CONTROL OF FLOWERING

AUTONOMOUS VERSES ENVIRONMENTAL REGULATION

The initiation of flowering is a critical life-history trait; plants have presumably evolved to flower at a time of
year that ensures maximal reproductive success in a given region. Decades of physiological studies have
revealed that flowering is initiated in response to both environmental cues and endogenous pathways.
Commonly studied environmental cues include changes in temperature and daylength. Endogenous pathways
function independently of environmental signals and are related to the developmental state of the plant; such
pathways are sometimes referred to as autonomous to indicate the lack of environmental influence. The
relative contributions of autonomous and environmental inputs to the flowering decision vary among, and
even within, species. For example, flowering is considered entirely due to autonomous pathways in a variety of
tobacco (Nicotiana tabacum) that forms a fixed number of nodes before flowering regardless of the
environment in which it is grown (McDaniel and Hsu, 1976). Yet, a single-gene change can cause tobacco to
require short days to flower (Allard, 1919), which indicates that the underlying biochemical differences between
environment-sensing and endogenous pathways can be minimal. Also, endogenous and environmental pathways
can interact. For example, some plants pass through a juvenile phase in which they are not responsive to
environmental cues that promote flowering (Poethig, 1990); that is, the transition from the juvenile to adult
phase is a type of endogenous pathway that is necessary to provide competence for environmental pathways to
promote flowering. The recent addition of molecular genetics to the range of approaches used to study the
initiation of flowering has provided some molecular insights into these endogenous and environment-sensing
pathways and has revealed how inputs from multiple pathways are integrated into the flowering decision.
Chemical Control
Flowering is regulated by chemicals produced in the plant, and a variety of plant hormones, including auxins,
ethylene, gibberellins, cytokinins, and abscisic acid, have been shown to influence flowering in different
species. The critical aspect of photoperiodism, however, is the measurement of seasonal time by detecting the
lengths of day and night.

The discovery of the night break phenomenon, which showed that interruption of the night period with light
inhibited flowering in SDPs, established that the length of the dark period is the most critical for initiating a
photoperiodic response.

The chemical phytochrome is responsible for measuring the dark period. Phytochrome, found in the leaves of
plants, exists in two forms, Pr and Pfr. Pr absorbs red light during the day and is converted to Pfr. Pfr absorbs far-
red light during the night and is converted to Pr.

The prevailing hypothesis is that Pfr inhibits flowering, and the length of the dark period has to be sufficient for
the Pfr to fall below some critical level. When the Pfr falls below this level, chemical messages are sent to the
floral regions, and flowering is initiated.

While phytochrome definitely has been shown to trigger the flowering response, it is not the only chemical
involved. It has been shown that a bluelight photoreceptor may also play a role in photoperiodism.

In addition, phytochrome is not translocated in the plant. It remains in the leaves. Hence, other chemicals which
have not been positively identified are responsible for signaling the photoperiodic response.
PHOTOPERIODISM AND FLORIGEN:
The annual fluctuations in daylength that occur over much of the surface of our planet provide a reliable
environmental cue regarding the time of year. It is not surprising, therefore, that the pathways that detect and
promote flowering in response to photoperiod are among the most ancient and conserved. Physiological
experiments first done in the 1930s (Knott, 1934) demonstrated that inductive photoperiods are sensed by
leaves. This raised two fundamental questions: how do leaves measure daylength, and what is the nature of the
flowering signal (known as florigen) that must travel from the leaves to the shoot apical meristem? After
another seven decades of research, we now have relatively clear and satisfying answers to these questions,
especially in Arabidopsis (Arabidopsis thaliana).
FlorigenA Hypothetical Flowering Hormone:
Evidence that a flowering hormone florigen exists in plants comes from the work of Naylor (1952), who
states that a plant can be made to bloom by grafting on it a leaf from another variety, species, genus, or even
from another family. A certain parasitic plant which grows on the roots of red clover is probably never exposed
to light and yet it blooms. It is assumed that this parasite obtains its stimulus for flowering from its host.
1. The metabolism of florigen is believed to be phytochrome-mediated.
2. Florigen has never been isolated. It is a hypothetical hormone.
3. The florigen is translocated to the vegetative bud through phloem, where it transforms vegetative but into
flower bud.
4. Florigen is a sort of stimulus. Unlike other phytohomones, it is neither growth promoter nor a growth
inhibitor.
5. The seat of synthesis and the seat of action of florigen are leaf and shoot tip respectively.
Chailakhyan (1968) demonstrated that the site of perception of light for photoperiodic inductions (stimulus) are
the green leaves. This is evident from the fact that a plant from which all leaves have been removed fails to
flower even under the inductive light conditions. Further confirmation was obtained from experiments with
Xanthium, a short-day plant, in which flowering occurred even when one-eighth of a leaf was exposed to short
days.
Photoperiodic induction received by a single leaf or its part in a plant is considered enough to induce flowering.
Further, a floral stimulus from an induced leaf in a long or short-day plant can be transmitted or trans-located to
another non-induced plant by grafting. Besides, the floral stimulus is not species-specific because grafting an
induced twig of Xanthium on to a vegetative soya bean plant can induce the latter to flower.
The nature of the flower-producing stimulus has been widely debated. Some plant physiologists have proposed
the existence of a flower-inducing growth hormone, the florigen (Naylor 1952 and Chailakhyan 1968). The
metabolism of florigen is believed to be phytochrome-mediated. Unfortunately, the florigen has never been
isolated.
The florigen is trans-located via phloem to the vegetative bud primordia which undergo transformation
(morphological changes) leading to the production of floral buds.
Four steps are involved in this transformation:
(i) Perception of the stimulus by phytochrome in the leaves (induction);
(ii) Change to new pattern of metabolism in the leaves leading to the production of flowering hormone, the
florigen;
(iii) Translocation of florigen (the stimulus) to the bud primordia; and
(iv) Transformation of vegetative bud primordia into floral buds (the response).
 LOCUS OF PHOTOPERIODIC REACTION
The photoperiodic response pathway the ability to respond to photoperiod requires a mechanism to detect
daylength. In Arabidopsis, which is a facultative LDP that is induced to flower earlier in LDs than in SDs, this
mechanism has been shown to involve the interaction of light signals which are perceived by photoreceptors
such as phytochromes, cryptochromes, and the blue light receptor F-box proteins ZEITLUPE (ZTL) and
FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1), with components of the circadian clock, and the
CONSTANS (CO) gene and protein whose rhythmic expression is driven by the circadian clock. The CO
protein is a major regulator of photoperiodic flowering and it directly induces the expression of the floral
integrator gene FT and the closely related TWIN SISTER OF FT (TSF) (Samach et al., 2000; Wigge et al.,
2005; Yamaguchi et al., 2005). The CO protein is expressed at very low levels and its abundance is the limiting
factor in the induction of flowering by photoperiod, as demonstrated by the fact that reducing CO levels by half
in heterozygous plants delays flowering (Robson et al., 2001). The photoperiodic pathway precisely regulates
levels of the CO protein during the course of the day, with levels of the CO protein increasing from c. 10 h after
dawn onwards, reaching high levels by 16 h after dawn or later (i.e. towards the end of a LD) (Valverde et al.,
2004). The coincidence of high levels of CO expression with light is necessary for floral induction, as was
demonstrated by experiments where flowering could be induced by altering the light/dark regime, or CO
expression, such that high levels of CO expression occurred in the light period in SDs (Roden et al., 2002;
Yanovsky & Kay, 2002).

Arabidopsis flowers more rapidly in long days than in short days and is thus a facultative long-day plant. The
regulation of the floral promoter CONSTANS (CO) is key in the perception of inductive long days (Turck et al.,
2008). The circadian clock regulates CO transcription such that peak expression occurs late in the day in long
days but after dusk in short days (Suarez-Lopez et al., 2001). CO protein, in turn, is stabilized by light and
rapidly degraded in darkness (Valverde et al., 2004). As a result, CO protein can only accumulate during
inductive long days. CO is expressed in the vasculature of leaves, and its role in flowering is to activate the
expression of FLOWERING LOCUS T (FT), which encodes a small protein that is florigen (Fig. 1). In both rice
(Oryza sativa) and Arabidopsis, FT is a strong promoter of flowering that is translocated from the vasculature of
leaves to the shoot apical meristem (Corbesier et al., 2007; Tamaki et al., 2007). In the meristem, FT forms a
complex with the bZIP transcription factor FD and initiates flowering by activating floral meristem-identity
genes such as APETALA1 and other floral promoters such as SUPPRESSOR OF OVEREXPRESSION OF
CONSTANS1 (SOC1; Michaels, 2009). Thus, FT up-regulation lies at the end of an environment-sensing
pathway and initiates flower development. In addition to the photoperiod pathway, FT and SOC1 are also
regulated by other flowering pathways (e.g. vernalization; see below) and therefore are referred to as floral
integrators.
The coupling of CO and FT appears to be an ancient and evolutionarily adaptable module. Unlike the situation
in Arabidopsis, in which long days lead to CO activation and FT induction, the rice CO/FT homologs
(HEADING DATE1/HEADING DATE3A) have evolved different circuitry that triggers flowering in response
to short days (Turck et al., 2008). It will be interesting to explore the possible role of CO and FT in more
complex photoperiod response types, such as various species of Bryophyllum, which require long days followed
by short days for flowering to occur (i.e. plants maintained under constant long or short days do not flower).
There is also evidence that the role of CO and FT extends beyond flowering. In poplar (Populus spp.) trees, CO
and FT are involved in the initiation of photoperiod-dependent dormancy (Turck et al., 2008). There is also
intriguing data demonstrating that the use of CO as a daylength indicator may predate flowering
plants. Chlamydomonas reinhardtii lacks FT but does contain a CO-like gene (CrCO) that is an output of the
circadian clock; remarkably, CrCO can partially rescue co mutants in Arabidopsis (Serrano et al., 2009). Given
that CO exists in a relatively large gene family (17 CO-like genes in Arabidopsis), it is possible that CO-related
genes play additional yet-to-be-discovered roles in plant responses to daylength.

PHOTOPERIODISM

The phenomenon of photoperiodism is a fairly recent discovery. Scientists first linked the onset of flowering
with day length in the 1920s, during experiments with soybeans and tobacco. During one experiment, plots of
soybeans were planted at two-week intervals throughout the spring and early summer. Surprisingly, all the
plants flowered at approximately the same time, no matter what their age. Based on this result, scientists
postulated that an environmental factor was triggering the flowering.
Further experiments on tobacco also pointed to this explanation. Most tobacco plants flower during the summer.
However, around 1920, a mutant appeared in a field of tobacco growing near Washington, D.C. The plant had
unusually large leaves and grew to an enormous height without ever flowering. This new variety was named
Maryland Mammoth, and was the subject of several experiments by two researchers from the USDA, W. W.
Garner and H. A. Allard. The researchers took cuttings of this new variety, and grew them in a greenhouse
where they would be protected from frost. These cuttings flowered in Decembereven though at that time they
were only half as tall as the field-grown specimen. Plants grown from seed also flowered in the winter.
Based on these and other experiments, scientists concluded that the flowering was related to day length, or the
number of hours of light the plants received. They termed this phenomenon photoperiodism, and categorized
plants as long-day, short-day, or day-neutral.
Long-Day and Short-Day Plants

Every plant for which flower initiation is light-dependent (and not all plants are) has
a critical day-length associated with it. The term long-day describes plants that begin
forming flower buds when the days are longerthan their critical day length. The
term short-day, on the other hand, describes plants that begin flowering when the
days are shorter than their critical day length. Day-neutral plants form flowers
independent of day length. Generally, long-day plants flower in summer; short-day
plants flower in spring or fall.
Here are some examples of light-dependent plants and their approximate critical day
lengths. There may, however, be cultivars of these plants which have been bred to
have shorter or longer critical day lengths, to meet market demand for flowers at a
certain timeor, in the case of spinach, to delay flowering to increase the length of
the harvest season. Also, in some cases other environmental factors such as
temperature can affect the time of flowering.
Two common long-day plants are dill and spinach. Both these plants will initiate
flowers when the day lengths are longer than their particular critical day length:
Dill critical day length: 11 hrs.
Spinach (some types) critical day length: 13 hrs.
Two familiar short-day plants are chrysanthemum and poinsettia. These plants will
initiate flowers when the day lengths are shorter than their critical day length:
Chrysanthemum (some types) critical day length: 15 hrs.
Poinsettia critical day length: 10 hrs.

Remember that the terms long-day and short-day dont refer to the length of the
critical day. Note that short-day chrysanthemums have a critical day length that
is longer than long-day spinach. The key to the concept is that the terms long-
day and short-day refer to whether the plant will begin flowering when the days
are longer or shorterthan their individual critical day lengths.
So, when the days (number of hours of daylight, that is) are 14 hours long, both
chrysanthemums and spinach will be stimulated to begin flowering.
Chrysanthemums will initiate flowers because the day length is shorter than their
critical day length of 15 hours; spinach will flower because the day length is longer
than its critical day length of 13 hours.
Other common long-day plants include foxglove, lettuce, petunia, sedum, and
hibiscus.
Familiar short-day plants include kalanchoe, onion, and viola.
To make things even more interesting, some plants respond to photoperiod when
they are young, but at maturity are day-neutral!
Remember that not all plants are photoperiodic (initiate flowers in response to day
length). Some plants simply begin flowering once theyve reached a certain age.
These plants are termed day-neutral. Familiar day-neutral plants include cucumber,
tomato, pea, corn, sunflowerand dandelion!
Eventually, scientists discovered that it was actually the hours of uninterrupted
darkness that triggered flowering, rather than the hours of light. Experiments
showed that even brief flashes of light during the dark period of the cycle could
interfere with flower development. Despite this new understanding of
photoperiodism, the terms long- and short-day, which refer to hours of light rather
than darkness, are still commonly used.

The reproductive cycles of many organisms, both plant and animal, are regulated by the length of the light and
dark period, called the photoperiod. In flowering plants (angiosperms), flowers are organs for sexual
reproduction, and photoperiodism refers to the process by which these plants flower in response to the relative
lengths of day and night.

Along the equator, the lengths of day and night remain constant because the sun rises and sets at the same time
throughout the year.

The lengths of the day and night are also equal (each is six months long) at the exact North and South Poles due
to the fact that the sun remains below the horizon for six months each year and above the horizon for the other
six months. Any place else in the world, the days become longer in the summer and shorter in the winter.

The reproductive cycles of many organisms, both plant and animal, are regulated by the length of the light and
dark period, called the photoperiod. In flowering plants (angiosperms), flowers are organs for sexual
 reproduction, and photoperiodism refers to the process by which these plants flower in response to the relative
lengths of day and night.
The synchronization of reproduction with seasonal time is a very important aspect of plant physiology.
Reproduction in many angiosperms is dependent on cross-pollination, the process of pollen being transferred
from one flower to another. Hence, it isimportant for all of the plants of the same species in a given region to
flower at the same time.

Even in nonflowering plants such as mosses, ferns, and some algae, it is usually beneficial for reproductive
structures to be formed in a given season. The ability to detect the length of the day or night or both makes it
possible to synchronize the reproductive event to a particular time of year.

While there have been hundreds of studies which show that many plants respond to changes in the photoperiod,
there have been no broad sweeping generalities to provide a better understanding of this phenomenon. Each
species, and often each cultivar or variety within a species, appears to have its own photoperiodic response.

Photoperiodic Classification
The photoperiodic classification of plants is usually made on the basis of flowering, but other aspects of their
development may also be affected by day length. Based on their flowering response, plants are classified as
short-day plants (SDPs), long-day plants (LDPs), intermediate-day plants, ambiphotoperiodic, or day-neutral
plants.

Photoperiodic Classification

Short-day plants flower when the days are relatively short (generally nine hours or less), such as
in the late fall or early winter.
 In some SDP species flowering is qualitative, meaning that short days are absolutely required,
while in other SDP species flowering is quantitative, which means flowering is accelerated under
short days, but short days are not an absolute requirement. Some examples of SDPs include rice,
cocklebur, and soybean.

Long-day plants flower when the days are relatively long (generally fifteen hours or greater), as
would occur in late spring and early summer. As with SDPs, there are qualitative and quantitative
species of LDPs.

Intermediate-day plants require quite narrow day lengths (between twelve and fourteen hours) in
order to flower, and flowering is inhibited by either short or long days. Sugarcane is an example
of an intermediate-day plant.

Ambiphotoperiodic plants are a specialized group of plants that will flower in either short days or
long days, but flowering is inhibited by intermediate day lengths.

In day-neutral plants, flowering is not regulated by day lengths. In other words, day-neutral plants
flower regardless of the day length. There are also many interesting interactions between
photoperiod and temperature.

A plant may respond to a certain day length at one temperature but exhibit a different response at
another temperature. For example, both the poinsettia and morning glory are absolute SDPs at
high temperature; however, they are absolute LDPs at low temperature and day-neutral
at intermediate temperatures.
PHOTOPERIODIC INDUCTION
Induction Period:
Induction period is the minimum period of exposure to a long day or a short day which is required
to induce flowering. Induction period differs in different plants. For instance, Xanthium requires
only one cycle of day plus night, but most plants require about ten such cycles.

Plants may require one or more inductive cycles for flowering. An appropriate photoperiod in 24
hours cycle constitutes one inductive cycle. If a plant which has received sufficient inductive
cycles is subsequently placed under unfavorable photoperiods, it will still flower. Flowering will
also occur if a plant receives inductive cycles after intervals of unfavorable photoperiods (i.e.,
discontinuous inductive cycles.) This persistence of photoperiodic after effect is
called photoperiodic induction.

1. An increase in the number of inductive cycles results in early flowering of the plant. For instance
Xanthium (a short day plant) requires only one inductive cycle and normally flowers after about
64-days. It can be made to flower even after 13 days if it has received 4-8 inductive cycles. In
such cases the number of flowers is also increased.
2. Continuous inductive cycles promote early flowering than discontinuous inductive cycles. Some
of the examples of plants which require more than one inductive cycle for subsequent flowering
 are Biloxi soybean (SDP) -2 inductive cycles; Salvia occidentalis(SDP)-17 inductive
cycles; Plantago lanceolata (LDP) 25 inductive cycles.

The Role of Photoperiodism in flowering

It is briefly discuss how photoperiodism affects a plants ability to survive in a particular environment.
First of all, lets think about the role flowers play in the life of a plant. We said in Week 1
that they are reproductive structures and are responsible for producing seeds. Now lets
think about why the timing of flowering might be important to a plant. Here are a few
possibilities:
Timing must be such that other plants of the same species are flowering at the same time,
to encourage cross-pollination.
The plant should flower when its pollinators, such as bees, are active.
The plant should flower early enough in the season for seeds to ripen before the cold
weather sets in.

Its easy to see that, as they say, timing is everything. Photoperiodism is a way that
plants can "tell time," and ensure that flowering occurs on schedule. (It is also a factor
in other plant responses such as dormancy; well look at this in the next section.) This
awareness, or measurement, of day length is also common in the animal kingdom. For
example, the mating season for many animals such as deer is in the fall. That way, the
gestation period lasts through the winter, and the young are born in the springand
they have all summer to mature before the cold weather returns. Scientists believe that
this timing is in response to photoperiodrather than being based on weather
conditions or other environmental factors. Photoperiodism also influences the timing
of animal migrations, and even seasonal changes in fur color by animals such as arctic
hares and foxes.
Role of Phytohormones in Flowering:
Researchers have indicated that flowering is also regulated by the interplay of the phytohormones, the
auxins, gbberellins, cytokinins and ethylene. Application of hormones can substitute for the necessary
photoperiod and can initiate floral development in certain plants. It is interesting to note that IAA
(auxin) inhibits flowering in most of the plants. An exception, however, is pineapple (Ananas).
Gibbereuic acid (GA) can substitute photoperiodic induction in many long day plants. It, however, is
almost ineffective in short-day plants except a few such as Impatiens balsamia (Balsam plant).
Significance of Photoperiodism:
1. Photoperiodism determines the season in which a particular plant shall come to
flower. For example, short-day plants develop flowers in autumn-spring period (e.g.,
Dahlia, Xanthium) while long-day plants produce flowers in summer (e.g.,
Amaranthus).
2. Knowledge of photoperiodic effect is useful in keeping some plants in vegetative
phase (e.g., many vegetables) to obtain higher yield of tubers, rhizomes etc., or keep
the plant in reproductive phase to yield more flowers and fruits.
3. A plant can be made to flower throughout the year by providing favourable
photoperiod.
4. Helps the plant breeders in effective cross-breeding in plants.
5. Enable a plant to flower in different seasons thus fruits can be produced during
their offseason by controlling photoperiod.

Circadian Rhythms in Plants

The earth rotates on its axis every 24 h, with the result that any position on the earth's
surface alternately faces toward or away from the sunday and night. That the
metabolism, physiology, and behavior of most organisms changes profoundly
between day and night is obvious to even the most casual observer. These biological
oscillations are apparent as diurnal rhythms. It is less obvious that most organisms
have the innate ability to measure time. Indeed, most organisms do not simply
respond to sunrise but, rather, anticipate the dawn and adjust their biology
accordingly. When deprived of exogenous time cues, many of these diurnal rhythms
persist, indicating their generation by an endogenous biological circadian clock. Until
recently, the molecular mechanisms by which organisms functioned in this fourth
dimension, time, remained mysterious. However, over the last 30 or so years, the
powerful approaches of molecular genetics have revealed the molecular
underpinnings of a cellular circadian clockwork as complicated and as beautiful as the
wonderful chronometers developed in the 18th century. Then, the need to accurately
measure time to precisely determine longitude sparked an international competition to
claim a prize, the princely sum of 20,000 pounds sterling, offered by the British
Crown (Sobel, 1995).
CHARACTERISTICS OF CIRCADIAN RHYTHMS
Circadian rhythms are the subset of biological rhythms with period, defined as the
time to complete one cycle (Figure 1 ) of 24 h (Dunlap et al., 2004). This defining
characteristic inspired Franz Halberg in 1959 to coin the term circadian, from the
Latin words circa (about) and dies (day). A second defining attribute of circadian
rhythms is that they are endogenously generated and self-sustaining, so they persist
under constant environmental conditions, typically constant light (or dark) and
constant temperature. Under these controlled conditions, the organism is deprived of
external time cues, and the free-running period of 24 h is observed. A third
characteristic of all circadian rhythms is temperature compensation; the period
remains relatively constant over a range of ambient temperatures (Pittendrigh, 1954).
This is thought to be one facet of a general mechanism that buffers the clock against
changes in cellular metabolism.
Figure 1.
Critical Terms Used to Describe Circadian Rhythms.
Period is defined as the time to complete one cycle. It is commonly measured from
peak to peak but could equally be measured from trough to trough or from any
specified phase marker. Phase is the time of day for any given event. For example, if
the peak in a rhythm occurred at dawn, the phase of the peak would be defined as 0 h.
If a rhythm peaked 6 h after dawn, its phase would be 6 h, and so on. Phase is often
defined in zeitgeber time (ZT). Zeitgeber is German for time giver, and any stimulus
that imparts time information to the clock is a zeitgeber. The onset of light is a
powerful zeitgeber, and dawn is defined as ZT0. The amplitude of the rhythm is
defined as one-half the peak-to-trough distance.
Only in exceptional circumstances, such as in the laboratory, is an organism deprived
of environmental time cues, such as light/dark cycles or temperature cycles, that
derive from the alternation of day and night. These environmental time cues, termed
zeitgebers (German for time givers), entrain the endogenous timing system to a period
of 24 h, precisely corresponding to the exogenous period of the earth's rotation. The
ability of a stimulus to reset the clock is a function of the time of day (phase;
see Figure 1) at which the stimulus is administered. A pulse of light given before
dawn will advance the phase of the clock, yet the same pulse of light given after dusk
will delay the phase. If given at noon, the same pulse of light will have no effect at all.
From this it is apparent that the clock regulates its own sensitivity to environmental
stimuli. This varying sensitivity can be quantified and displayed as a phase response
curve, in which one plots the shift in phase in response to a stimulus applied at
different times across the circadian cycle (Dunlap et al., 2004).
Previous SectionNext Section
ARABIDOPSIS DISPLAYS MANY CIRCADIAN RHYTHMS
Arabidopsis exhibits myriad rhythmic outputs or hands of the clock (McClung,
2001; McClung et al., 2002; Staiger, 2002). Like many plants, Arabidopsis displays
rhythmic cotyledon and leaf movement, although this rhythm in Arabidopsis is based
on differential growth and thus differs from the rhythmic turgor-driven expansion and
contraction of the pulvinus that underlies rhythmic leaf movement in legumes,
including Tamarindus and Mimosa (Kim et al., 1993). In Arabidopsis, there is a
circadian rhythm in the elongation rate of the abaxial and adaxial cells of the petiole
that confers an oscillation in position of cotyledons and leaves (Engelmann and
Johnsson, 1998). Arabidopsis also exhibits a circadian rhythm in the rate of hypocotyl
elongation (Dowson-Day and Millar, 1999) and in the elongation rate of inflorescence
stem (Jouve et al., 1998).
Circadian control of transcription is widespread (Dunlap, 1999), and the list of plant
genes regulated by the circadian clock is extensive. Microarray analyses suggest that
10% of all Arabidopsis genes regulated at the level of mRNA abundance and have
identified multiple metabolic pathways under circadian control (Harmer et al.,
2000; Schaffer et al., 2001). Circadian-regulated transcripts are enriched in the subset
of transcripts with short half-lives (Gutierrez et al., 2002); it may be that high
transcript stability may obscure some transcriptional oscillations when one simply
monitors steady state transcript abundance. Indeed, enhancer trapping suggests that up
to 35% of the transcriptome may show clock regulation (Michael and McClung,
2003).
Although the study of circadian rhythms has focused on constant conditions, it is
important to remember that plants in nature grow in a changing world. In plants
grown in diurnal cycles, there is an important interaction with sugar metabolism that
strongly influences cycling gene expression (Blsing et al., 2005). In addition, recent
data make it clear that the circadian clock modulates the ability to respond to abiotic
stresses, such as cold (Fowler et al., 2005). Clock modulation of response to biotic
stresses has been the subject of speculation but remains to be established.