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MEETING REVIEW 4335
June bloom in Maratea
François Parcy1,2,3,4 and Jan U. Lohmann5,*
Summary
The International Workshop on Molecular Mechanisms
Controlling Flower Development took place in the secluded
southern Italian village of Maratea in June 2011. This meeting,
which takes place biennially, gathers researchers in the fields of
flowering time and flower and fruit development from both
Europe and overseas to enjoy the sun, the sea and, most
importantly, the science. As we summarise here, the results
presented at this workshop underlined how mechanistic studies
of both model and diverse species are deepening our
understanding of the cellular processes involved in flowering.
Key words: Evolution, Flower development, Flowering time, Fruit
development, Plant hormone, Transcriptional control
Introduction
The study of flowers, in particular how they develop and become
elaborated in diverse species, has attracted scientists for hundreds
of years. However, only in recent decades, since the advent of
genetics and molecular biology in model systems such as
Arabidopsis, have we been able to take a quantum leap forward in
understanding the molecular mechanisms underlying flowering.
Flower development can be broadly divided into several
interconnected steps (Fig. 1): the repression of reproduction under
non-favourable conditions, the induction of flowering sensor
pathways that integrate environmental and endogenous cues, the
specification of floral identity to young stem cell centres by
meristem identity genes, and, finally, the elaboration and
patterning of floral organs. The International Workshop on
Molecular Mechanisms Controlling Flower Development, which
took place in Maratea, Italy, earlier this year, provided researchers
in this field with the opportunity to present their latest insights into
the molecular mechanisms that control these important steps of
flower development.
Since flowering represents sexual reproduction in plants, it is
imperative that the pathways leading up to the generation of seeds
are synchronised with both the growth status of the plant and its
external environment, in order to maximise the survival rate of
offspring (reviewed by Amasino, 2010). One particularly important
external input that is connected to repression of flowering is winter
experience, or vernalisation, and many plants will not flower unless
they have experienced an extended exposure to cold. This behaviour
is driven by FLOWERING LOCUS C (FLC), which encodes a
potent transcription factor that represses the expression of floral
inducers and integrators and whose expression is reduced by a
polycomb-dependent epigenetic silencing mechanism in response
1
CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble,
France. 2CNRS, UMR5168, F-38054 Grenoble, France. 3Université Joseph FourierGrenoble I, UMR5168, F-38041 Grenoble, France. 4INRA, UMR1200, F-38054
Grenoble, France. 5Centre for Organismal Studies, University of Heidelberg, 69121
Heidelberg, Germany.
*Author for correspondence ([email protected])
to cold (Bastow et al., 2004). In addition, plants have evolved
elaborate mechanisms to trigger flowering at reproducible times of
the growing season in response to environmental cues. Temperature
and day length appear to be the most relevant inputs for this
behaviour, and work over recent decades has uncovered some of the
mechanisms that control how these inputs regulate flowering. These
studies have shown, for example, that the day-length response is
mediated by circadian expression of CONSTANS (CO) mRNA,
coupled to the light-dependent stabilisation of CO protein (Valverde
et al., 2004). This system ensures that CO mRNA coincides with
light only under long days, leading to the long-day-specific
stabilisation of CO. Light sensing, and thus day length detection,
occurs in the leaves, whereas developmental decisions, such as floral
induction, are undertaken by cells of the apical stem cell niche. Thus,
the information generated in the leaves must be transmitted over a
substantial distance, and this activity has been termed florigen.
Genetics and genomics have shown that FLOWERING LOCUS T
(FT) encodes a small mobile protein that carries out florigen
function (Mathieu et al., 2007; Wigge et al., 2005). Interestingly, it
has emerged that the CO transcription factor directly activates FT
mRNA expression in leaves, while a number of floral repressors,
including the transcription factors APETALA 2 (AP2),
SCHNARCHZAPFEN (SNZ) and FLOWERING LOCUS M (FLM),
counteract this activity to balance inductive and repressive inputs
into FT gene activity (Yant et al., 2010). After translation, FT protein
moves via the phloem sap to the apex and, once unloaded from the
phloem, FT interacts with basic leucine zipper (bZIP) transcription
factors, including FLOWERING LOCUS D (FD), to act as a
transcriptional regulator that potently induces flower formation
(Wigge et al., 2005).
Once the floral inductive signals have overcome the repressive
inputs, as described above, newly arising stem cell centres are
specified to become flowers by floral meristem identity genes such
as LEAFY (LFY) and APETALA 1 (AP1) (reviewed by Liu et al.,
2009). The activity of these transcription factors is a prerequisite for
the formation of floral primordia and for the appropriate expression
of floral organ identity genes, which in turn take over the patterning
of the emerging organs (reviewed by Lohmann and Weigel, 2002).
The ABC model elegantly describes how floral organs are specified
in a combinatorial fashion in which three overlapping genetic
activities specify the four distinct organ types that are arranged in
four concentric rings, termed whorls (Coen and Meyerowitz, 1991).
The floral organ identity genes, which include the A-class genes
AP1 and AP2 required for sepal and petal development in whorls 1
and 2, respectively, the B-class genes AP3 and PISTILLATA (PI) that
are responsible for specifying petal identity in whorl 2 and stamen
identity in whorl 3, and the C-class gene AGAMOUS (AG), which is
essential for stamen and carpel fate in whorls 3 and 4, respectively,
are expressed in specific subdomains of the developing flower. With
the exception of AP2, these regulators belong to the MCM1,
AGAMOUS, DEFICIENS and SRF (MADS) domain family of
transcription factors, and recent research has shown that these
proteins act in higher-order complexes to direct target gene
expression and thus organ specification. Essential co-factors for the
formation of these complexes are the SEPALLATA (SEP) proteins,
which are also members of the MADS domain protein family and
which extend the ABC model to the ABCE model (reviewed by
Gutierrez-Cortines and Davies, 2000). Once the basic floral pattern
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Development 138, 4335-4340 (2011) doi:10.1242/dev.067215
© 2011. Published by The Company of Biologists Ltd
4336 MEETING REVIEW
Development 138 (20)
Environmental cues
e.g. light, day length, temperature
Sensor pathways
Sensor pathways
Cold
FLC
Endogenous cues
Floral pathway integrators
e.g. FT, FD
Floral repressors,
e.g. AP2, SNZ, FLM
Fig. 1. The regulatory steps of flower
development. Environmental and endogenous cues
are detected by sensor pathways, which in turn act on
floral pathway integrators (such as FT and FD). These
then activate genes and proteins involved in specifying
meristem identity (e.g. LFY, ABC genes, SEP proteins),
eventually leading to floral and organ patterning.
Hormones, such as auxin and jasmonic acid, can also
influence flowering in various ways. AP2, APETALA 2;
FD, FLOWERING LOCUS D; FLC, FLOWERING LOCUS
C; FLM, FLOWERING LOCUS M; FT, FLOWERING
LOCUS T; LFY, LEAFY; SEP, SEPALLATA; SNZ,
SCHNARCHZAPFEN.
Meristem identity regulators
e.g. LFY, ABC genes, SEP proteins
Hormones
e.g. auxin, jasmonic acid
has been laid down by organ identity genes, organs are elaborated
by intricate regulatory networks that involve plant hormones and
other transcription factors (reviewed by Østergaard, 2009).
Although most of the mechanisms described above (as
summarised in Fig. 1) have been elucidated using the power of
genetics and molecular approaches in Arabidopsis, we are currently
witnessing a trend to study these processes in diverse species that
exhibit divergent flowering behaviours or morphologies, using the
molecular knowledge established in model systems as a steppingstone. The results presented at the Maratea meeting, which was
organised by Lucia Colombo and Martin Kater (University of Milan,
Italy), mirrored this trend, but also underlined the importance of
mechanistic studies of model systems for expanding and deepening
our understanding of the cellular processes involved in flowering.
Several major themes emerged during course of the workshop, and,
in the following sections, we summarise the data that was presented
relating to each of these themes.
Evolution of regulatory networks
One exciting concept that emerged during the meeting was that
conserved regulatory networks have been rewired during evolution,
leading to differential responses to environmental cues in diverse
species. Thus, despite the fact that the same regulators act on the
same biological process, the developmental outcome of a network
can be modified during adaptation. In this context, Richard
Macknight (University of Ontago, New Zealand) presented
collaborative work with Jim Weller (University of Tasmania,
Australia) showing that legumes have three distinct subclades of FT
genes. In the legume Medicago truncatula, these FT genes respond
differentially to day length and vernalisation, and the combined
action of at least two of these FTs determines flowering time (Laurie
et al., 2011). Studies presented by Ove Nilsson (Umeå Plant Science
Centre, Sweden) on the regulation of flowering time demonstrated
that, in sugar beet (Beta vulgaris), gene duplication has given rise to
two FT paralogues that have evolved antagonistic functions. One
gene (BvFT2) behaves as all previously described FT-like genes,
activating flowering, whereas the other paralogue (BvFT1) is a
strong repressor of flowering. BvFT1 appears to have a central role
in the regulation of vernalisation in biennial sugar beet, and
overexpression of BvFT1 leads to non-flowering vernalisationinsensitive plants that appear to fulfil all the requirements of a
‘winter beet’ that can be planted in the autumn without flowering the
next spring (Pin et al., 2010). In addition, Timo Hytönen (University
of Helsinki, Finland) reported that the TERMINAL FLOWER 1
(TFL1) gene, which controls inflorescence architecture in
Arabidopsis and other species, appears to be a key regulator of
flowering in strawberry, thus explaining the major differences
between seasonal and continuously flowering accessions.
Several talks dealt with the evolution of inflorescence
architecture. These included three presentations on plants that bear
an inflorescence called cyme, in which the primary meristem
terminates in a flower and growth continues due to a lateral structure
called the sympodial meristem. Ronald Koes (University of
Amsterdam, The Netherlands) and Claire Périlleux (University of
Liège, Belgium) unravelled the central role of the Petunia EXTRA
PETALS (EXP) and tomato JOINTLESS genes, two MADS domain
family genes that prevent the sympodial meristem from acquiring
floral fate. Serena Della Pina (University of Amsterdam, The
Netherlands) presented evidence to suggest that the differences in
the expression patterns observed between Arabidopsis and Petunia
for LFY and UNUSUAL FLORAL ORGANS (UFO) in Arabidopsis
and ABERRANT LEAF AND FLOWER (ALF) and DOUBLE TOP
(DOT) in Petunia are due to differences in cis-elements between
UFO and DOT and to differences in trans factors acting on the LFY
and ALF promoters.
Several laboratories focusing on fruit development in Arabidopsis
and rape seed presented their work on the evolution of regulatory
networks. Central regulators of Arabidopsis fruit development have
been isolated in genetic screens in the past, and recent work aimed
to link these regulators together. Monica Colombo from the
laboratory of Cristina Ferrandiz (University of Valencia, Spain)
showed that the formation of the apical part of the gynoecium, the
style, is dependent on a higher-order protein complex involving the
NGATHA (NGA), STYLISH (STY) and YABBY (YAB)
transcription factors (Trigueros et al., 2009). NGA factors are also
able to interact with other factors that play a role in apical
gynoecium development, such as AINTEGUMENTA (ANT),
suggesting that a combinatorial NGA complex code might dictate
tissue identity in the fruit.
Work from Robert Sablowski and Lars Østergaard (John Innes
Centre, Norwich, UK) pinpointed a single nucleotide regulatory
mutation in the REPLUMLESS (RPL) gene as the molecular origin
DEVELOPMENT
Flower
development
of developmental variation in Brassicaceae seed dispersal (Arnaud
et al., 2011). An equivalent mutation in RPL has been selected to
limit seed dispersal during rice domestication (Konishi et al., 2006),
suggesting that a common genetic toolkit regulates both
domestication and natural evolution, highlighting how plant
evolutionary developmental biology studies and breeding research
can inform each other.
Transcription factor behaviour
Since flowering is controlled largely by transcriptional mechanisms,
the development of novel genome-wide techniques, such as
chromatin immunoprecipitation-sequencing (ChIP-seq), has deeply
impacted work in this field. The laboratories of Gerco Angenent
(University of Wageningen, The Netherlands) and Markus Schmid
(Max-Planck Institute for Developmental Biology, Tübingen,
Germany) presented genome-wide transcription factor binding
profiles for several key regulators of flower development, including
the AP1, SEP3 and FLM MADS domain proteins, as well as AP2
and LFY (Moyroud et al., 2011; Yant et al., 2010; Kaufmann et al.,
2010; Kaufmann et al., 2009). These studies revealed a multitude of
potential new direct targets for these factors and further work is now
needed to confirm their regulation and to study their function.
Because ChIP-seq combined with expression studies usually yields
a wealth of targets, the results of ChIP-seq studies of the
FRUITFULL (FUL) MADS domain protein presented by Marian
Bemer (University of Zurich, Switzerland) came as a surprise: very
few of the potentially regulated genes were identified as direct
targets using the ChIP-seq approach. Although FUL is known to
negatively regulate the valve margin identity genes
SHATTERPROOF 1 and 2 (SHP1 and SHP2), INDEHISCENT
(IND) and ALCATRAZ (ALC), only SHP2 was identified as a direct
FUL target.
Genome-wide data are not only useful for compiling extensive
lists of target genes, but they can also be used to understand the rules
governing DNA binding and transcriptional logic. To this end, Jose
Muiño (University of Wageningen, The Netherlands) presented
tools that allow multiple ChIP-seq datasets to be processed, analysed
and compared (Muiño et al., 2011). François Parcy (University
Joseph Fourier, Grenoble, France) also showed how, based on in
vitro biochemical studies combined with ChIP-seq analysis, a
biophysical model can be constructed to predict binding sites of the
LFY master floral regulator (Moyroud et al., 2011). Such a tool can
efficiently track regulatory evolution based on the analysis of
primary genome sequence.
Given their central roles in most steps of flower development,
understanding the regulatory logic for complexes of MADS domain
transcription factors is a key issue. Günter Theissen and Rainer
Melzer (University of Jena, Germany) along with Gerco Angenent
presented exciting results obtained by combining in vitro
experiments and computational analyses of ChIP-seq data. They
demonstrated that the DNA-binding ability of MADS complexes
(dimer or tetramers) not only depends on DNA sequence but also on
DNA shape, the orientation of binding sites, the distance between
binding sites and even temperature (Melzer et al., 2009; Melzer and
Theissen, 2009). Along these lines, the existence of MADS protein
tetramers in vitro and in vivo has been substantiated by data from
the Angenent laboratory: using affinity purification and mass
spectrometry
followed
by
bimolecular
fluorescence
complementation (BiFC) validation, they showed that five major
floral homeotic MADS domain proteins (AP1, AP3, PI, AG and
SEP3) interact in floral tissues as suggested in the ‘floral quartet’
model, which predicts the interaction of floral homeotic ABC
MEETING REVIEW 4337
regulators with SEP proteins in a tetrameric complexes (Honma and
Goto, 2001; Theissen and Saedler, 2001). In addition to the
interactions between MADS domain proteins, the Angenent
laboratory discovered a number of other transcription factors and
chromatin-remodelling factors that are associated with the floral
MADS proteins, taking us a substantial step closer to understanding
how the floral pattern is translated into organ specification.
MADS domain transcription factors are represented by large and
diverse gene families in all land plants, and floral patterning is not
their only role. Thus, several talks were devoted to functional
analyses of MADS domain transcription factors in diverse species.
The take-home message was that, despite the conserved role of this
gene family in flower development, the number of genes in each
subclade of the MADS domain family and the degree of
subfunctionalisation of these proteins differ greatly between species.
Martin Kater (University of Milan, Italy) presented genetic
interactions between the four AG subfamily genes present in rice and
showed that carpel identity was completely lost in an osmads3
osmads58 double-mutant stamen, similar to the carpel identity loss
observed in the Arabidopsis ag mutant. Dabing Zhang’s group
(Shanghai Jiao Tong University, China) identified several key floral
organ regulators in the monocot rice, including the C-class gene
OsMADS3 (Hu et al., 2011), the E-class gene OsMADS34 (Gao et
al., 2010), an ancient AGAMOUS-LIKE 6 gene OsMADS6 (Li et al.,
2010) and the CYCLOIDEA-like homologue RETARDED PALEA 1.
More recently, they have investigated the interactions between
OsMADS3, OsMADS13 (a D-class gene) and DROOPING LEAF
(DL) during floral organ identity specification and floral meristem
determinacy (Li et al., 2011). Furthermore, the Zhang group showed
that OsMADS6 is able to positively regulate the expression of B-,
C- and E-class floral patterning genes during early flower
development, and proposed a working model to explain the role of
floral homeotic genes in the specification of flower organ identity
and meristem determinacy in rice.
Teemu Teeri (University of Helsinki, Finland) showed that Eclass floral patterning genes show a higher level of
subfunctionalisation in Gerbera than in Arabidopsis, with individual
genes specialised for either stamen development or carpel
development. Brendan Davies (University of Leeds, UK) showed
how a single amino acid change in the K (keratin) domain of a
MADS box factor can modify the identity of its interacting partners,
thereby explaining the functional difference between the
FARINELLI and PLENA proteins from Antirrhinum (Airoldi et al.,
2010). Lucia Colombo (University of Milan, Italy) explained how
the SEEDSTICK (STK) MADS gene acts redundantly with the
ARABIDOPSIS B-SISTER (ABS) gene in controlling several aspects
of ovule and seed development, demonstrating that MADS
regulators play essential roles in all steps of flower development,
from the control of flowering time to the final stages of flower
development.
Integration of transcriptional and hormonal
signals
Another topic that emerged during the course of the workshop was
the importance of interactions between local transcriptional
networks and hormonal signals during the regulation of diverse
processes, ranging from stem cell regulation in the shoot apical
meristem to patterning the fruit for seed dispersal. Jan Lohmann
(University of Heidelberg, Germany) identified a basic helix-loophelix (bHLH) transcription factor as a direct transcriptional target of
the meristem regulator WUSCHEL (WUS) (Busch et al., 2010).
Interestingly, this factor is able to uncouple stem cell proliferation
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from the well-characterised WUSCHEL-CLAVATA system of
meristem maintenance (Brand et al., 2000; Schoof et al., 2000).
Gain- and loss-of-function studies highlighted both auxin-dependent
and -independent functions for this transcription factor, suggesting
that auxin could be directly involved in stem cell control (Zhao et
al., 2010). Rüdiger Simon (University of Düsseldorf, Germany)
presented new results on the control of KNOTTED1-LIKE
HOMEOBOX (KNOX) and of PIN-FORMED (PIN), which encodes
an auxin transporter, expression in Arabidopsis shoot meristems.
Genetic analysis and direct molecular studies revealed that
LATERAL ORGAN BOUNDARY DOMAIN (LBD) proteins, a
class of plant-specific transcription factors, interact with each other
and form different heteromeric complexes that jointly act at the
boundary region, a cleft that separates the meristem from laterally
arising organs. Meristems that lack LBD protein activity, such as
those present in jagged lateral organs mutants, fail to support further
organ growth and arrest activity at early stages. Moving on to floral
meristems, David Smyth (Monash University, Melbourne,
Australia) reported novel insights into petal emergence. He proposed
an elegant mechanism by which the tri-helix transcription factor
PETAL LOSS (PTL) mediates growth suppression between sepals,
thus allowing auxin signalling from neighbouring cells to trigger
petal outgrowth. Ptl enhancer screens identified the auxin
transporter AUX1, further substantiating the role of auxin during
petal emergence. Once the petal has been specified, its growth and
shape need to be defined. The group of Mohammed Bendahmane
(Ecole Normale Supérieure, Lyon, France) demonstrated that the
bHLH transcription factor BIG PETALp is involved in controlling
postmitotic cell expansion during petal development by functioning
in the jasmonate pathway and through an interaction with AUXIN
RESPONSE FACTOR 8 (Brioudes et al., 2009; Varaud et al., 2011).
The intricate connection between hormone signalling and
transcriptional regulation became further apparent in talks that
focused on the development of reproductive organs. Maura
Cardarelli (Sapienza University of Rome, Italy) showed how auxin
and jasmonic acid work hand in hand in late stamen development
(Cecchetti et al., 2008). She showed that auxin first controls the
timing of endothecium lignification, an early event of the anther
opening process during which jasmonic acid has no role. Auxin then
activates jasmonic acid biosynthesis, which in turn stimulates anther
opening. Auxin is also essential for patterning the gynoecium and
Eva Sundberg (University of Uppsala, Sweden) presented data on
the direct transcriptional regulation of the YUCCA class of auxin
biosynthesis genes and other transcription factor genes by SHORT
INTERNODES (SHI)/STY zinc-finger transcription factors (Eklund
et al., 2010a). Interestingly, the regulatory interaction between
SHI/STY genes and auxin biosynthesis in Arabidopsis is conserved
in moss, and SHI/STY expression overlaps with auxin responses in
the moss Physcomitrella (Eklund et al., 2010b). Charles Gasser
(University of California, Davis, USA) reported that, in the complex
regulatory network of ovule patterning, the KANADI transcription
factor ABERRANT TESTA SHAPE physically interacts with the
ETTIN auxin response factor and that both are essential for
integument growth. Thus, auxin appears to play a role not only in
ovule initiation, but also in later morphogenetic events. Even later
in flower development, when the fruit is fine-patterned to allow seed
dispersal, localised hormonal activity is essential. The laboratory of
Lars Østergaard identified the IND and SPATULA (SPT)
transcription factors as key regulators of auxin transport in both early
gynoecium development and later during fruit opening. This
regulation occurs through direct interactions of IND and SPT with
target genes involved in the control of polar auxin transport.
Development 138 (20)
Furthermore, this core genetic network underlying Arabidopsis fruit
development was shown to be conserved in Brassica, and this
knowledge is now being used to improve yield in oilseed rape.
From these presentations, it is clear that the local modulation of
hormone signalling represents a widely used regulatory regime. This
would suggest that, in contrast to many animal systems, hormones
primarily act as regional signals and thus represent efficient
morphogenetic executors. Furthermore, the presentations made it
clear that intricate feedback and feedforward loops operate in many
of the described signalling circuits. Thus, for a complete mechanistic
understanding of these regulatory events, mathematical modelling
is likely to become even more important if we are to uncover the
wiring and layouts of these complex networks.
Imaging, morphodynamics and biophysical
modelling
Although transcription factors and hormones play key roles in
diverse processes during plant development, their activity alone is
not sufficient to define the shape of complex organs. Several
exciting talks addressed the issue of plant morphogenesis using
advanced imaging and mathematical modelling. Robert Sablowski
demonstrated how quantitative three-dimensional analysis of cell
geometry and DNA replication can be used to monitor how cell
growth and the cell cycle are coupled in the meristem and in organ
primordia, and how this coupling is modified by regulatory genes
that affect organ growth. The presentation by Jan Traas (Ecole
Normale Supérieure, Lyon, France) focused on the biophysical
properties of cells during the early stages of flower development.
Using a combined imaging-modelling approach, he showed that the
local modulation of cellular parameters, such as cell wall stiffness
and anisotropy, can be sufficient to produce organ outgrowth.
Zooming in on organogenesis during floral patterning, Susana
Sauret-Gueto (John Innes Centre, Norwich, UK) presented a
quantitative staging system of petal development over time, which
was used as a framework for extracting local growth parameters
through clonal analysis. She used computational models of genetic
factors that locally control growth rate and the direction of growth
through the establishment of an organ polarity field (Fig. 2). These
talks clearly showed that, despite the fact that Arabidopsis has been
a major reference species for investigating plant development, many
aspects of Arabidopsis morphogenesis are still poorly understood
and poorly described. However, it is clear that the ever-improving
imaging techniques and the development of mathematical models to
describe plant tissues at the biophysical level will open new avenues
of research that will help to elucidate the mechanisms that regulate
plant morphogenesis.
Data analysis and network reconstruction
Throughout the meeting, it became clear that both the complexity of
genetic, regulatory and biochemical interactions and the amount of
data derived from high-throughput and genome-wide approaches are
increasing at exponential rates. Thus, the importance of systematic
data handling, analysis and modelling of networks emerged as a
major theme of the meeting. Elena Alvarez-Buylla (University of
Mexico City, Mexico) demonstrated that a complex mathematical
model based on experimental data obtained from Arabidopsis can
be used not only to recapitulate flower development in this species,
but also to predict the regulatory changes that underlie macroevolutionary modulations in flower morphology. As an example, she
presented data on Lacandonia, a Mexican plant species that uniquely
has male reproductive organs in the centre of the flower (AlvarezBuylla et al., 2010). Focusing on data integration and analysis, Yves
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Acknowledgements
We apologise to our colleagues whose work we could not describe owing to
space constraints.
Funding
Work in the F.P. laboratory is funded by ANR, CNRS, INRA and UJF and work in
the J.U.L. laboratory is funded by HSFP, EMBO and the Max Planck Society.
Fig. 2. Modelling tissue growth in Arabidopsis. Image of an
Arabidopsis petal model generated with the MATLAB Growing
Polarised Tissue framework software (Keenaway et al., 2011). In this
approach, the petal tissue is treated as continuous material within
which genetically controlled factors can locally control growth rates and
directions. In this example, two different regional factors (indicated in
orange and yellow) control local growth parameters across the tissue
(white). Image provided by Susana Sauret-Gueto (John Innes Centre,
Norwich, UK).
Van de Peer (VIB, Ghent, Belgium) demonstrated how to
successfully mine large-scale datasets to extract transcriptional
modules and regulatory pathways. He presented studies that have
utilised the Learning Module Networks (LeMoNe) tool
(Vermeirssen et al., 2009) to analyse transcriptomics data together
with protein-protein interaction data, and convincingly showed that
the integration of multiple, diverse datasets in a unified analysis
pipeline represents a quantum leap over more limited approaches
that use one-dimensional data sources. The talks by Antonio Costa
de Oliveira (Federal University of Pelotas, Brazil) and Pedro
Madrigal (Polish Academy of Science, Poznan, Poland) showed
how completely different computational strategies can help to
uncover important cis-regulatory elements: Costa de Oliveira and
co-workers made use of evolutionary conservation to identify
candidate regions across diverse floral regulators, whereas Madrigal
and colleagues applied functional principal component analysis
(PCA) to a genome-wide protein binding dataset to uncover new
AP1 target regions.
Conclusion
In summary, the Molecular Mechanisms Controlling Flower
Development workshop provided an exciting opportunity for the
latest results and experimental strategies in flowering research to be
exchanged and discussed. Six major conclusions can be distilled
from this year’s meeting: (1) do not take regulatory logic identified
in Arabidopsis for granted if you look at other species; (2) we still
have a long way to go before we can fully understand the
transcriptional regulation of flowering, even in the established
model systems; (3) plant hormones are commonly used in local
regulatory circuits, giving rise to diverse morphological structures;
(4) we need to invest heavily in phenotypic analysis at the cellular
and subcellular level in order to resolve the biophysical properties
of target tissues; (5) biologists can no longer neglect systematic data
analysis and modelling; and (6) southern Italy is a beautiful place to
be in late spring.
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Competing interests statement
The authors declare no competing financial interests.
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