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First published online September 12, 2008; 10.1104/pp.108.125542 Plant Physiology 148:1425-1435 (2008) © 2008 American Society of Plant Biologists Ehd2, a Rice Ortholog of the Maize INDETERMINATE1 Gene, Promotes Flowering by Up-Regulating Ehd11,[C],[W]National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan (K.M., U.Y., T.I., M.Y.); and Plant Genome Center, Tsukuba, Ibaraki 305–0856, Japan (Z.-X.W., Y.M.)
Recent research into the flowering of rice (Oryza sativa) has revealed both unique and conserved genetic pathways in the photoperiodic control of flowering compared with those in Arabidopsis (Arabidopsis thaliana). We discovered an early heading date2 (ehd2) mutant that shows extremely late flowering under both short- and long-day conditions in line with a background deficient in Heading date1 (Hd1), a rice CONSTANS ortholog that belongs to the conserved pathway. This phenotype in the ehd2 mutants suggests that Ehd2 is pivotal for the floral transition in rice. Map-based cloning revealed that Ehd2 encodes a putative transcription factor with zinc finger motifs orthologous to the INDETERMINATE1 (ID1) gene, which promotes flowering in maize (Zea mays). Ehd2 mRNA in rice tissues accumulated most abundantly in developing leaves, but was present at very low levels around the shoot apex and in roots, patterns that are similar to those of ID1. To assign the position of Ehd2 within the flowering pathway of rice, we compared transcript levels of previously isolated flowering-time genes, such as Ehd1, a member of the unique pathway, Hd3a, and Rice FT-like1 (RFT1; rice florigens), between the wild-type plants and the ehd2 mutants. Severely reduced expression of these genes in ehd2 under both short- and long-day conditions suggests that Ehd2 acts as a flowering promoter mainly by up-regulating Ehd1 and by up-regulating the downstream Hd3a and RFT1 genes in the unique genetic network of photoperiodic flowering in rice.
Flowering is one of the fundamental events in the life cycle of many higher plants and is a very important trait for determining the ability of a species to adapt to various environmental conditions. Flowering time is largely determined by the timing of the transition from vegetative to reproductive growth and is controlled by both environmental signals and developmental programs. Photoperiod (i.e. daylength) is an important environmental signal that determines flowering time in plants and recent molecular genetic research in Arabidopsis (Arabidopsis thaliana) has revealed how plant sensitivity to photoperiod controls flowering time (Kobayashi and Weigel, 2008
A genetic pathway similar to that in Arabidopsis is conserved in the photoperiodic control of flowering in rice (Oryza sativa), a short-day (SD) plant. Heading date1 (Hd1) is one of the first flowering-related genes to have been cloned from a natural variant of rice (Yano et al., 2000
Although the recent rapid accumulation of knowledge about the genetic control of flowering in rice has been largely based on the analysis of natural variations (Yano et al., 2001
In this study, we discovered an ehd2 mutant that flowers extremely late compared with wild-type plants under both SD and LD conditions. The presence of this phenotype in the ehd2 mutants suggested that the wild-type gene (Ehd2) essentially acts as a flowering promoter. In this article, we describe molecular cloning of Ehd2 and the gene's role in the control of photoperiodic flowering in rice. No significant morphological aberration was observed in the vegetative and reproductive organs of the ehd2 mutants. Map-based cloning revealed that Ehd2 encodes a putative transcription factor with zinc finger motifs, which is orthologous to the INDETERMINATE1 (ID1) gene in maize (Zea mays). Mutations in ID1 have severe effects on the floral transition (Singleton, 1946
Phenotypes of the ehd2 Mutant
The ehd2 mutant was identified as a late-flowering variant of the M2 plants from a
To test whether the flowering times of the ehd2 mutants differed among photoperiodic conditions, we grew the mutants and corresponding wild-type plants under SD conditions (10 h light/14 h dark) and LD conditions (14.5 h light/9.5 h dark). Under SD conditions, flowering time of the ehd2 mutants was 206.5 d, an increase of 145 d compared with the wild-type plants (61.5 ± 1.3 d; Fig. 1A). Under LD conditions, the ehd2 mutants never flowered during more than 365 d, whereas the wild-type plants flowered at 73.7 ± 2.1 d (Fig. 1A). The difference in flowering time in the wild-type plants under the SD and LD conditions was small (12 d; Fig. 1A). Thus, the ehd2 mutants showed extremely late flowering compared with the wild-type plants under both conditions, although the mutation had a more severe effect on flowering time under LD conditions. To examine whether a reduction in growth rate or a prolonged plastochron might have caused the late flowering in the ehd2 mutants, we next compared the leaf emergence rate between the ehd2 mutants and the wild-type plants until 144 d. The wild-type plants flowered after 12 leaves had emerged under SD conditions and after 15 leaves had emerged under LD conditions (Fig. 1B). Before flowering of the wild-type plants, the leaf emergence rate of the ehd2 mutants was almost indistinguishable from that of the wild-type plants under both SD and LD conditions (Fig. 1B). Under both conditions, the ehd2 mutants had developed 20 leaves by 144 d after germination. By the time the wild-type plants flowered, the leaf size and plant height in the ehd2 mutants were similar to those in the wild-type plants under ND conditions (Fig. 1C). The ehd2 mutants eventually flowered under ND and SD conditions (Fig. 1A). No significant morphological aberration was evident in the ehd2 mutants, although the inflorescences with ripened seeds were smaller than those of the wild-type plants (Fig. 1D). Thus, the growth rate and development of the inflorescences were not affected by the ehd2 mutation. These results demonstrate that Ehd2 controls the floral transition in rice, but not its growth rates.
We then performed map-based cloning of ehd2. The ehd2 mutant was first crossed with an indica cultivar (Guang Lu Ai 4), and the resultant F1 was backcrossed with cv Guang Lu Ai 4. It was easy to obtain sufficient DNA marker polymorphisms between japonica and indica rice. The ehd2 phenotype segregated as a monogenic recessive trait in the BC1F2 population (Supplemental Fig. S1). Because the mutant phenotype behaved as a complete recessive, the mutation appears to have been caused by an absence of Ehd2 function. We next performed bulked segregant analysis using plants with normal and mutant phenotypes from the BC1F2 population. The result of the analysis revealed that a simple sequence repeat (SSR) marker (RM6124) on chromosome 10 was linked to the gene for the mutant phenotype (Fig. 2A
). Furthermore, a high-resolution linkage analysis demonstrated that ehd2 is delimited within a 13.9-kb genomic region between two single-nucleotide polymorphisms, SNP-1 and SNP-2, on chromosome 10 (Fig. 2B; Supplemental Table S1). An SSR marker (SSR-1) showed cosegregation with the mutant phenotype (Supplemental Table S1). In this candidate region, two putative proteins, a zinc finger protein (Os10g0419200) and a heat shock transcription factor (Os10g0419300), were annotated in the Rice Annotation Project Database (http://rapdb.dna.affrc.go.jp; zinc finger and heat shock transcription factor, respectively; Fig. 2B). Comparison of the sequence of the candidate region between the ehd2 mutant and the wild-type Ehd2 plants revealed a 4-bp insertion within the second exon of the putative zinc finger protein in the ehd2 mutant (Fig. 2C), resulting in a premature stop codon in the open reading frame (ORF). No other nucleotide polymorphisms were observed in this 13.9-kb candidate region. A homology search using tBLASTn software (http://blast.ddbj.nig.ac.jp/top-j.html) revealed that the putative zinc finger protein is a rice homolog of the maize ID1 protein (accession no. AF058757) that is involved in the transition to flowering (Colasanti et al., 1998
The 3,496-bp Ehd2 gene consisted of three exons and two introns (Fig. 2C). The deduced sequence of 475 amino acids in the protein had a nuclear localization signal motif (KKKR) and four zinc finger motifs (two C2H2-type and two C2HC-type), previously designated as the ID domain (Fig. 2D; Supplemental Fig. S2; Kozaki et al., 2004 To demonstrate that the ehd2 mutant phenotype was caused by a loss-of-function mutation in the putative zinc finger protein, we complemented ehd2 by transforming it with the corresponding cv Nipponbare genomic fragment; cv Nipponbare had a sequence for the putative Ehd2 ORF identical to that of cv Tohoku IL9. The 5.0-kb fragment consisted of a 0.9-kb upstream sequence, the putative coding region, and a 0.7-kb downstream sequence digested by XbaI and KpnI. In these transgenic plants, the Ehd2 phenotype was restored under SD conditions (Fig. 2E). These results confirmed that Ehd2 encodes the ID1 ortholog.
Previous studies in maize revealed that ID1 mRNA appears exclusively in developing leaves (Colasanti et al., 1998
Ehd2 Promotes Flowering by Up-Regulating Ehd1, Hd3a, and RFT1 To identify potential downstream genes that are regulated by Ehd2, we examined the transcript levels of five flowering-related genes (Ehd2, Hd1, Ehd1, Hd3a, and RFT1) by means of quantitative RT-PCR. Leaf samples were collected from 3-week-old and 30-d-old plants grown under SD and LD conditions, respectively. The developmental stage of these plants was about 40 d before flowering. We found that the ehd2 mutant and the wild type both carried a defective Hd1 allele (accession no. AB433218) derived from the japonica cv Sasanishiki. The defective allele had a 43-bp deletion and a 36-bp insertion in the first exon compared with the functional cv Nipponbare Hd1 allele (accession no. AB041837), resulting in a premature stop codon (Fig. 4A ). Nonetheless, the Hd1 mRNA expression was observed in the wild-type plants and the mutants under both SD and LD conditions with a clear diurnal change (Supplemental Fig. S4). However, the level of the Hd1 transcripts in the ehd2 mutants was reduced under both SD and LD conditions compared with that of the wild-type plants. The results suggested that Ehd2 up-regulates Hd1 mRNA expression.
In the wild-type plants under SD conditions, the level of Ehd2 transcripts started to increase after dusk and reached a peak before dawn (Fig. 4B). Then the Ehd2 transcript level decreased once and increased again just before dawn. The Ehd2 transcript level decreased gradually after dawn. Thus, Ehd2 mRNA expression showed a clear diurnal change. The patterns of accumulation of Ehd1, Hd3a, and RFT1 mRNAs appeared to parallel Ehd2 expression, with a short delay, suggesting transcriptional regulation of these genes by Ehd2, although these transcripts remained abundant during the daytime, gradually decreasing until dusk. In contrast, Ehd2 mRNA in the ehd2 mutants remained at very low levels all day, with no sign of diurnal variation, possibly as a result of nonsense-mediated decay of the mRNA. Levels of Ehd1, Hd3a, and RFT1 mRNAs decreased dramatically to nearly undetectable levels in the ehd2 mutants. Under LD conditions, Ehd2 mRNA showed diurnal changes in the wild-type plants and, to a much lesser extent, in the ehd2 mutants (Fig. 4B). The pattern of accumulation of Ehd1, Hd3a, and RFT1 in the wild-type plants was apparently more synchronized with Ehd2 expression under LD conditions than under SD conditions, except that a second peak of RFT1 expression was apparent during the daytime. In the ehd2 mutants, the accumulation of Ehd1, Hd3a, and RFT1 mRNAs was also repressed, at a significantly lower level, as was the case under SD conditions. These results demonstrated that Ehd2 up-regulates the transcription of Ehd1 and of the downstream FT-like genes, Hd3a and RFT1, under both SD and LD conditions, thereby promoting the floral transition.
To further examine whether Ehd2 regulates any other genes, we performed a microarray analysis of wild-type plants and ehd2 mutants grown under LD conditions, with approximately 44,000 rice gene probes. Leaf samples were collected from 30-d-old plants 2 h after dawn. As expected, the level of Ehd2 transcripts was dramatically less in the ehd2 mutants than in the wild-type plants (Supplemental Table S2). The difference in levels of Ehd1 transcripts between the wild-type plants and the ehd2 mutants showed the greatest down-regulation among the genes we examined (Supplemental Table S2). In addition to transcripts of Ehd1, the transcript levels of putative NO APICAL MERISTEM (NAM) protein domain-containing protein (Os08g0200600; Supplemental Fig. S5) and of
To examine the accumulation of Ehd2, Ehd1, Hd3a, and RFT1 mRNAs during development, we harvested developed leaves from wild-type plants and ehd2 mutants at different developmental stages and analyzed them by means of quantitative RT-PCR. The samples were collected 2 h after dawn under SD and LD conditions. In the wild-type plants under SD conditions, Ehd2 mRNA was observed by 1 week after germination and reached a peak by 2 weeks (Fig. 5 ). Subsequently, the level gradually decreased, but transcripts were detected continuously at low levels even after flowering of the wild-type plants (about 9 weeks). The accumulation of Ehd1 mRNA was detected at 2 weeks after germination, and increased greatly thereafter to reach a peak at 8 weeks. Hd3a mRNA was also observed at 2 weeks, then began to increase, and reached a peak at 6 weeks. RFT1 mRNA was present at very low levels until 4 weeks, then began to increase, and reached a peak at 6 weeks. After flowering, levels of Ehd1, Hd3a, and RFT1 mRNAs decreased. Under LD conditions in wild-type plants, the level of Ehd2 transcripts was low during all developmental stages (Fig. 5), although transcription was detected from at least 1 week after germination. Ehd1, Ehd3a, and RFT1 mRNAs were less abundant than under SD conditions, although transcription increased after 4 weeks.
In contrast, the transcription of Ehd2 was very low in the ehd2 mutants, and Ehd1, Hd3a, and RFT1 transcripts were almost undetectable throughout all stages of development under both SD and LD conditions. These results further suggest that Ehd2 functions upstream of Ehd1 and of the FT-like genes.
Because cv Tohoku IL9 (the wild-type of the ehd2 mutant) carried a defective allele at the Hd1 locus, the functional relationship between Ehd2 and Hd1 remained unconfirmed (Fig. 4A). Therefore, we screened Tos17-induced mutant lines (http://tos.nias.affrc.go.jp/
Under ND conditions, the wild-type plants (cv Nipponbare) flowered at 116.6 ± 2.8 d and the Tos17-induced mutants of Ehd2 (hereafter referred to as ehd2-Tos17) flowered at 144.1 ± 4.3 d without significant morphological aberration (Fig. 6B). We grew the ehd2-Tos17 mutants and the wild-type plants under SD and LD conditions also. Under SD conditions, the wild-type plants flowered at 47.5 ± 1.1 d and the ehd2-Tos17 mutants flowered at 132.7 ± 4.3 d. Under LD conditions, the wild-type plants flowered at 80.6 ± 3.4 d, but the ehd2-Tos17 mutants did not flower for more than 365 d (Fig. 6B), as was the case for the ehd2 mutants of cv Tohoku IL9 (Fig. 1A). The flowering time of the ehd2-Tos17 mutants was significantly delayed (by more than 85 d) compared with the wild-type plants under SD conditions. However, as in the case of the ehd2 mutants of cv Tohoku IL9, the ehd2-Tos17 mutants grown under SD conditions flowered dramatically earlier than those under LD conditions, suggesting that some unidentified gene other than Hd1 and Ehd1 can promote flowering under SD conditions in the ehd2 mutants (Fig. 6B).
We further examined the levels of Hd1 transcripts in the ehd2-Tos17 mutants and the wild-type plants. First, we analyzed the accumulation of Ehd2 and Ehd1 mRNAs to confirm that the late-flowering phenotype was caused by the Tos17-induced mutation of Ehd2 and the consequent reduced abundance of Ehd1 mRNA. The leaf samples were harvested 2 h after dawn from plants that had been grown for 4 weeks under SD and LD conditions and expression analysis was performed. Ehd2 and Ehd1 transcripts were abundant in the wild-type plants, but were nearly undetectable in the ehd2-Tos17 mutants (Fig. 6C). This result confirmed that the late flowering was caused by the ehd2 mutation. Next, we compared Hd1 mRNA expression between the ehd2-Tos17 mutants and the wild-type plants. The leaf samples were harvested 6 h after dusk under SD conditions or at 1.5 h after dusk under LD conditions because it has been reported that the accumulation of Hd1 mRNA increases after dusk (Izawa et al., 2002
In this article, we cloned a rice ortholog of the maize ID1 gene, Ehd2, and demonstrated that it plays a critical role in the photoperiodic control of flowering in rice. Comparison of mRNA accumulation between the ehd2 mutants and wild-type plants (cv Tohoku IL9, carrying a deficient allele of Hd1) revealed that Ehd2 function is required for the expression of Ehd1 and of downstream FT-like genes under both SD and LD conditions (Figs. 4B and 5). Furthermore, expression analysis to compare Tos17-induced mutants of Ehd2 with wild-type plants (cv Nipponbare carrying a functional allele of Hd1) revealed that Ehd2 could up-regulate Hd1 (Fig. 6C). However, Hd1 may remain functional in the ehd2-Tos17 mutant because the reduction of Hd1 mRNA accumulation in the mutants was less severe than the reduction of Ehd1 mRNA (Fig. 6C). In this situation, flowering was severely delayed in the ehd2-Tos17 mutant under SD conditions (Fig. 6B). Therefore, Hd1 may not compensate for the late flowering caused by the ehd2-Tos17 mutation. Instead, Ehd2 and Hd1 may act additively because the ehd2-Tos17 mutants with a cv Nipponbare background flowered sooner than the ehd2 mutants with a cv Tohoku IL9 background. We cannot yet confirm this because we did not compare quantitative trait loci (QTL) between the two backgrounds. Note that either Hd1 or Ehd1 alone can promote rice flowering under SD conditions (Doi et al., 2004
A diurnal change in Ehd2 mRNA accumulation was observed under both SD and LD conditions, although we did not define whether this pattern was controlled by a circadian clock or by an acute response to light signals (Fig. 4B). In addition, Ehd2 mRNA did not exhibit any photoperiodic responses because the expression of Ehd1 did not appear to be affected much by photoperiod under our study conditions. During development, the accumulation of both Ehd1 and Hd3a mRNAs was observed at 2 weeks under SD conditions, although it was low level (Fig. 5). The mRNA accumulation of these genes might follow the rise of Ehd2 mRNA level and might be related to floral transition because, under SD conditions, the floral transition of wild-type plants (cv Tohoku IL9) should occur at about 3 weeks after germination. On the other hand, the level of Ehd1 and Hd3a mRNAs clearly reached a peak after the floral transition, although we do not have any knowledge about the increase in level of Ehd1 and Hd3a mRNAs after floral transition for now. Under LD conditions, the mRNA accumulation pattern of Ehd2 and the downstream genes showed a similar trend as under SD conditions with short delay.
Ehd2 is not the only gene that functions upstream of Ehd1. Recently, it has been reported that a type I MADS box gene, OsMADS51, also up-regulates Ehd1 and subsequently activates Hd3a mRNA expression (Kim et al., 2007
In maize, two genes other than ID1 that play a role in flowering have been cloned and characterized thus far: delayed flowering1 (dlf1; Muszynski et al., 2006
The orthologous relationship between rice Ehd2 and maize ID1, which show a very high identity (82%) between their zinc finger domains, had been previously inferred by Colasanti et al. (2006)
The amount of ID1 mRNA and its protein showed no obvious diurnal changes even if the maize plants were subjected to different light and dark cycles (Wong and Colasanti, 2007 In summary, Ehd2 promotes floral transition by up-regulating Ehd1 primarily and by up-regulating the downstream Hd3a and RFT1 genes (Fig. 7), demonstrating that Ehd2 is a key factor in the genetic network that controls photoperiodic flowering in rice. Like Ehd1, there is no obvious ortholog of rice Ehd2 or maize ID1 in Arabidopsis. Moreover, some functional differences are likely to be present even between the orthologous genes of rice and maize in their floral induction pathways. Further clarifying how these differences contribute to the control flowering time in rice, maize, and Arabidopsis will improve our understanding of the diversification of photoperiodic control of flowering in higher plants at a molecular level.
Plant Materials and Growth Conditions
Two japonica rice (Oryza sativa) cv Tohoku IL9 and cv Nipponbare, were used as the wild-type controls; cv Tohoku IL9 is a near-isogenic derivative of the japonica cv Sasanishiki. The ehd2 mutant was identified in an M2 generation of
To map the ehd2 locus, the ehd2 mutant was first crossed with the indica cv Guang Lu Ai 4 to obtain sufficient DNA marker polymorphisms and the resultant F1 population was backcrossed with cv Guang Lu Ai 4. We then performed bulked segregant analysis by pooling equal amounts of DNA from 10 BC1F2 plants with a late-flowering phenotype (homozygous for the recessive allele at ehd2) or 10 BC1F2 plants with a normal flowering phenotype (heterozygous or homozygous for the dominant Ehd2 allele). A total of 93 SSR markers, which were distributed evenly across all 12 chromosomes, were selected to examine SSR marker polymorphism between the late-flowering phenotype with the ehd2 mutant and the normal flowering phenotype in cv Guang Lu Ai 4. For the high-resolution mapping, the progeny (2,047 plants) of heterozygotes of the initial mapping population were used. To test the complementation of Ehd2, we cloned a 5.0-kb genomic fragment of cv Nipponbare, which was digested by XbaI and KpnI and transformed into the pPZP2H-lac binary vector (Fuse et al., 2001
To identify the Tos17-induced mutation of Ehd2, we extracted genomic DNA using a cetyltrimethylammonium bromide method (Murray and Thompson, 1980
Total RNA was extracted from leaves by using the SDS-phenol method (Shirzadegan et al., 1991 Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers AB359195, AB359196, AB359197, and AB359198.
The following materials are available in the online version of this article.
We thank Dr. Kazuhiko Sugimoto for valuable advice regarding the experimental procedures. We also thank Dr. Hirohiko Hirochika and Dr. Akio Miyao for the DNA pools used to screen the Tos17 lines, Ms. Meenu Gupta for screening the ehd2-Tos17 line, Dr. Yoshiaki Nagamura and Ms. Ritsuko Motoyama for performing the microarray analysis, Ms. Kazuko Ono for the Agrobacterium-mediated transformation, and Ms. Kanako Takeyama for technical assistance. Received July 7, 2008; accepted September 5, 2008; published September 12, 2008.
1 This work was supported by the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated Research Project for Plant, Insect and Animal using Genome Technology [grant no. IP1001] and Genomics for Agricultural Innovation [grant no. GPN0001]). The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Masahiro Yano (myano{at}nias.affrc.go.jp).
[C] Some figures in this article are displayed in color online but in black and white in the print edition.
[W] The online version of this article contains Web-only data. www.plantphysiol.org/cgi/doi/10.1104/pp.108.125542 * Corresponding author; e-mail myano{at}nias.affrc.go.jp.
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