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First published online January 25, 2008
doi: 10.1242/10.1242/dev.008631
Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma 630-0101, Japan.
Author for correspondence (e-mail:
simamoto{at}bs.naist.jp)
Accepted 21 November 2007
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SUMMARY |
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TOP
SUMMARY
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES |
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Key words: FT-like gene family, Photoperiodic flowering, Epigenetic regulation, Rice
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INTRODUCTION |
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TOP
SUMMARY
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES |
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;
Baurle and Dean, 2006). Plants
generally fall into one of three photoperiod-sensing classes: long-day plants
(LDP), which promote flowering by sensing long-day (LD) photoperiods;
short-day plants (SDP), which promote flowering by sensing short-days (SD);
and day-neutral plants, which are not regulated by photoperiod.
The signaling cascades of photoperiodic flowering have been studied in the
LDP Arabidopsis thaliana. CONSTANS (CO) encodes a
zinc-finger transcriptional activator and induces expression of the floral
integrator FLOWERING LOCUS T (FT) under LD conditions
(Kardailsky et al., 1999;
Kobayashi et al., 1999;
Yanovsky and Kay, 2002).
FT expression is regulated by both the circadian clock and light
(Yanovsky and Kay, 2003;
Imaizumi and Kay, 2006). The
CO-FT pathway is conserved in rice, which is a SDP [Heading date
1 (Hd1)
Heading date 3a (Hd3a)]
(Yano et al., 2000;
Hayama et al., 2003).
Hd3a, which was identified as a quantitative trait locus (QTL) for
flowering time, is a key activator of flowering in rice
(Kojima et al., 2002). Recent
studies suggest that FT/Hd3a represents a florigen-type
mobile flowering signal (Tamaki et al.,
2007; Corbesier et al.,
2007; Jaeger and Wigge,
2007; Mathieu et al.,
2007; Lin et al.,
2007). Hd3a expression is regulated by Hd1, and
by Ehd1, a B-type response regulator that functions independently of
Hd1 (Yano et al.,
2000; Hayama et al.,
2003; Doi et al.,
2004). Hd3a is also regulated by light via the
phytochrome B sensory system. These two functional pathways merge at
Hd3a (Izawa et al.,
2002; Ishikawa et al.,
2005). Key regulators for photoperiodic flowering in rice and
Arabidopsis are conserved, but differences in their regulation result
in either SDP or LDP (Hayama et al.,
2003).
In addition to the photoperiodic pathway, vernalization, autonomous and
gibberellin pathways are integrated into the transcriptional regulation of
downstream target genes such as FT, TWIN SISTER OF FT (TSF),
SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and
LEAFY (LFY) in Arabidopsis
(Boss et al., 2004;
Imaizumi and Kay, 2006).
Prolonged exposure to cold, a process known as vernalization, promotes
flowering in winter annual Arabidopsis. FLOWERING LOCUS C
(FLC), a MADS-box transcription factor, suppresses floral transition
by repressing the expression of floral activators
(Michaels and Amasino, 1999).
FLC expression is repressed by the vernalization pathway through
epigenetic mechanisms at the FLC locus
(Sung and Amasino, 2004a;
He and Amasino, 2005).
Vernalization requires VERNALIZATION INSENSITIVE 3 (VIN3), a
member of a plant-specific protein family with plant homeodomain and
fibronectin domains, VERNALIZATION 2 (VRN2), a homologue of
polycomb group protein, and VERNALIZATION 1 (VRN1), a
protein containing a DNA-binding domain
(Levy et al., 2002;
Bastow et al., 2004;
Sung and Amasino, 2004b).
These genes are involved in H3K9-mediated deacetylation, and H3K9- and
H3K27-mediated dimethylation chromatin modifications at the first intron of
FLC, and promote flowering by the suppression of FLC.
Furthermore, HETEROCHROMATIN PROTEIN 1 (LHP1)/TERMINAL
FLOWER II (TFLII) is required to maintain the increased level of
H3K9 dimethylation at the FLC locus
(Sung et al., 2006). In
rapid-cycling accessions of Arabidopsis, FLC expression is also
regulated by the autonomous pathway, which constitutively represses flowering.
In this pathway, FLOWERING LOCUS D (FLD) and FVE,
plant homologues of a protein found in the histone deacetylase (HDAC) complex
of mammals, partly regulate flowering by histone deacetylation at the
FLC locus (He et al.,
2003; Ausin et al.,
2004). Chromatin modifications at the SOC1 locus have
also been observed (Bouveret et al.,
2006). However, chromatin modifications at the FT locus
have not been reported (Sung et al.,
2006), although FT expression is regulated by
FLC. In Arabidopsis, flowering is regulated by many floral
activators through multiple pathways, but there is no FLC orthologue
in the rice genome (Goff et al.,
2002; Doi et al.,
2004), and rice does not require vernalization for flowering.
Photoperiodic flowering is thus the key pathway in rice, but no report on
floral regulation through chromatin modification has as yet been
published.
In Arabidopsis, TSF, an FT homologue, acts redundantly
with FT to promote floral transition, because ft tsf double
mutants flower slightly later than ft single mutants
(Michaels et al., 2005;
Yamaguchi et al., 2005). The
rice genome contains thirteen members of the Hd3a gene family
(Chardon and Damerval, 2005).
RFT1/FT-L3 is the closest homologue of Hd3a, and
FTL/FT-L1 is the second closest homologue. Transgenic rice plants
overexpressing RFT1 or FTL flower early, much like
Hd3a-overexpressing plants (Izawa
et al., 2002; Kojima et al.,
2002). However, because there are no mutants of FT-like
genes available, including Hd3a, it is unclear whether
FT-like genes other than Hd3a function as floral activators.
In this study, we show that double RFT1-Hd3a RNAi plants do
not flower for up to 300 days after sowing (DAS), indicating that these two
genes are essential for flowering in rice. Moreover, RFT1 functions
as a floral activator in Hd3a RNAi plants. OsMADS14 and
OsMADS15 were shown to be downstream of Hd3a and
RFT1 in rice flowering under SD conditions. On the basis of these
results, we propose a model for the regulation of rice flowering under SD
conditions.
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MATERIALS AND METHODS |
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SUMMARY
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES |
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). Plants were grown in climate chambers at 70% humidity under
SD conditions with daily cycles of 10 hours of light at 30°C and 14 hours
of dark at 25°C, or LD conditions with 14 hours of light and 10 hours of
dark. Light was provided by fluorescent white light tubes (400 to 700 nm, 100
µmol m-2 s-1).
Hd3a RNAi, RFT1 RNAi, double RFT1-Hd3a RNAi and RFT1::GUS constructs
To generate RNAi transgenic plants, the gene sequences of Hd3a and
RFT1, for which inverted repeats were made, were amplified using
specific primers (see Table 1)
and subcloned into the pENTR/D-TOPO cloning vector (Invitrogen) to yield entry
vectors. The final RNA silencing vectors were produced by an LR clonase
reaction between each of the entry vectors and pANDA
(Miki and Shimamoto, 2004). A
1.7 kb promoter region of the RFT1 gene was used to construct
RFT1::GUS, including an intron to enhance GUS expression
(Tanaka et al., 1990).
Transgenic rice plants were generated by Agrobacterium-mediated
transformation of rice calli (cv. Norin 8), performed according to a published
protocol (Hiei et al.,
1994).
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).
Samples were embedded in paraffin and sectioned at a thickness of 10 µm
using an ULTRACUT UCT ultramicrotome (Leica). Sections were photographed using
a BX50 microscope (Olympus).
RNA extraction and real-time PCR analysis
Leaves were harvested at various times of the day, and total RNA was
extracted using an RNeasy plant mini kit (Qiagen) and treated with DNase I
(Invitrogen). cDNA was synthesized from 1 µg of total RNA using
SuperScriptII Reverse Transcriptase (Invitrogen). One microlitre of cDNA was
used for the quantitative analysis of gene expression performed with SYBR
Green PCR master mix (Applied Biosystems) with gene-specific primers (see
Table 1). Data were collected
using the ABI PRISM 7000 sequence detection system in accordance with the
instruction manual.
Chromatin immunoprecipitation (ChIP) assay
ChIP analysis was performed as described previously
(Nagaki et al., 2003;
Nagaki et al., 2004;
Okano et al., 2008) using
whole leaves harvested 35 or 70 DAS (zeitgeber time; ZT 0) under SD conditions
from Hd3a RNAi and wild-type plants. Isolated nuclei were digested
with micrococcal nuclease (Sigma) instead of sonication and, after the
recovery of nucleosomes, we confirmed that monomer nucleosome (
160 bp)
was most abundant by electrophoresis. ChIP-PCR products were quantified by
real-time PCR. Quantitative ChIP-PCR was normalized to Actin1 in each
experiment. Regions I-VII of the RFT1 locus were amplified by
real-time PCR using specific primers (see
Table 1). ChIP assays were
performed three times with at least two replicates each for each sample.
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).
Genomic DNA (1 µg) was digested with McrBC as recommended by the supplier
(New England BioLabs). McrBC is an endonuclease, which cleaves DNA containing
methylcytosine. Digested DNA template (1 µl) was then amplified, using PCR,
for 25 cycles of 30 seconds at 94°C, 30 seconds at 58°C and 60 seconds
at 72°C with gene-specific primers (see
Table 1). M65, which is a
transgenic line of cv. Nipponbare that carries non-methylated 35S-GFP
(Hashizume et al., 1999), and
the 35S-Pi line, which carries a silencer construct and methylated
35S-GFP (Okano et al.,
2008), served as controls. Methylation status of 35S-GFP
was determined by bisulfite sequencing
(Okano et al., 2008). |
RESULTS |
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SUMMARY
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MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES |
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;
Chardon and Damerval, 2005;
Faure et al., 2007).
RFT1 also lies adjacent to Hd3a, separated by only 11.5 kb
on chromosome 6 (Fig. 1A). To
examine RFT1 expression during different developmental stages under
SD and LD conditions, we sampled leaves from wild-type plants every 10 days
from 25 DAS until flowering. Levels of Hd3a and RFT1 mRNA
were examined by quantitative RT-PCR. Under SD conditions, levels of
RFT1 and Hd3a transcripts were highest 30 days before
flowering, concurrent with floral transition, although absolute transcript
levels of RFT1 were much lower than those of Hd3a
(Fig. 1B). Expression of no
other FT-like gene peaked 30 days before flowering (data not shown).
Hd3a expression is diurnal with a peak before dawn, and a gradual
decrease during the day under SD conditions
(Izawa et al., 2002). Our
analysis showed that RFT1 expression is also diurnal, with a peak
before dawn (Fig. 1D). It is
known that Hd3a acts downstream of the photoperiod pathway via
Hd1 transcriptional regulation
(Kojima et al., 2002;
Hayama et al., 2003).
Expression of RFT1 in hd1 mutants was significantly reduced
under SD conditions, as is Hd3a
(Fig. 1E,F), indicating that
RFT1 and Hd3a are partially regulated by Hd1 under
SD conditions. Under LD conditions, expression of Hd3a and
RFT1 was barely detectable in any developmental stage in wild-type
plants (Fig. 1C).
To study the spatial pattern of RFT1 expression, RFT1 and
Hd3a expression was measured in leaf blades, sheaths and roots under
SD conditions. Expression of RFT1 and Hd3a was observed in
leaf blades, but not in leaf sheaths or roots
(Fig. 2A,B). An
RFT1::GUS reporter fusion protein was detected in leaf blade vascular
tissues 35 DAS under SD conditions (Fig.
2C). This expression pattern is similar to that of
Hd3a::GUS (Tamaki et al.,
2007). The similarity of Hd3a and RFT1
expression patterns under SD and LD conditions, and in vascular tissues,
suggests that RFT1 could function redundantly with Hd3a in
promoting floral transition under SD conditions.
Hd3a and RFT1 are essential for flowering in rice under SD conditions
To test whether RFT1 affects floral induction under SD conditions,
we produced transgenic plants that suppress RFT1, Hd3a, or both
(Fig. 3D). Because homology
between RFT1 and Hd3a is low in the 5' and 3'
non-coding regions, the 5'UTR of RFT1 was used for the RNAi
construct to specifically suppress RFT1 expression and the
3'UTR of Hd3a was used to specifically suppress Hd3a
expression (Fig. 3A,B). The
flowering time of RFT1 RNAi plants (T1) was essentially
the same as in wild type (59±3.5 DAS, n=9 for wild type versus
62±8.3 DAS, n=18 for RFT1 RNAi plants) under SD
conditions (Fig. 3C). This
result indicates that Hd3a acts as the primary activator of flowering
in RFT1 RNAi plants, and that RFT1 does not contribute
significantly to floral transition under SD conditions. By contrast,
Hd3a RNAi plants (T1) flowered 95±6.4 DAS
(n=9) under SD conditions, about 30 days later than did wild type
(Fig. 3C). New leaves are not
normally produced after floral transition in rice. Until 60 DAS, Hd3a
RNAi and wild-type plants had the same number of leaves, indicating that the
growth rates of Hd3a RNAi and wild-type plants are about the same
(data not shown). However, Hd3a RNAi plants produced two or three
more leaves than did wild-type plants after 60 DAS, suggesting that floral
transition is delayed in Hd3a RNAi plants. It is likely, then, that
Hd3a, but not RFT1, promotes floral transition under SD
conditions. Double RFT1-Hd3a RNAi plants did not flower up
to 300 DAS (n=10) under SD conditions
(Fig. 3C). These plants
continued to produce leaves for 300 days and reached a height of 110-130 cm,
about double the height of wild-type plants
(Fig. 3E). The absence or
extended delay of flowering in double RFT1-Hd3a RNAi plants
is apparently due to a complete defect in floral transition. These results
suggest that Hd3a and RFT1 are essential for flowering in
rice.
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;
Michaels et al., 2005;
Teper-Bamnolker and Samach,
2005). In rice, OsMADS1, OsMADS14 and OsMADS15
are upregulated in the floral meristem when it begins to differentiate into
primary panicle branch primordia (Furutani
et al., 2006). To identify genes acting downstream of
Hd3a and RFT1, we examined the expression of OsMADS14,
OsMADS15 and OsMADS50 at 35 and 70 DAS in leaves of
Hd3a RNAi and double RFT1-Hd3a RNAi plants under SD
conditions. OsMADS14 and OsMADS15 are orthologues of
AP1, and OsMADS50 is a rice orthologue of SOC1
(Jeon et al., 2000;
Lee et al., 2004).
OsMADS14 and OsMADS15 were suppressed in Hd3a RNAi
plants 35 DAS (Fig. 5A,B).
OsMADS14 and OsMADS15 thus apparently act downstream of
Hd3a. Expression of OsMADS14 and OsMADS15 was
higher at 70 DAS, when RFT1 expression was also higher in
Hd3a RNAi plants (Fig.
5A,B). Furthermore, OsMADS14 and OsMADS15 were
suppressed at all stages (35, 70 and 120 DAS) in double RFT1-Hd3a
RNAi plants (Fig. 5A,B),
suggesting that RFT1 activates the expression of OsMADS14
and OsMADS15. The expression of OsMADS50 in Hd3a
RNAi and double RFT1-Hd3a RNAi plants was similar to that in
wild-type plants (Fig. 5C).
These results show that, under SD conditions, Hd3a and RFT1
promote floral transition and induce the expression of OsMADS14 and
OsMADS15, but not of OsMADS50.
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We first assessed DNA methylation at the RFT1 locus at 35 and 70 DAS, because RFT1 expression was very low at 35 DAS and very high at 70 DAS in Hd3a RNAi plants. After digestion of genomic DNA with McrBC, an endonuclease that cleaves DNA containing methylcytosine, specific primers were used to amplify the MI, MII and MIII regions of the RFT1 locus (see Table 1). DNA methylation was not detected in any region of the RFT1 locus at any stage in either wild-type or Hd3a RNAi plants (see Fig. S1 in the supplementary material). We obtained similar results when DNA methylation at the RFT1 locus was analyzed by PCR after treatment with methylation-sensitive restriction enzymes (data not shown). DNA methylation was not altered 35 or 70 DAS in wild-type plants or Hd3a RNAi plants, suggesting that the increased expression of RFT1 in Hd3a RNAi plants was not associated with DNA methylation.
Chromatin immunoprecipitation (ChIP) assays were used to examine histone
modifications at the RFT1 locus. H3K9 or H4 acetylation and H3K4
dimethylation cause major modifications of active chromatin, whereas H3K9
dimethylation and H3K27 dimethylation are heterochromatic markers
(Fuchs et al., 2006).
Chromatin modifications in regions I through VII of the RFT1 locus in
Hd3a RNAi plants were compared with those in wild-type plants at 35
and 70 DAS by ChIP, using antibodies against H3K9 acetylation
(Fig. 6A). At 70 DAS, when
RFT1 expression is highly activated in Hd3a RNAi plants,
levels of H3K9 acetylation were higher than wild-type plants in region III,
the region around the start site of transcription
(Fig. 6C). By contrast, there
was no increase in H3K9 acetylation 35 DAS in Hd3a RNAi plants, a
stage at which RFT1 expression is low
(Fig. 6B). Increased H3K9
acetylation at the RFT1 locus may thus be correlated with the
activation of RFT1 transcription.
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DISCUSSION |
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SUMMARY
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES |
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; Lifschitz et al.,
2006; Faure et al.,
2007; Gyllenstrand et al.,
2007). Double mutants of TSF, a close
Arabidopsis homologue of FT, and FT flower late,
but they do eventually flower (Michaels et
al., 2005; Yamaguchi et al.,
2005).
There are 13 rice genes in the FT-like gene family
(Chardon and Damerval, 2005;
Faure et al., 2007). In double
RFT1-Hd3a RNAi plants, expression of FT-L4, FT-L5, FT-L6 and
FT-L12 was similar to that of wild-type plants at 35 DAS and later
stages. Expression of FT-L7, FT-L8, FT-L9, FT-L10, FT-L11 and
FT-L13 was barely detectable in wild-type plants. Interestingly,
expression of FT-L1/FTL, which was the second closest homologue of
Hd3a in rice, was suppressed in the leaves of double
RFT1-Hd3a RNAi plants (data not shown). In the shoot apex of
wild-type plants, expression of FT-L1/FTL was not increased during
the transition to the reproductive stage, but was later increased during
spikelet and floral organ initiation in the inflorescence meristem (R.K. and
K.S., unpublished). Expression of RFT1 and Hd3a was not
detected at any stage in the shoot apex (R.K. and K.S., unpublished).
Furthermore, in Hd3a RNAi plants, expression of FT-L1/FTL
was suppressed at 35 DAS, and not increased at 70 DAS. These results indicate
that RFT1 is the only member of rice FT-like gene family
that was upregulated in Hd3a RNAi plants
(Fig. 4). However, the
possibility that FT-L1/FTL is involved in the extremely late
flowering of the double RFT1-Hd3a RNAi plants cannot be
completely excluded.
Phylogenetic analysis of cereal FT-like genes indicates that
RFT1 is unique to the rice genome, although other FT-like
genes are found in other cereals (Chardon
and Damerval, 2005). RFT1 and Hd3a are
physically very close on chromosome 6, separated by only 11.5 kb
(Fig. 1A), suggesting that
RFT1 may have arisen by tandem duplication of Hd3a after the
divergence of rice from some progenitor cereal. Therefore, RFT1 may
function as an auxiliary to Hd3a in the flowering developmental
pathway when Hd3a is suppressed. Regulation by two members of the
FT/Hd3a gene family involved in flowering may be a rice-specific
mechanism, or an as yet undiscovered auxiliary mechanism in other plants.
Molecular mechanism model for RFT1 activation in Hd3a RNAi plants
Two mechanisms were initially considered to explain the activation of
RFT1 in Hd3a RNAi plants: one was the direct interaction of
Hd3a mRNA or protein with RFT1 mRNA; and the other was a de
novo adaptive pathway, which arises due to the extended vegetative stage
caused by a lack of Hd3a. Direct suppression by Hd3a mRNA or
protein was ruled out by co-transfection assays. RFT1::GUS and
Ubq::bar:GFP (control) or Ubq::Hd3a:GFP were co-transfected
into rice protoplasts and the effect of RFT1::GUS fusion
protein activity on Ubq::Hd3a:GFP was measured. The absence of
RFT1::GUS suppression suggested that neither Hd3a
mRNA nor Hd3a protein acts directly on the RFT1 promoter (data not
shown).
|
), expression
of RFT1 is not increased at 70 DAS under SD conditions (see Fig. S2
in the supplementary material). These results suggest that activation of
RFT1 requires Hd1 and Ehd1, and a novel adaptive
pathway induced by the loss of Hd3a expression
(Fig. 7). To test the possible involvement of epigenetic phenomena in this pathway, we examined histone modifications at the RFT1 locus by ChIP assays and found that H3K9 acetylation increased in the region around the transcription start site of RFT1 when RFT1 was highly expressed in Hd3a RNAi plants (Fig. 6C). This suggests that some chromatin-associated factor(s) regulates RFT1 transcription.
Ehd1 has a GARP [Golden2, Arabidopsis RESPONSE REGULATOR
(ARR), and Chlamydomonas regulatory protein of P-starvation
acclimatization response (Psr1)] DNA-binding motif, which
specifically recognizes 5-bp oligonucleotides in vitro
(Sakai et al., 2000). Binding
sites of Ehd1 are present in RFT1 promoter region II, in
which H3K9 acetylation was slightly increased. H3K9 acetylation of region III
(5'UTR), which is adjacent to region II, was highly increased in
Hd3a RNAi plants. Therefore, chromatin modification at region III of
the RFT1 locus may allow Ehd1 to bind to the promoter region
of RFT1 and thus induce transcription. Because region III of the
RFT1 locus has no homology with the Hd3a 5'UTR used
for the Hd3a RNAi construct, siRNA derived from the Hd3a RNA
constructs was not likely to be involved in chromatin modification of the
RFT1 locus in Hd3a RNAi plants. RFT1 expression
also increased in plants in which Hd3a expression was decreased by a
construct using the coding region of Hd3a (data not shown). These
results suggest that the activation of RFT1 expression in
Hd3a RNAi plants is not induced by some unknown factor(s) associated
with the RNAi method used in our study.
A model for the regulation of photoperiodic flowering in rice
Hd3a is the main promoter of floral transition and flowering at
about 60 DAS under SD conditions in wild-type plants. RFT1, like
Hd3a, is regulated by Hd1 under SD conditions, and its
expression is diurnal with a peak at dawn
(Fig. 1). Expression of
RFT1, which is similar in time and space to Hd3a expression,
is much lower than that of Hd3a (Figs
1,
2). However, when Hd3a
expression is suppressed, as in Hd3a RNAi plants, RFT1
expression increases at a later stage, and RFT1 appears to complement
or replace Hd3a as a floral activator (Figs
3,
4). The increase of
RFT1 expression induces the expression of two rice AP1
orthologues, OsMADS14 and OsMADS15, and also promotes
flowering 30 days later than in wild-type plants
(Fig. 5). Furthermore, when
RFT1 expression is activated in Hd3a RNAi plants, the level
of H3K9 acetylation was higher than in wild-type plants, but not when
RFT1 expression is low (Fig.
6). This chromatin modification at the RFT1 locus may
lead to increased RFT1 expression in Hd3a RNAi plants
(Fig. 6). Suppression of both
Hd3a and RFT1 resulted in no flowering even 300 DAS
(Fig. 3). These results
indicate that Hd3a and RFT1 are the major floral activators,
and one or the other is essential for photoperiodic flowering in rice under SD
conditions (Fig. 7). The
molecular mechanism for RFT1 expression in Hd3a RNAi plants
and the function of RFT1 under other environmental conditions remain
to be studied. There may be an adaptive mechanism of plants to adjust to
changes in the gene expression of a major regulator of flowering to secure
flowering for the production of offspring.
Supplementary material
Supplementary material for this article is available at
http://dev.biologists.org/cgi/content/full/135/4/767/DC1
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ACKNOWLEDGMENTS |
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Footnotes |
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Present address: Faculty of Agriculture, Iwate University, Morioka
020-8550, Japan
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REFERENCES |
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TOP
SUMMARY
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
REFERENCES |
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