plants display a pronounced vernalization response when subjected to relatively short cold periods, which are insufficient to elicit a strong flowering response in the wild type, despite producing a large reduction in FLC levels. MAF2 expression is less sensitive to vernalization than that of FLC, and its repressor activity is exerted independently or downstream of FLC transcription. Thus, MAF2 can prevent premature vernalization in response to brief cold spells. Overexpression of MAF3 or MAF4 produces alterations in flowering time that suggest that these genes also act as floral repressors and might contribute to the maintenance of a vernalization requirement. However, the final gene in the cluster, MAF5, is upregulated by vernalization. Therefore, MAF5 could play an opposite role to FLC in the vernalization response.

Expression profiling and bioinformatic analyses of a novel stress-regulated multispanning transmembrane protein family from cereals and Arabidopsis

Cold acclimation is a multigenic trait that allows hardy plants to develop efficient tolerance mechanisms needed for winter survival. To determine the genetic nature of these mechanisms, several cold-responsive genes of unknown function were identified from cold-acclimated wheat (Triticum aestivum). To identify the putative functions and structural features of these new genes, integrated genomic approaches of data mining, expression profiling, and bioinformatic predictions were used. The analyses revealed that one of these genes is a member of a small family that encodes two distinct groups of multispanning transmembrane proteins. The cold-regulated (COR)413-plasma membrane and COR413-thylakoid membrane groups are potentially targeted to the plasma membrane and thylakoid membrane, respectively. Further sequence analysis of the two groups from different plant species revealed the presence of a highly conserved phosphorylation site and a glycosylphosphatidylinositol-anchoring site at the C-terminal end. No homologous sequences were found in other organisms suggesting that this family is specific to the plant kingdom. Intraspecies and interspecies comparative gene expression profiling shows that the expression of this gene family is correlated with the development of freezing tolerance in cereals and Arabidopsis. In addition, several members of the family are regulated by water stress, light, and abscisic acid. Structure predictions and comparative genome analyses allow us to propose that the cor413 genes encode putative G-protein-coupled receptors.

Phytochrome control of flowering is temperature sensitive and correlates with expression of the floral integrator FT

In Arabidopsis flowering is accelerated by reduced red:far-red (R:FR) ratio which signals the presence of neighbouring vegetation. Hastened flowering is one component of the shade-avoidance syndrome of responses, which alter many aspects of development in response to the threat of potential competition. Of the red/far-red-absorbing photoreceptors it is phyB that plays the most prominent role in shade-avoidance, although other related phytochromes act redundantly with phyB. It is well established that the phyB mutant has a constitutively early flowering phenotype. However, we have shown that the early flowering phenotype of phyB is temperature-dependent. We have established that this temperature-sensitive flowering response defines a pathway that appears to be independent of the autonomous-FLC pathway. Furthermore, we have demonstrated that the phytochromes control the expression of the floral promoter FT. We have also shown that other phyB-controlled responses, including petiole elongation, are not sensitive to the same temperature change. This suggests that discrete pathways control flowering and petiole elongation, components of the shade-avoidance response. This work provides an insight into the phytochrome and temperature interactions that maintain flowering control.

Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis

Phytochrome-mediated perception of the ratio of red to far-red wavelengths in the ambient light environment is fundamental to plant growth and development. Such monitoring enables plants to detect neighboring vegetation and initiate avoidance responses, thus conferring considerable selective advantage. The shade avoidance syndrome in plants is characterized by elongation growth and early flowering, responses that are fully induced by end-of-day far-red light treatments. Elucidating the roles of individual phytochromes in mediating responses to red to far-red has however always been confounded by synergistic and mutually antagonistic coactions between family members. The creation of triple and quadruple mutants in Arabidopsis, deficient in multiple phytochromes, has revealed functional redundancy between phyB, D, and E in controlling flowering time, leaf development, and regulation of the homeobox gene, ATHB-2. In addition, mutant analysis suggests a possible novel role for phyC in suppressing ATHB-2 transcription in the light.

Transgenic expression of a putative calcium transporter affects the time of Arabidopsis flowering

PPF1 is a gibberellin-induced, vegetative growth-specific gene, first isolated from short-day (SD)-grown G2 pea plants. In the current work, we found that transgenic Arabidopsis plants overexpressing the PPF1 gene (PPF1 (+)) flowered much later and had a significantly longer lifespan compared to control plants, whereas suppression of this gene (PPF1 (-)) resulted in a very rapid reproductive cycle. Western blotting analyses of PPF1 (+) and (-) plant lines revealed a positive correlation between the amount of antibody-reactive protein and the time of flowering. Green fluorescent protein (GFP) co-expression assays showed that the PPF1 protein is likely localized in chloroplast membranes. Transgenic expression of PPF1 affected the calcium storage capacities since chloroplasts isolated from PPF1 (+) plants contained high Ca2+ levels while chloroplasts of PPF1 (-) plants contained very low amounts of calcium ion. Using Novikoff human hepatoma cells, we demonstrated that expression of PPF1 leads to a significant inward calcium ion current that was absent in untransformed cells. We conclude that, as a putative calcium ion carrier, PPF1 affects the flowering time of higher plants by modulating Ca2+ storage capacity within chloroplasts.

Endogenous alpha-ketol linolenic acid levels in short day-induced cotyledons are closely related to flower induction in Pharbitis nil

Alpha-ketol linolenic acid [KODA, 9,10-ketol-octadecadienoic acid, that is 9-hydroxy-10-oxo-12(Z),15(Z)-octadecadienoic acid] is a signal compound found in Lemna paucicostata after exposure to stress, such as drought, heat or osmotic stress. KODA reacts with catecholamines to generate products that strongly induce flowering, although KODA itself is inactive [Yokoyama et al. (2000) Plant Cell Physiol. 41: 110; Yamaguchi et al. (2001) Plant Cell Physiol. 42: 1201]. We examined the role of KODA in the flower-induction process of Pharbitis nil (violet). KODA was identified for the first time in seedlings of P. nil grown under a flower-inductive condition (16-h dark exposure), by means of LC-SIM and LC-MS/MS. In addition, the changes in endogenous KODA levels (evaluated after esterification of KODA with 9-anthryldiazomethane) during the flower-inductive phase in short day-induced cotyledons were closely related to flower induction. The KODA concentration sharply increased in seedlings during the last 2 h of a 16-h dark period, while the KODA level showed no significant elevation under continuous light. The increase of KODA level occurred in cotyledonal blades, but not in other parts (petiole, hypocotyls and shoot tip). When the 16-h dark period was interrupted with a 10-min light exposure at the 8th h, flower induction was blocked and KODA level also failed to increase. The degree of elevation of KODA concentration in response to 16-h dark exposure was the highest when the cotyledons had just unfolded, and gradually decreased in seedlings grown under continuous light for longer periods, reaching the basal level at the 3rd day after unfolding. Flower-inducing ability also decreased in a similar manner. These results suggest that KODA may be involved in flower induction in P. nil.

AGAMOUS-LIKE 24, a dosage-dependent mediator of the flowering signals

The most dramatic phase change in plants is the transition from vegetative to reproductive growth. This flowering process is regulated by several interacting pathways that monitor both the developmental state of the plants and environmental cues such as light and temperature. The flowering-time genes FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1), together with the floral meristem identity gene LEAFY (LFY), are three essential regulators integrating floral signals from multiple pathways in Arabidopsis thaliana. Part of the crosstalk among these genes is mediated by a putative transcription factor, AGAMOUS-LIKE 24 (AGL24). This gene is gradually activated in shoot apical meristems during the floral transition and later located in the whole zone of both inflorescence and floral meristems. Loss and reduction of AGL24 activity by double-stranded RNA-mediated interference result in late flowering, whereas constitutive overexpression of AGL24 causes precocious flowering. The correlation between the level of AGL24 accumulation and the alteration of flowering time suggests that AGL24 is a dosage-dependent flowering promoter. Analysis of AGL24 expression in various flowering-time mutants shows that it is regulated in several floral inductive pathways. Further genetic analyses of epistasis indicate that AGL24 may act downstream of SOC1 and upstream of LFY.

Independent control of gibberellin biosynthesis and flowering time by the circadian clock in Arabidopsis

Flowering of the facultative long-day plant Arabidopsis is controlled by several endogenous and environmental factors, among them gibberellins (GAs) and day length. The promotion of flowering by long days involves an endogenous clock that interacts with light cues provided by the environment. Light, and specifically photoperiod, is also known to regulate the biosynthesis of GAs, but the effects of GAs and photoperiod on flowering are at least partially separable. Here, we have used a short-period mutant, toc1, to investigate the role of the circadian clock in the control of flowering time by GAs and photoperiod. We show that toc1 affects expression of several floral regulators and a GA biosynthetic gene, but that these effects are independent.

Sequence variation and haplotype structure at the putative flowering-time locus COL1 of Brassica nigra

Motivated by a previous study indicating that polymorphism at an indel, Ind2, within the Brassica nigra COL1 gene is significantly associated with flowering time, we searched for evidence of selection in a sample of 41 complete sequences of B. nigra COL1. The within-gene population recombination rate is moderate, and all neutrality tests used in the present study failed to detect departure from the standard neutral model or evidence of selection. The haplotype structure of the 5'-half of the gene is primarily associated with the demographic history of the species and more specifically with the split between European and Ethiopian populations, whereas the structure of the 3'-half reflects the polymorphism at Ind2. This could be the result of selection or a combination of recombination and migration during the history of the sample of sequences. Without additional information on polymorphism in flanking areas, these two alternatives are difficult to tell apart. If selection acted on the gene, we suggest that if the indel itself is not the target of selection, among the polymorphic sites cosegregating with the polymorphism at Ind2, replacement polymorphisms around sites 890 and 1260 are the most likely quantitative trait nucleotides within the gene.

VFL, the grapevine FLORICAULA/LEAFY ortholog, is expressed in meristematic regions independently of their fate

The flowering process in grapevine (Vitis vinifera) takes place in buds and extends for two consecutive growing seasons. To understand the genetic and molecular mechanisms underlying this process, we have characterized grapevine bud development, cloned the grapevine FLORICAULA/LEAFY (FLO/LFY) ortholog, VFL, and analyzed its expression patterns during vegetative and reproductive development. Flowering induction takes place during the first season. Upon induction, the shoot apical meristem begins to produce lateral meristems that will give rise to either inflorescences or tendrils. During the second season, after a winter dormancy period, buds reactivate and inflorescence meristems give rise to flower meristems. VFL is expressed in lateral meristems that give rise to inflorescence and flower meristems, consistent with a role in reproductive development. Furthermore, VFL is also detected in other meristematic regions such as the vegetative shoot apical meristem and the lateral meristems that will give rise to tendrils. VFL is also expressed in leaf primordia and in growing leaf margins until later stages of development. Accumulation of VFL transcripts in cell-proliferating regions suggests a role for VFL not only in flower meristem specification, but also in the maintenance of indeterminacy before the differentiation of derivatives of the apical meristem: flowers, leaves, or tendrils.

The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of FLOWERING LOCUS C

The late-flowering, vernalization-responsive habit of many Arabidopsis ecotypes is mediated predominantly through repression of the floral programme by the FLOWERING LOCUS C (FLC) gene. To better understand this repressive mechanism, we have taken a genetic approach to identify novel genes that positively regulate FLC expression. We identified recessive mutations in a gene designated VERNALIZATION INDEPENDENCE 4 (VIP4), that confer early flowering and loss of FLC expression in the absence of cold. We cloned the VIP4 gene and found that it encodes a highly hydrophilic protein with similarity to proteins from yeasts, Drosophila, and Caenorhabditis elegans. Consistent with a proposed role as a direct activator of FLC, VIP4 is expressed throughout the plant in a pattern similar to that of FLC. However, unlike FLC, VIP4 RNA expression is not down-regulated in vernalized plants, suggesting that VIP4 is probably not sufficient to activate FLC, and that VIP4 is probably not directly involved in a vernalization mechanism. Epistasis analysis suggests that VIP4 could act in a separate pathway from previously identified FLC regulators, including FRIGIDA and the autonomous flowering promotion pathway gene LUMINIDEPENDENS. Mutants lacking detectable VIP4 expression flower earlier than FLC null mutants, suggesting that VIP4 regulates flowering-time genes in addition to FLC. Floral morphology is also disrupted in vip4 mutants; thus, VIP4 has multiple roles in development.