Cold kick-start for flowering

by Aalt-Jan van Dijk
Wageningen University, The Netherlands

When I started writing this commentary, I looked out of my window and decided a good way to start would be to mention that here in the Netherlands winter had finally arrived. Snow had fallen and ice was beginning to be visible on the pond in the park. However, by the time I was finishing writing this a few days later, the situation had already changed and the temperature was again above zero degrees Celsius. Hence, instead of referring to the current weather, I’ll use an old Dutch work of art (Figure 1). It was painted in a time of severe winters and illustrates the impact of winter on the landscape and on human behaviour.

Fig. 1. Painting by Hendrick Avercamp (1609).

Fig. 1. Painting by Hendrick Avercamp (1609). Rijksmuseum, Amsterdam

Winter also influences plants, and flowering is a prime example of a trait under control of environmental cues such as light and temperature. Temperature influences flowering both via small fluctuations in ambient temperature and via longer periods of winter cold. In the latter case, the promotion of flowering in response to a prolonged exposure to cold is called vernalization. In the model plant Arabidopsis thaliana, a lot is known about regulation of this process. In particular, the transcription factor FLC is known to be a central player in the vernalization response. FLC is a repressor of flowering which has to be repressed itself in order to allow vernalization. In a recent paper, Helliwell et al. (2015) propose a hypothesis on how the influence of winter cold on flowering is initiated.
Increasingly, there is a role for computational approaches in understanding the regulation of flowering time, including vernalization (Angel et al. 2011). As recently described in a review on gene regulatory networks involved in Arabidopsis reproduction (Pajoro et al. 2014), computational models come in a variety of flavours. Examples include two models for the Arabidopsis flowering time integration network (Valentim et al. 2015), which integrate computational modelling with experimental data in order to understand the function of a gene regulatory network. Helliwell et al. (2015) made a different use of models. Here, the main purpose is to generate hypotheses which then still await experimental validation. Their hypothesis deals with the question of how repression of FLC is initiated. As mentioned above, FLC is the main player in Arabidopsis’ response to vernalization. Although a lot is known about FLC repression, it still seems unclear what is the very first step in this repression.
Their central proposal is that the initial response to temperature change is physical, in the sense that there would be reorganization of the folding or looping of the chromatin polymer which would derive from a polymer entropy effect. Such a physical response is quite a general effect, different from a response enabled by a particular gene or protein, which changes its behaviour upon temperature change. To clarify the idea of a physical response, you could look again at the scene visualized in Figure 1. Ice is clearly visible, and this is the result of the physical response of freezing. In this process, molecules themselves do not change, but their configuration change with respect to each other (Figure 2).

Figure 2. Physical responses to temperature change. (Top) Water changes structure upon the transition from liquid water (right) to ice (left). Red indicates oxygen atom, black hydrogen atom. (Bottom) Polymer phase transition from high temperature (right) to low temperature (left). Green circles indicate monomeric subunits of polymer.

Figure 2. Physical responses to temperature change. (Top) Water changes structure upon the transition from liquid water (right) to ice (left). Red indicates oxygen atom, black hydrogen atom. (Bottom) Polymer phase transition from high temperature (right) to low temperature (left). Green circles indicate monomeric subunits of polymer.

Ideas on how the physical response of chromatin to temperature would be relevant for FLC repression are provided by Helliwell et al. (2015) referring to polymer physics models. These are described from a mathematical perspective as well as more visually by a video recording of the relaxation of a rubber band. One aspect of this hypothesis, which I think is beautiful, is how it connects different ‘levels’. This is actually an important aspect of computational models: on which scale or level do they operate? Models can, for instance, describe a whole plant, they can be tissue-based, or at the other extreme, models can be molecule-based such as the above-mentioned gene regulatory network models. Modelling chromatin via polymer physics models involves molecules but is clearly at a higher level than the scale of individual proteins or genes. In fact, the exact nature of the DNA and proteins involved in chromatin is not considered. These components are aggregated simply as ‘polymer’. The polymer scale is then connected to the molecular and cellular scale via its proposed influence on FLC expression and finally to the macroscopic level as it would influence flowering time upon vernalization.
What still puzzles me is how such a physical response could specifically influence FLC and not a lot of genes all over the genome. What would be special about FLC related chromatin? Helliwell et al. (2015) mentioned that ‘it is likely that the combination of DNA sequence and chromatin topology of the FLC locus make this locus uniquely responsive to changes in temperature’, but to me it is not clear how that could be accomplished for such a general physical response. Of course, any type of hypothesis or model should ultimately be tested with experiments. They also discussed a few examples of how analysis of kinetics of gene expression would enable this testing to be done. This would involve analysis of the kinetics of FLC repression after transfer to different low temperatures, and the kinetics of repression of genes neighbouring FLC. It will be interesting to see how data obtained in this way will validate or falsify the hypothesis on the importance of the physical response of chromatin to temperature for vernalization.
From my perspective here in the Netherlands, it is very timely to read Helliwell et al. (2015) paper. Even if we are not aware of it, plants around us are already preparing for the time after winter. The question what is the initial kick-start by which cold enables this response is clearly of fundamental importance to understand the regulation of flowering– and this paper generates fresh ideas on this issue.

Helliwell CA, Anderssen RS, Robertson M, Finnegan EJ
. 2015. How is FLC repression initiated by cold? Trends in Plant Sciences. 20(2) 76-82.
Angel A, Song J, Dean C, Howard M. 2011. A Polycomb-based switch underlying quantitative epigenetic memory. Nature 476(7358):105-108.
Pajoro A, Biewers S, Dougali E et al. 2014. The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history. Journal of Experimental Botany. 65, 4731-4745.
Jaeger KE, Pullen N, Lamzin S, Morris RJ and Wigge PA. 2013 Interlocking feedback loops govern the dynamic behaviour of the floral transition in Arabidopsis. The Plant Cell. 25(3), 820-833.
Valentim FL, van Mourik S, Posé D, Kim MC, Schmid M, van Ham RCHJ, Busscher M, Sanchez-Perez GF, Molenaar J, Angenent GC, Immink RGH, van Dijk ADJ. 2015. A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network. PLoS ONE, in press.

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Flowers under attack by phytoplasmas

by Frank Wellmer

Smurfit Institute of Genetics, Trinity College Dublin, Ireland

Phytoplasmas are cell wall-less bacteria that infect plants when they are transferred via sap-feeding insects such as leafhoppers. Plants infected with phytoplasmas can show a range of defects. One of them is the well-known Witches’ Broom, a massive overproliferation of shoots, often seen in nature on trees and shrubs. Another common defect of phytoplasma infection is termed phyllody, which is a conversion of floral organs into leaf-like structures (Figure 1).  This phenomenon is interesting from an evolutionary point of view as floral organs are thought to be modified leaves (Pelaz et al., 2001; von Goethe, 1790). Thus, phytoplasmas convert floral organs into something that resembles their developmental ground state.

MacLean AM et al. (2014). Phytoplasma Effector SAP54 Hijacks Plant Reproduction by Degrading MADS-box Proteins and Promotes Insect Colonization in a RAD23-Dependent Manner. PLoS Biol 12(4): e1001835.

Figure 1. From MacLean AM, et al. (2014). PLoS Biol 12(4): e1001835.

The molecular basis of phyllody is largely unknown but a recent paper by MacLean et al. (2014) has begun to shed light on the underlying mechanism. The authors elucidated how one effector of phytoplasma, a protein called SAP54 (MacLean et al., 2011), induces phyllody in Arabidopsis thaliana. Using a yeast two-hybrid approach, they found that SAP54 physically interacts with several transcription factors of the MADS-domain family, which contains many key floral regulators. Among them are the APETALA1 (AP1) and SEPALLATA1 to 4 (SEP1-4) proteins that have important functions during the onset of flower development and/or the specification of floral organ identity, respectively (O’Maoileidigh et al., 2014; Sablowski, 2010).

How does the interaction of SAP54 with floral regulators of the MADS-domain family lead to phyllody? Given that plants with mutations in genes coding for certain MADS-domain proteins exhibit transformations of floral organs into leaves it appeared likely the SAP54 might render these transcription factors inactive. In fact, it was found that the MADS-domain proteins AP1 and SEP3 are less abundant in plants infected with phytoplasmas than in the wild type. This reduced protein accumulation appears to be a consequence of a higher rate of protein turnover because addition of a proteasome inhibitor resulted in a restoration of MADS-domain protein levels.

This finding brought the authors back to the results of their yeast two-hybrid screen, in which they had also identified two RAD23 proteins as interacting with SAP54. RAD23 proteins are thought to play a role in directing ubiquitinated proteins for degradation by the 26S proteasome. Thus, SAP54 may bridge between components of the ubiquitin-proteasome system and floral regulators.

That RAD23 proteins are indeed important for phyllody was shown through experiments in which SAP54 was ectopically expressed in plants. While SAP54 over-expression leads to a strong degree of phyllody in the wild type, the expression of phyllody is suppressed in mutants in which several RAD23 genes are disrupted. Similarly, infection of higher-order rad23 mutants with phytoplasma does not lead to phyllody nor to a degradation of MADS-domain proteins, albeit other aspects of phytoplasma infection, such as the formation of Witches’ Broom, are unaffected. Taken together, these data provide convincing evidence that SAP54 induces phyllody by targeting MADS-domain transcription factors for degradation through interactions with RAD23 proteins.

What benefit does inducing phyllody in their host plants have for phytoplasmas? When male and female leafhoppers were given the choice between plants with normal flowers and plants that exhibited phyllody, they produced significantly more progeny on the latter. While the exact reason for this preference is currently unclear, it appears from these results that phytoplasmas modify flower architecture primarily to attract their insect vector to infected plants and thus ensure the spread of the pathogen.


Figure 1: An Arabidopsis wild-type flower (left) and a flower from a plant after phytoplasma infection showing phyllody (right). Figure taken from (MacLean et al., 2014).


MacLean AM, Sugio A, Makarova OV, Findlay KC, Grieve VM, Toth R, Nicolaisen M, Hogenhout SA. 2011. Phytoplasma effector SAP54 induces indeterminate leaf-like flower development in Arabidopsis plants. Plant Physiol 157, 831-841.

MacLean AM, Orlovskis Z, Kowitwanich K, Zdziarska AM, Angenent GC, Immink RG, Hogenhout SA. 2014. Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner. PLoS Biol 12, e1001835.

O’Maoileidigh DS, Graciet E, Wellmer F. 2014. Gene networks controlling Arabidopsis thaliana flower development. New Phytol 201, 16-30.

Pelaz S, Tapia-Lopez R, Alvarez-Buylla ER, Yanofsky MF. 2001. Conversion of leaves into petals in Arabidopsis. Curr Biol 11, 182-184.

Sablowski R. 2010. Genes and functions controlled by floral organ identity genes. Semin Cell Dev Biol 21, 94-99.

von Goethe JW. 1790. Versuch die Metamorphose der Pflanzen zu erklären. Ettinger, Gotha, Germany.


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On gibberellins and life decisions…

by Cristina Ferrándiz
Instituto de Biología Molecular y Celular de Plantas. CSIC-UPV.Valencia, Spain

In spite of what their sessile lifestyle could suggest, or maybe perhaps as a consequence of it, plants appear to be big decision-makers. Developmental decisions such as dormancy/germination, growth/arrest, branching/suppression-of-branches, vegetative-growth/flowering, senescence, fate … are key factors for their survival and reproductive success. Clearly, messengers are crucial to take action in a coordinated manner, and therefore the central role that plant hormones play in this coordination is no wonder. Among plant hormones, and among decisions too, a strong connection can be made between those that involve fate determination or life cycle transitions and gibberellins (GAs). The role of GAs in organ growth, cell differentiation and flowering promoting pathways has been well established and, somehow, GAs can be viewed as ‘coaches’ towards a grown-up stage.
Arabidopsis thaliana is an annual species that forms a vegetative rosette before entering into the reproductive phase. Flowering involves the bolting of the stem, which bears a small number of cauline leaves with axillary inflorescences, and above these the flowers grow. This particular type of growth, where in the bolting stem two different zones can be easily delimited, has led to two contrasting models to explain flowering transition, each of them based on different experimental evidence (Figure 1).

Figure 1. The two models that explain inflorescence architecture and flowering transition in Arabidopsis

Figure 1. The two models that explain inflorescence architecture and flowering transition in Arabidopsis

The acropetal model proposes that the shoot apical meristem undergoes two consecutive transitions: at bolting, the vegetative (V) meristem takes a first-phase-inflorescence identity (I1) and laterally produces leaves subtending flowering branches before undergoing a second phase change, where the I1 becomes an I2 meristem that directly produces flowers (Ratcliffe et al., 1998). Alternatively, the bidirectional model proposes that there is a single transition (V-to-I), after which the I meristem produces flowers acropetally while promoting internode elongation and branch development basipetally (Hempel and Feldman, 1994). No definitive proof has been found yet that fully supports one model over the other. One of the consequences is that many studies consider rosette leaf number as an indicator of flowering time, while many others quantify total leaf number (rosette+cauline).
The recent paper by Yamaguchi et al. (2014), which nicely advances our knowledge on GAs’ role in reproductive transition, might also shed light on this discussion. Or maybe not. The authors find that LEAFY (LFY), a floral meristem identity gene, directly up-regulates ELA1, a cytochrome P450 involved in GA4 catabolism. ELA1 up-regulation allows accumulation of gibberellin-sensitive DELLA proteins that, through their interaction with the flowering promoting factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9), activate the transcription of APETALA1 (AP1), another meristem identity gene that ultimately confers floral identity to the lateral primordia produced by the apical meristem. Therefore, it would appear that GAs act as floral repressors, since they have to be inactivated to produce flowers. However, it has been known for a long time that GAs are essential to promote flowering under short days in Arabidopsis and that they work in part by up-regulating LFY expression (Blázquez and Weigel, 2000). So there is an apparent contradiction here: GAs are important to switch on LFY, at least in some conditions, but after that, they have to be eliminated to allow flower formation. Accordingly, this paper shows how GA defective mutants or treatments that cause DELLA accumulation have more rosette leaves but less cauline leaves. This and other evidence in the paper can be easily integrated in the biphasic acropetal model of flowering: GAs contribute to the V-to-I1 transition and LFY up-regulation. Once this is established, LFY in turn directs GAs degradation and allows AP1 up-regulation and thus I1-I2 transition. In addition, and under this view, this work contributes another nice example of dual behaviour in floral business. So far, several transcription factors have been characterized to show this type of ‘mercurial’ temperament. For example, AP1 itself works promoting floral meristem identity and then, by changing interacting partners goes on to repress meristem identity and directs the differentiation of floral organs (Gregis et al., 2009)
While this dual biphasic behaviour seems to be a likely scenario, other interpretations could also be proposed that similarly fit the single-transition bidirectional model. It is possible that after GAs promote the reproductive transition, LFY action on GAs degradation could be local, restricted to acropetal lateral primordia, while basipetally GAs are not depleted from the stem and act on internode elongation. GA defective mutants would delay transition as a whole (explaining the increase observed in total leaf number described in Yamaguchi et al. paper) but then the basipetal signal to promote internode elongation would be weak and could explain the reduction on cauline leaf number of these mutants.
In any case, in addition to food-for-thought, this work provides new and interesting evidence and further confirms our impression: transition to adulthood is also a hormonal matter.


Blázquez M, Weigel D. 2000. Integration of floral inductive signals in Arabidopsis. Nature 404, 889-892.

Gregis V, Sessa A, Dorca-Fornell C, Kater MM. 2009. The Arabidopsis floral meristem identity genes AP1, AGL24 and SVP directly repress class B and C floral homeotic genes. The Plant Journal 60, 626-637.

Hempel FD, Feldman LJ. 1994. Bi-directional inflorescence development in Arabidopsis thaliana: Acropetal initiation of flowers and basipetal initiation of paraclades. Planta 192, 276-286.

Ratcliffe O, Amaya I, Vincent C, Rothstein S, Carpenter R, Coen E, Bradley D. 1998. A common mechanism controls the life cycle and architecture of plants. Development 125, 1609-1615.

Yamaguchi N, Winter CM, Wu MF, Kanno Y, Yamaguchi A, Seo M, Wagner D. 2014. Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis. Science 344, 638-641.

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Cereal crops see things differently

by Ben Trevaskis CSIRO Plant Industry, Black Mountain ACT 2601, Australia

Our knowledge of plant molecular biology is biased towards the model plant Arabidopsis, the focus of intense genetic study and the first plant genome sequenced. The general assumption is that understanding developed in this model system can be applied directly to other plant species. While this is often true, it is becoming increasing clear that perspectives developed from this single plant species should be applied cautiously to other systems. This is particularly true for distantly related monocot plants, such as wheat and barley.
The molecular pathways controlling vernalization-induced flowering illustrate this point. In Arabidopsis the FLC gene plays the pivotal role in controlling the induction of flowering by the prolonged cold of winter (see Amasino 2010). After intensive study of temperate cereals and related grasses it seems that the key gene controlling the vernalization response of these plants is VRN1, an APETALA1/FRUITFUL-like (AP1/FUL-like) MADS box gene (see Trevaskis 2010). AP1/FUL-like genes do not have the same role in Arabidopsis.
Recent studies indicate that mechanisms that accelerate flowering in response to long days might also differ between Arabidopsis and the grasses. A study by Chen et al. (2014) shows that PHYTOCHROME C (PHYC) is critical for long-day induced flowering in wheat. Phytochrome proteins act as photoreceptors. Loss of PHYC function in durum wheat (Triticum turgidum) delays flowering in long days. The late flowering phenotype is associated with altered circadian rhythms and reduced FLOWERING LOCUS T-like 1 (FT1) expression (Chen et al., 2014). FT1 normally promotes flowering in long days, so an inability activate expression of this gene might explain the phenotype of the PHYC mutant. Other recent studies show that natural variation in PHYC underlies differences in daylength sensitivity amongst barley cultivars, reinforcing the importance of this gene in the photoperiod flowering response of temperate cereals (Nishida et al., 2013, Pankin et al., 2014).
The major role of PHYC in the long-day flowering-response extends to other grasses. In Brachypodium distachyon, a model grass related to temperate cereal crops, loss of PHYC function also delays flowering in long days (Woods et al., 2014). Like the wheat PHYC mutants, Brachypodium PHYC mutants show altered expression of circadian clock genes and reduced FT1 expression (Woods et al., 2014). Constitutive expression of FT1 in a Brachypodium PHYC mutant promotes early flowering, supporting the idea that FT1 acts downstream of PHYC to accelerate flowering in long days.
PHYC does not play a role in accelerating flowering in long days in Arabidopsis, so the findings of these recent studies raise an important question: to what extent do the pathways controlling the long-day flowering response of temperate grasses overlap with those of Arabidopsis? Long-days induce expression of FLOWERING LOCUS T (FT) genes to accelerate flowering in both Arabidopsis and the temperate grasses (Amasino 2010; Turner et al., 2005; Lv et al., 2014). It is possible that there are only minor differences between the mechanisms that sense daylength to activate FT genes in these different plant lineages. Different phytochromes potentially function in a shared daylength sensing pathway, for example. Alternatively, there might be more radical differences in the way that Arabidopsis and the cereals sense and respond to daylength. There are indications that this might be the case. For example, a PSEUDORESPONSE REGULATOR (PHOTOPERIOD1) regulates daylength sensitivity in cereals but has no direct functional equivalent in Arabidopsis (Turner et al., 2005).
The unexpected importance of PHYC in regulating the long-day flowering response of grasses highlights the need to place understanding of the functions of genes developed in Arabidopsis into a broader context of how these functions are recruited into biological roles in other plants. The study of Chen et al. (2014) also provides a clear demonstration that molecular genetic approaches that have proven so successful in the study of Arabidopsis can be applied directly to a polyploid crop with a large genome. This type of research is essential if we are to understand the pathways controlling seasonal flowering-responses of temperate cereal crops and apply this knowledge to crop improvement.

Amasino R. (2010) Seasonal and developmental timing of flowering. Plant Journal, 61: 1001-1013.

Chen A, Li C, Hu W, Lau MY, Lin H, Rockwell NC, Martin SS, Jernstedt JA, Lagarias JC, Dubcovsky J. (2014) PHYTOCHROME C plays a major role in the acceleration of wheat flowering under long-day photoperiod. Proceedings of the National Academy of Science 111:10037–10044

Lv B, Nitcher R, Han X, Wang S, Ni F, Li K, Pearce S, Wu J, Dubcovsky J, Fu D. (2014) Characterization of FLOWERING LOCUS T1 (FT1) gene in Brachypodium and wheat. PLoS ONE 9:e94171, Doi: 10.1371/journal.pone.0094171

Nishida H, Ishihara D, Ishii M, Kaneko T, Kawahigashi H, Akashi Y, Saisho D, Tanaka K, Handa H, Takeda K, Kato K. (2013) Phytochrome C is a key factor controlling long-day flowering in barley. Plant Physiology 163: 804-814.

Pankin A, Campoli C, Dong X, Kilian B, Sharma R, Himmelbach A, Saini R, Davis SJ, Stein N, Schneeberger K, von Korff M. (2014) Mapping-by-Sequencing Identifies HvPHYTOCHROME C as a candidate gene for the early maturity 5 Locus modulating the circadian clock and photoperiodic flowering in barley. Genetics 198:383-396

Trevaskis B. (2010) The central role of the VERNALIZATION1 gene in the vernalization response of cereals. Functional Plant Biology 37: 479-487.

Turner A, Beales J, Faure S, Dunford RP, Laurie DA. (2005) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 11: 1031-1034.

Woods DP, Ream TS, Minevich G, Hobert O, Amasino R. M. (2014) PHYTOCHROME C Is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon. Genetics 198: 397-408

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Farewell to Ko Shimamoto

Paula Suárez-López1, Hiroyuki Tsuji2 and George Coupland3

1Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain. 2Graduate School of Biological Sciences, Nara Institute of Science and Technology, Japan. 3Max Planck Institute for Plant Breeding Research, Cologne, Germany.

We were deeply saddened to learn that Ko Shimamoto passed away on 28 September 2013. Ko was an esteemed colleague, mentor and supervisor and his tremendous contributions to the flowering field have changed our view of photoperiodic control of flowering. We wished to pay tribute to him and have written an obituary, which has now been published in the Flowering Newsletter (Suárez-López et al., 2014).

Ko Shimamoto

Professor Ko Shimamoto

Ko was very active and productive, continuing to write manuscripts even when very ill. His scientific production encompasses many aspects of rice biology and biotechnology. Early in his career he produced the first fertile transgenic rice plants from protoplasts, when working at the Plantech Research Institute (Shimamoto et al., 1989). Then he moved to the Nara Institute of Science and Technology to establish his own laboratory. Since then, he worked mainly on three topics, plant innate immunity, gene silencing and flowering, using rice as a model plant.

His contributions to the flowering field are especially remarkable. Plants sense and respond to environmental factors, including seasonal changes in day length, in order to flower under optimal conditions. Ko’s group showed that the short-day flowering habit of rice results from the use of essentially the same components as those that determine long-day flowering in other species, exemplified by Arabidopsis. In both species, GIGANTEA acts under inductive photoperiods and up-regulates the expression of two highly related genes, CONSTANS (CO) in Arabidopsis and HEADING DATE 1 (Hd1) in rice. CO and Hd1, in turn, regulate the expression of a gene that is essential for floral induction, FLOWERING LOCUS T (FT) in Arabidopsis and its rice homologue HEADING DATE 3a (Hd3a). While CO promotes FT expression under inductive photoperiods, Hd1 represses Hd3a expression under non-inductive photoperiods (Hayama et al., 2003). In this way, Ko’s group showed that the opposite roles of Hd1 and CO account for the opposite photoperiodic responses of rice and Arabidopsis, a key contribution to understanding the evolution of photoperiodic control of flowering.

Another ground-breaking discovery from Ko’s group was the identification of Hd3a protein as a mobile signal that travels from the leaf to the shoot apical meristem, where Hd3a induces flowering (Tamaki et al., 2007). Hd3a is therefore an essential component of florigen, the long-sought after flowering signal, a result supported by studies in other species (Kobayashi and Weigel, 2007; Turck et al., 2008). In Arabidopsis, FT interacts with the transcription factor FD after reaching the shoot apical meristem. Ko’s laboratory showed that Hd3a and the rice FD homologue OsFD also form a complex and their interaction is bridged by a 14-3-3 protein (Taoka et al., 2011). While Hd3a is crucial for flowering under inductive short days, another FT-like protein, RICE FLOWERING LOCUS T 1 (RFT1), plays an essential role in flowering of rice under long days and acts as a long-day florigen (Komiya et al., 2008; Komiya et al., 2009).

In addition to his outstanding findings in flowering biology, Ko’s group also made major contributions to many other areas of plant science, most importantly plant innate immunity and gene silencing. His group also developed diverse tools for the study of rice. We had the double privilege of knowing Ko and enjoying his science. We encourage the readers of this blog to learn about him and his remarkable scientific achievements.


Hayama R, Yokoi S, Tamaki S, Yano M, Shimamoto K. 2003. Adaptation of photoperiodic control pathways produces short-day flowering in rice. Nature 422, 719-722.

Kobayashi Y, Weigel D. 2007. Move on up, it’s time for change – mobile signals controlling photoperiod-dependent flowering. Genes and Development 21, 2371-2384.

Komiya R, Ikegami A, Tamaki S, Yokoi S, Shimamoto K. 2008. Hd3a and RFT1 are essential for flowering in rice. Development 135, 767-774.

Komiya R, Yokoi S, Shimamoto K. 2009. A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice. Development 136, 3443-3450.

Shimamoto K, Terada R, Izawa T, Fujimoto H. 1989. Fertile transgenic rice plants regenerated from transformed protoplasts. Nature 338, 274-276.

Suárez-López P, Tsuji H, Coupland G. 2014. A tribute to Ko Shimamoto (1949–2013). Journal of Experimental Botany. doi:10.1093/jxb/eru104.

Tamaki S, Matsuo S, Wong HL, Yokoi S, Shimamoto K. 2007. Hd3a Protein Is a Mobile Flowering Signal in Rice. Science 316, 1033-1036.

Taoka K-i, Ohki I, Tsuji H, Furuita K, Hayashi K, Yanase T, Yamaguchi M, Nakashima C, Purwestri YA, Tamaki S, Ogaki Y, Shimada C, Nakagawa A, Kojima C, Shimamoto K. 2011. 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature 476, 332-335.

Turck F, Fornara F, Coupland G. 2008. Regulation and Identity of Florigen: FLOWERING LOCUS T Moves Center Stage. Annual Review of Plant Biology 59, 573-594.


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Tell me who your sister is and I’ll tell who you are

by Aalt-Jan van Dijk
Wageningen University, The Netherlands

After spending time with family during the Christmas holidays, it became clear to me how much we learn about ourselves by watching our relatives. This involves both similarities and striking differences. Although at a completely different time scale, a similar principle holds when analysing plant species and their genomes: depending on the goal of the analysis, a judicious choice of species to be compared with can be extremely helpful. In particular, it can be very useful to focus on a ‘sister species’, the closest relative of the group of species of interest. As I’ll describe using two examples, this is of clear relevance for flowering research.

A few months ago, one example of such sister lineage genome analysis was presented through the Tarenaya hassleriana (Figure 1) genome (Cheng et al. 2013). Tarenaya hassleriana belongs to the Cleomaceae, which is the phylogenetic sister family of the Brassicaceae, including Arabidopsis thaliana and Brassica crops. One finding of notice in the comparison involved MADS-box transcription factors, which have various roles in flower development. The fate of these flowering regulators after a genome triplication that occurred independently in T. hassleriana and in Brassica was analysed. In general, after a genome multiplication many of the new gene copies get lost. However, a striking difference was observed between Brassica and Tarenaya: Brassica retained twice as many floral MADS genes as Tarenaya. Although further analysis is required, morphological diversity in Brassica was speculated to be related to this difference.
More recently, a second example was reported in the final 2013 issue of Science with the publication of the Amborella trichopoda genome sequence (Amborella Genome Project, 2013). Amborella is a shrub endemic to New Caledonia in the southwest Pacific Ocean. It has previously been indicated that it is the single sister species to all other flowering plants (Figure 2). In addition to analysis of structural aspects of genome evolution (which I will not discuss here), the Amborella genome enabled analysis of how flowering-relevant gene functions developed during flower evolution.

Figure 2. (Left) Amborella trichopoda, sister to all flowering plants. (Right) Simplified land plant phylogeny

Figure 2. (Left) Amborella trichopoda, sister to all flowering plants.(Right) Simplified land plant phylogeny

By comparing the Amborella genome to other available plant genomes, the ancestral gene content at key nodes in land plant phylogeny could be reconstructed. Roughly 25% of 5,210 gene families were specific to flowering plants and not found in non-flowering plants. This suggests that a diverse collection of novel gene functions was likely associated with the origin of flowering plants. Gene Ontology (GO) annotations related to reproduction were indeed overrepresented in this set of gene families. However, GO terms related to homeostasis and related to response to environmental cues, including herbivory, were even stronger enriched in these flowering-specific gene families. The latter was rationalised in the paper by referring to the importance of plant-herbivore coevolution in the diversification of flowering plants. As a side note, it is good to remember that there are many uncertainties associated with GO term analysis, including the fact that for many genes there is no experimental evidence for their function (Kourmpetis et al. 2011; Rhee and Mutwil). The remaining 75% of the 5,210 gene families were found in the common ancestor of all seed-bearing plants, both flowering and non-flowering. This suggested that flowering plants co-opted many pre-existing genes to the business of making flowers. One specific example discussed in the paper is again for the MADS-box genes. The data supports the hypothesis that duplication and diversification of floral MADS-box genes likely occurred before the origin of flowering plants, despite MADS-box genes being tightly associated with the origin of the flower. Apparently, as with us humans, what makes plants unique in comparison even with close relatives is not only which genetic components are present, but also the way in which these components are utilised!

Amborella Genome Project .2013. The Amborella genome and the evolution of flowering plants. Science 342(6165):1241089.

Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Kuelahoglu C, et al. 2013. The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. The Plant Cell 25(8):2813-30.

Kourmpetis Y, van Dijk ADJ, van Ham RCHJ, ter Braak CJF. 2011. Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources. Plant Physiology 155(1):271-81.

Rhee S. and Mutwil M. 2014. Towards revealing the functions of all genes in plants. Trends in Plant Science 19:212-221.

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At the swing of a pendulum: reversals from monosymmetry to radial symmetry are a frequent phenomenon in angiosperms

by Louis Ronse De Craene
Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK.

Monosymmetric flower: Westringia fruticosa (Lamiaceae). Note the 3:2 pattern of the corolla and sequential stamen maturation.

Fig 1. Early monosymmetric flower: Westringia fruticosa (Lamiaceae). Note the 3:2 pattern of the corolla and sequential stamen maturation.

Changes in floral symmetry are an important evolutionary process in flowers. In general four forms of symmetry are recognized in flowers (Endress 1999, Citerne et al. 2010): flowers are either polysymmetric (actinomorphic, with more than one mirror-images if divided in half – very much like slicing a cake), bisymmetric (with two mirror images), or monosymmetric (zygomorphic, with a single mirror image, often called bilateral symmetry: Fig. 1); The final form is asymmetry, which is fairly rare in angiosperms. I also refer to the previous post by Beverley Glover on The mechanisms of symmetry. Monosymmetry is the most frequent flower shape besides polysymmetric flowers. The condition has evolved independently in all major groups of angiosperms, especially in rosids and asterids (Jabbour et al. 2009). Monosymmetry is generally associated with insect (especially bee) pollination, necessitating a landing platform for visitors. Interestingly, genera or even families that are mainly polysymmetric rarely have monosymmetric species, and if they occur, monosymmetry is usually a late-developmental event in the flower (Fig. 2). On the other hand, genera or families that are mainly monosymmetric will have an early onset of monosymmetry in the development, affecting the shape and number of organs being developed (Fig. 1) (Endress 1999, Ronse De Craene 2010). Developmentally, the onset of monosymmetry is regulated by several factors, such as the initiation sequence and subsequent growth of organs, as well as external parameters, such as the orientation of the flower and the opposing pressure of subtending bracts and inflorescence axis (e.g. Endress 1999, Tucker 1999).

Late monosymmetric flower: Iberis sempervirens (Brassicaceae)

Fig. 2. Late monosymmetric flower: Iberis sempervirens (Brassicaceae)

It is clear that monosymmetry evolved at an early stage in some groups of plants and represents a major evolutionary change. What is interesting is that a reversal has frequently arisen from monosymmetry to polysymmetry.
Most Lamiales are monosymmetric, with a constant pattern of three anterior and two posterior petals (Donoghue et al. 1998, Endress 1999, Ronse De Craene 2010). The posterior stamen is generally reduced or lost, and this corresponds typically to the flower of Antirrhinum (Plantaginaceae). Although most Lamiales have monosymmetric flowers, there are several independent derivations of polysymmetry (Soltis et al. 2005).
Reversals to actinomorphic flowers are strongly correlated with the degree of reduction of the posterior side of the flower. In Gesneriaceae the posterior staminode is well developed and reversals to actinomorphic flowers are relatively straightforward, as in Ramonda (Endress 1998; Fig. 3). Actinomorphic flowers in Lamiales are frequently tetramerous (e.g. Plantago, Buddleja).

Fig. 3. Ramonda myconi(Gesneriaceae): the return of a polysymmetric flower in a monosymmetric family

Fig. 3. Ramonda myconi (Gesneriaceae): the return of a polysymmetric flower in a monosymmetric family

A mechanical explanation is linked with a strong polarity between the anterior side and the posterior side of the flower. The posterior side is strongly compressed and this is accompanied by the progressive loss of the staminode and possibly posterior sepal. At the same time the two posterior petals can fuse into a single petal, leading to a tetramerous flower (Endress 1999, Bello et al. 2004).

The mechanical explanation is linked to a genetic cause. As shown for Antirrhinum, monosymmetry is regulated by the antagonistic expression of the TCP transcription factors CYCLOIDEA (CYC) and DICHOTOMA (DICH) against the MYB transcripton factor DIVARICATA (DIV) (Luo et al. 1996). CYC is responsible for the dorsal identity of the corolla and androecium in monosymmetric flowers, while DIV acts on the ventral identity. In a number of case-studies of mutants of Antirrhinum, monosymmetric flowers become polysymmetric either by expansion of DIV at the expense of CYC (Luo et al. 1996), by methylation of CYC, effectively neutralizing its activity (e.g. peloria of Linaria: Cubas et al. 1996), or by expansion of CYC at the expense of DIV, creating fully dorsalized flowers (Luo et al. 1999). This is accompanied by an increase in merism to hexamery. The genetic pathways described for Antirrhinum appear to be conserved in diverse groups of angiosperms outside Lamiales that have been investigated for homologues of CYC (CYCLOIDEA-like genes), with an increased complexity by repeated duplication events (Howarth and Donoghue 2005, Citerne et al. 2010, Preston et al. 2011).
Changes in symmetry can thus be explained in two ways:
-as a loss-of-function event (downgrading of CYC) leading to a reversal to actinomorphy (Luo et al. 1996). Preston et al. (2011) suggested that radially symmetrical flowers of Plantago evolved through loss of CYC-like genes, although they did not explain how tetramery came about;
-as a gain-of-function event (expansion of CYC) leading to actinomorphy (Donoghue et al. 1998). In Gesneriaceae, a reversal to actinomorphy is either an expansion (e.g. Tengia: Peng et al. 2010) or a downgrading of CYC (e.g. Bournea: Zhou et al. 2008). Both processes may result in similar floral morphology.
A similar scenario of dorsal or ventral expansion has been shown to be reproduced in other core eudicots outside Lamiales, such as Lonicera in the Dipsacales (Howarth et al. 2011), or Cadia in Leguminosae (Citerne et al. 2006). Most of these examples relate to families or orders that are highly monosymmetric.

Fig. 4.Bunchosia sp. (Malpighiaceae): example of Neotropical polysymmetric flower. Note the equal paddle-shaped petals. Photo Kyle Dexter

Fig. 4. Neotropical polysymmetric flower: Bunchosia sp. (Malpighiaceae). Note the equal paddle-shaped petals. Photo Kyle Dexter

However, it is interesting to see that a similar process occurs in groups of plants with little or no monosymmetry, emphasizing the universality of CYC expression in the angiosperms. In an interesting paper Zhang et al. (2013) described this for Malpighiaceae, a member of the mainly polysymmetric order Malpighiales. Malpighiaceae is a medium-sized tropical family occurring in the New and Old World. Flowers are typically pentamerous with paddle-shaped petals and are either polysymmetric (Fig. 4) or weakly to strongly monosymmetric (Figs. 5, 6). As monosymmetry is a late-developmental event, all floral organs are present in flowers (even as some may be staminodial) and zygomorphy is often reflected in a small difference in length of one petal (banner*). Zygomorphic flowers tend to be found as a specialization associated with Neotropical bees foraging for oil produced on external glands of the sepals (Figs 5, 6; Vogel 1990).

Fig. 5. Berysonima chrysophylla (Malpighiaceae): example of Neotropical monosymmetric flowers catering for oil-collecting bees. Note the paired glands on the outside of the calyx on the younger flowers at the top. Photo Toby Pennington

Fig. 5. Berysonima chrysophylla (Malpighiaceae): Neotropical monosymmetric flowers catering for oil-collecting bees. Note the paired glands on the outside of the calyx on the younger flowers at the top. Photo Toby Pennington

Zhang et al. (2013) demonstrated that zygomorphy in Malpighiaceae is linked with a duplication of the CYC2 lineage in CYC2A and CYC 2B, which may influence monosymmetry in different degrees (cf. Zhang et al. 2010). Interestingly, with the loss of oil bee specialisations there was a reversal to actinomorphy in four independent cases. Zhang et al. (2013) demonstrated that this reversal was always accompanied by changes in the CYC2 expression. A derived actinomorphy is in some cases accompanied by the expansion the CYC2A expression to the anterior petals, in a similar way as Cadia in Leguminosae (Citerne et al. 2006). In the other cases actinomorphy is attained by loss of CYC2B expression. These results indicate that CYC expression appears to be more widespread in actinomorphic flowers than originally thought.

Fig. 6. Stigmaphyllon sp. (Malpighiaceae): detail of monosymmetric flower with two longer petals. Photo Tiina Sarkinen

Fig. 6. Stigmaphyllon sp. (Malpighiaceae): detail of monosymmetric flower with two longer petals. Photo Tiina Sarkinen

Research of Howarth and Donoghue (2005) and Howarth et al. (2011) suggests that CYC is expressed in all petals of basal Dipsacales, even actinomorphic morphs, such as Viburnum, and that monosymmetry is related to a restriction of CYC to the dorsal side of the flower. Zhang et al. (2013) also suggested that Arabidopsis may not be the best representative for actinomorphic flowers, in that CYC expression has been lost in this model genus (see Busch and Zachgo 2007). As CYC2 is expressed in Elatinaceae, the sister family to Malpighiaceae, it can be assumed that this is also the case for basal Malphighiaceae. However, the reconstruction of the ancestral condition is equivocal and it remains uncertain whether a broad expression of CYC2 or an absence of it is ancestral in the family (Zhang et al. 2013).

In conclusion, evolution of symmetry appears to be an exciting research topic. There is a need to better understand the effects of CYC on other parameters than the petals, such as floral merism, stamen reductions, and the polarization of the shape of the flower. The close correlation between the expression of CYC2 and floral morphology as seen for Malpighiaceae reflects a highly conserved genetic developmental program. However, patterns of change of symmetry are totally unpredictable, as a reflection of the twists of evolution. The pendulum keeps swinging…

*Monosymmetry in Malpighiaceae is not running along a median line, but is oblique, as one of the two posterior petals is longest but becomes displaced along the median line by a torsion of the pedicel (Ronse De Craene 2010). In other cases two petals are longer (Fig. 6).

Thanks to Toby Pennington, Kyle Dexter and Tiina Sarkinen for providing photographs of Malpighiaceae.

Bello MA, Rudall PJ, González F, and Fernández-Alonso JL. 2004. Floral morphology and development in Aragoa (Plantaginaceae) and related members of the order Lamiales. International Journal of Plant Science 165: 723-738.

Busch A and Zachgo S. 2007. Control of corolla monosymmetry in the Brassicaceae Iberis amara. Proceedings of the National Academy of Science USA 104, 16714-16719.

Citerne H, Jabbour F, Nadot S, and Damerval C. 2010. The evolution of floral symmetry. In: J.C. Kader and M. Delseny (eds.), Advances in Botanical Research. London: Elsevier, pp. 85-137.

Citerne HL, Pennington RT, and  Cronk QCB. 2006. An apparent reversal in floral symmetry in the legume Cadia is a homeotic transformation. Proceedings of the National Academy of Science USA 103: 12017-12020.

Cubas P, Vincent C, and Coen E. 1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157-161.

Donoghue MJ, Ree RH and Baum DA. 1998. Phylogeny and the evolution of flower symmetry in the Asteridae. Trends in Plant Science 3: 311-317.

Endress PK 1998. Antirrhinum and Asteridae – evolutionary changes of floral symmetry. Society for Experimental Biology. Symposium Series 51: 133-140.

Endress PK 1999. Symmetry in flowers. Diversity and evolution. International Journal of Plant Science 160 [6 Suppl]: S3-S23.

Howarth DG and  Donoghue MJ. 2005. Duplications in cyc-like genes from Dipsacales correlate with floral form. International Journal of Plant Science 166: 357-370.

Howarth DG. Martins T, Chimney E, and Donoghue MJ. 2011. Diversification of CYCLOIDEA expression in the evolution of bilateral flower symmetry in Caprifoliaceae and Lonicera (Dipsacales). Annals of Botany 107: 1521-1532.

Jabbour F, Nadot S, Damerval C. 2009. Evolution of floral symmetry: a state of the art. C. R. Biologies 332: 219–231

Luo D, Carpenter R, Vincent C, Copsey L, and Coen E. 1996. Origin of floral asymmetry in Antirrhinum. Nature 383: 794-799.

Luo D, Carpenter R, Copsey L, Vincent C, Clark J, and Coen E. 1999. Control of organ asymmetry in flowers of Antirrhinum. Cell 99: 367-376.

Preston JC, Martinez CC, and Hileman LC. 2011. Gradual disintegration of the floral symmetry gene network is implicated in the evolution of a wind-pollination syndrome. Proceedings of the National Academy of Science USA 108: 2343-2348.

Ronse De Craene LP. 2010. Floral diagrams. An aid to understanding flower morphology and evolution. Cambridge, Cambridge University Press.

Soltis DE, Soltis PS, Endress PK, and Chase MW. 2005. Phylogeny and evolution of angiosperms. Sinauer, Mass., USA.

Tucker, S. C. 1999. Evolutionary lability of symmetry in early floral development. International Journal of Plant Science 160, 6 Supplement: S25-S39.

Vogel, S. 1990. History of the Malpighiaceae in the light of pollination ecology. Memoirs of the New York Botanical Garden 55: 130-142.

Zhang W, Kramer EM, and C.C. Davis. 2010. Floral symmetry genes and the origin and maintenance of zygomorphy in a plant-pollinator mutualism. Proceedings of the National Academy of Science USA 107: 6388-6393.

Zhang W, Steinmann VW, Nikolov L, Kramer EM, and Davis CC. 2013. Divergent genetic mechanisms underlie reversals to radial floral symmetry from diverse zygomorphic flowered ancestors. Frontiers in Plant Science 4: doi: 10.3389/fpls.2013.00302.

Zhou X-R, Wang Y-Z, Smith JF, and Chen R. 2008. Altered expression patterns of TCP and MYB genes relating to the floral developmental transition from initial zygomorphy to actinomorphy in Bournea (Gesneriaceae). New Phytologist 178: 532-543.

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Adaptative walk or random walk?

by Martin Lascoux
Department of Ecology and Genetics, EBC, Uppsala University, Uppsala University, Sweden

The search for the genetic factors controlling phenological traits in Arabidopsis thaliana, in particular flowering time, started in a candid and optimistic mood, with the rapid identification of FRI and FLC as two of the main culprits. Further studies, however, have consistently led to a far more complex picture, with more genes involved and sometimes either FRI, FLC, or both missing. Given what is today known about the genetic basis of complex traits this is perhaps hardly surprising. The new emerging picture is also a consequence of a shift in the type of experiments that are carried out. There are three main differences between recent studies and earlier ones. First, in contrast to early studies that used a single individual per population, recent studies often incorporate local genetic variation. Second, phenology tends today to be measured under more natural conditions. Finally, earlier studies were based on unstructured worldwide samples while more recent studies have considered different geographical scales. In a recent and very interesting study, Brachi and collaborators focus on the latter. Using a hierarchical sampling of French Arabidopsis thaliana populations together with a worldwide sample, they investigated the association of phenology with environmental ecological variables, on the one hand, and variation at 135 SNPs, on the other hand, at different geographical scales. Three main conclusions emerge, none of which is particularly reassuring with regards to our ability to one day reach a generic understanding of the control of phenology in Arabidopsis. First, history matters and it matters a lot: most of phenological variation can simply be explained by neutral genetic variation. It is worth pointing out that, in this respect, A. thaliana might be a particularly difficult species. Other species might not have been disturbed to the same extent. Second, local selective agents such as edaphic conditions or interspecific competition, play an important role in shaping adaptive variation. Third, different genes control phenology in different places and at different geographical scale. I would tend to be a bit more pessimistic than the authors and think that all this would seem to seriously complicate the reconstruction of “the adaptive walks that natural populations follow towards local phenotypic optima”. Hopefully I am wrong and they are right.

Brachi B, Villoutreix R, Faure N, Hautekèete N, Piquot Y, Pauwels M, Roby D, Cuguen J, Bergelson J, Roux F. (2013) Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana. Mol Ecol 22: 4222-4240

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The mechanics of symmetry

by Beverley Glover
Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.

Flowers come in many different shapes and sizes, but their symmetry is usually described in a binary fashion. Some flowers are bilaterally symmetrical, also known as zygomorphic or monosymmetric (for example, sweet peas). These flowers have a clear top (dorsal side) and bottom (ventral side), and it is only possible to draw a single line of symmetry through them. The alternative state is to be radially symmetrical, also known as actinomorphic or polysymmetric (for example, poppies). It is possible to draw many different lines of symmetry through an actinomorphic flower.

Ophrys speculum has a highly zygomorphic flower, with inner tepals and both whorls of reproductive organs affected

Fig.1. Ophrys speculum has a highly zygomorphic flower, with inner tepals and both whorls of reproductive organs affected

Although we generally think of flowers as having only one of two options when it comes to their symmetry, in fact the overall form of a flower can arise from differential development of organs in one or more whorls of the floral meristem. Many orchids, for example, show extreme bilateral symmetry, with the inner tepals clearly zygomorphic, and the stamens and carpels fused into a single gynostemium, itself often dorsally positioned (Fig 1). The flower of snapdragon (Antirrhinum majus) is the classic genetic model in which zygomorphy has been studied, and its symmetry is based on expansion of the dorsal petals relative to the lateral and ventral ones but abortion of the dorsal stamen (Fig 2).
Fig 2. Antirrhinum majus is the classic genetic model for studies of zygomorphy. The petals and stamens are affected in this species

Fig 2. Antirrhinum majus is the classic genetic model for studies of zygomorphy. The petals and stamens are affected in this species

In contrast the flowers of a number of species of Solanum show zygomorphy only in the stamen whorl, with differential development of anthers to fill feeding or pollinating roles in their interaction with pollen-collecting bees (De Luca and Vallejo-Marin, 2013). These variations in symmetry can be most dramatic in the Asteraceae (the daisy family), where in different species or varieties different combinations of actinomorphic, slightly zygomorphic and strongly zygomorphic florets combine in a condensed inflorescence to produce a flower head (capitulum) that appears fully radially symmetrical (Fig 3; Chapman et al. 2012).
The presence of many subtly different forms of zygomorphy suggests a developmental mechanism that is flexible in both its spatial position within the flower and the strength with which it acts. We have known for over 15 years that the zygomorphy of the Antirrhinum
Fig 3. Daisies, such as this Gorteria diffusa, produce an apparently radially symmetrical capitulum (flower head) by combining central actinomorphic disk florets with an outer ring of highly zygomorphic ray florets

Fig 3. Daisies, such as this Gorteria diffusa, produce an apparently radially symmetrical capitulum (flower head) by combining central actinomorphic disk florets with an outer ring of highly zygomorphic ray florets

flower is dependent on the actions of both dorsalising factors (the partially redundant TCP transcription factors CYCLOIDEA (CYC) and DICHOTOMA (DICH)) and ventralising factors (the MYB transcription factor DIVARICATA (DIV)) (Luo et al. 1996; Almeida et al. 1997). In 2005 Corley et al. used a combination of genetic and molecular approaches to define a further MYB protein, RADIALIS (RAD), as a target of CYC/DICH and the antagonist to the ventralising signals provided by DIV, which is transcribed in all regions of the floral meristem. A model in which RAD and DIV competed to bind promoter regions of downstream ventral-specific genes was the simplest explanation, with DIV outcompeted by RAD in the dorsal parts of the flower as RAD is activated by CYC/DICH in this region.
Recent work by Raimundo et al. (2013) has dissected the molecular interaction between DIV and RAD in more detail, and has shown that the mechanism of symmetry determination is a little more complicated than initially supposed. The authors determined the optimal DNA binding site of the DIV protein, and found that RAD did not bind the same motif. Moreover, RAD did not displace DIV from a DIV-DNA complex, and RAD and DIV proteins did not interact in a yeast 2 hybrid assay. Having effectively disproven the earlier model, the authors then reasoned that RAD and DIV might interact through a third protein. Using RAD as bait in a yeast 2 hybrid screen they identified a pair of novel MYB proteins, which they termed DRIF1 and DRIF2. Tests with DRIF1 showed that it also bound to DIV, and that the DIV-DRIF1-DNA complex was disrupted by the addition of RAD, which competed with DIV not for the DNA but for the DRIF1 protein. Analysis of the subcellular localisation of these proteins revealed that RAD is present in both cytoplasm and nucleus, while DIV is found in the nucleus only. DRIF1 was found to be nuclear localised in the presence of DIV, but cytoplasmically localised in the presence of RAD. In combination these data show that the antagonism between dorsal and ventral activities that occurs when RAD and DIV are both present in the dorsal part of the floral meristem is due to the ability of RAD to sequester the DRIF proteins in the cytoplasm, preventing their interaction with DIV and consequently preventing the DIV protein from activating transcription when bound to DNA.
This mechanism is not unique to floral symmetry. The sequestration of key components of transcriptional complexes in the cytoplasm is a common theme in many aspects of both plant and animal development, including in the processes (such as the floral transition) that occur in response to light signals. It is a system that is both robust and flexible, and has the potential to be adapted to suit a variety of specific requirements. It is perhaps fitting, given that complexity of zygomorphic flowers in their many forms, that the control of floral symmetry operates through a similarly complex molecular interaction.

Almeida J, Rocheta M & Galego L 1997. Genetic control of flower shape in Antirrhinum majus. Development 1244, 1387-1392.
Chapman MA, Tang S, Draeger D, Nambeesan S, Shaffer H, Barb J, Knapp S & Burke J. 2012. Genetic analysis of floral symmetry in Van Gogh’s sunflowers reveals independent recruitment of CYCLOIDEA genes in the Asteraceae. PLoS Genetics 8, (3), e1002628.
Corley S, Carpenter R, Copsey L & Coen E. 2005. Floral asymmetry involves an interplay between TCP and MYB transcription factors in Antirrhinum. PNAS 102, 5068-5073.
De Luca PA & Vallejo-Marín M. 2013. What’s the “buzz” about? The ecology and evolutionary significance of buzz-pollination. Current Opinion in Plant Biology 16, 429-435.
Luo D, Carpenter R, Vincent C, Copsey L & Coen E. 1996. Origin of floral asymmetry in Antirrhinum. Nature 383, 794-799.
Raimundo J, Sobral R, Bailey P, Azevedo H, Galego L, Almeida J, Coen E & Costa M. 2013. A subcellular tug of war involving three MYB-like proteins underlies a molecular antagonism in Antirrhinum flower asymmetry. The Plant Journal 75, 527-538.

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Forecasting flowering phenology

Aalt-Jan van Dijk
Plant Research International, Wageningen University

A prominent example of the role computational predictions play in everyday life is that of the weather forecast – will the weather allow your outdoor activities, and how about the weather during holidays? A similar situation is faced by plants in their decision when to start flowering: they should take information from the environment into account, in other words, they should forecast the weather. From a scientific point of view, there is a second layer of “forecasting” related to flowering: how do changes in the climate influence the choices made by plants? On-going interest in assessing the impact of global warming is clear – note that in a couple of days (end of September) the next Intergovernmental Panel on Climate Change (IPCC) Assessment Report is due.
Recently, a novel approach towards forecasting the influence of temperature on flowering was published (Satake et al. 2013). Before discussing this paper, I will briefly describe a bit of context. A popular approach to model the influence of the environment on flowering has been to use information about e.g. average temperatures and/or the number of days with temperature above a certain level, to find thresholds after which flowering would start. In the last few years, molecular and mechanistic aspects have been introduced to such approaches. In one example, mutants impaired in different signalling pathways in Arabidopsis thaliana were grown in field experiments (Wilczek et al. 2009). A variant of the above mentioned modelling approach was used, in which the accumulation of appropriately scaled “photothermal units” describes the progression of plants towards the initiation of reproductive growth. In this variant, individual scaling factors were linked to the activities of specific genes. In this way, each genotype accumulated photothermal units on the basis of day lengths and temperature averages in each experimental planting, modified according to the environmental sensitivity of the line. A second example presented a two-year census of the expression of a temperature-dependent flowering-time gene, AhgFLC, in a natural population of perennial Arabidopsis halleri (Aikawa et al. 2010). This revealed that the regulatory system in which this gene is involved, extracts seasonal cues as if it memorizes temperatures over the past six weeks.

Flowering forecast

Flowering forecast – information about the weather (left-hand arrow) is taken into account in a computational model of a gene regulatory network (bottom panel); this in turn predicts flowering time (right-hand arrow).FLC and FT indicate the two genes modelled by Satake et al.; red arrow indicates repression activity.

Now, a follow-up on this work forecasts flowering phenology under the influence of temperature changes, again for Arabidopsis halleri (Satake et al. 2013). This time, not only the influence of the environment was included, but also a mechanistic model of a gene regulatory network that influences flowering time. The parameters describing the interactions in this network were fitted to data obtained in controlled experiments in the lab. Importantly, this was done separately for different natural populations. The resulting sets of parameters capture differences in how these populations respond to temperature change, as mediated by the gene regulatory network. Subsequently, these models were tested by predicting how these populations would respond to temperature conditions measured in the field, where the models show a convincing ability to predict flowering. One striking so far untested prediction of the model is that it forecasts that under climate warming, the shift in the return time to vegetative growth is greater than that in floral initiation. This would correspond to a significant reduction of the flowering period and ultimately to losing the opportunity to flower at all.
From a computational point of view, it is interesting that the parameters of the gene regulatory network model presented by Satake et al. capture information about responses to the environment, and how these responses differ between natural populations. This extends recent efforts towards modelling flowering time gene regulatory networks, such as (Dong et al. 2012 and Jaeger et al. 2013). Nevertheless, genetic information is not yet explicitly present in the Satake et al. model, in the sense that no connection is made to causal variants in the genome that presumably are present in the different natural populations. Hence, for a novel population of interest, this approach is not directly able to predict its behaviour based on genetic information. I expect that we will see in the near future modelling approaches that use such knowledge on which genetic changes underlie differences between populations. One recent example of an underlying causal variant for Arabidopsis thaliana is given by (Méndez-Vigo et al. 2013) and such information could in principle be incorporated as influencing the parameters in the model. That being said, this work provides an important step towards describing how plants deal with the weather forecast!

Satake A, Kawagoe T, Saburi Y, Chiba Y, Sakurai G, Kudoh H. 2013. Forecasting flowering phenology under climate warming by modelling the regulatory dynamics of flowering-time genes. Nat Commun 4:2303.

Wilczek AM, Roe JL, Knapp MC, Cooper MD, Lopez-Gallego C, Martin LJ, Muir CD, Sim S, Walker A, Anderson J, Egan JF, Moyers BT, Petipas R, Giakountis A, Charbit E, Coupland G, Welch SM, Schmitt J. 2009. Effects of genetic perturbation on seasonal life history plasticity. Science 323(5916):930-4.

Aikawa S, Kobayashi MJ, Satake A, Shimizu KK, Kudoh H. 2010. Robust control of theseasonal expression of the Arabidopsis FLC gene in a fluctuating environment. Proceedings of the National Academy of Sciences 107(25):11632-7.

Dong Z, Danilevskaya O, Abadie T, Messina C, Coles N, Cooper M. 2012. A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modelling. PLoS One 7(8):e43450.

Jaeger KE, Pullen N, Lamzin S, Morris RJ, Wigge PA. 2013. Interlocking feedback loops govern the dynamic behavior of the floral transition in Arabidopsis. Plant Cell 25(3):820-33.

[6] Méndez-Vigo B, Martínez-Zapater JM, Alonso-Blanco C. 2013. The flowering repressor SVP underlies a novel Arabidopsis thaliana QTL interacting with the genetic background. PLoS Genet 9(1):e1003289.

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