Gene Details:

Functional Descriptions:

  • Spin1 overexpression causes late flowering independently of daylength; expression analyses of flowering marker genes in these lines suggested that SPIN1 represses flowering by downregulating the flowering promoter gene Heading date3a (Hd3a) via Hd1-dependent mechanisms in short days and by targeting Hd1-independent factors in long days.
  • The CONSTANS (CO) and Heading date 1 (Hd1) genes are known to be central integrators of the photoperiod pathway in Arabidopsis and rice, respectively.
  • The expression of Hd3a and FTL decreased in these transgenic plants, whereas the expression of Hd1, Early heading date 1 (EHd1), OsMADS51, and OsMADS50 did not significantly change.
  • RT-PCR analyses of the OsMADS50 KO and ubiquitin (ubi):OsMADS50 plants showed that OsMADS50 is an upstream regulator of OsMADS1, OsMADS14, OsMADS15, OsMADS18, and Hd (Heading date)3a, but works either parallel with or downstream of Hd1 and O.
  • Therefore, two key flowering time genes, Hd1 and EHd1, can control panicle development in rice; this may affect crop yields in the field through florigen expression in leaf.
  • Meanwhile, the transcription of DTH8 has been proved to be independent of Ghd7 and Hd1, and the natural mutation of this gene caused weak photoperiod sensitivity and shorter plant height.
  • In addition, QTLs near Hd2, Hd16, and Ghd7, which are involved in inhibition of heading under long-day conditions, function in the same pathway that controls heading date.
  • The results revealed that the combination of Heading-date 1 (Hd1) and Early heading date 1 (EHd1) can reduce the number of primary branches in a panicle, resulting in smaller spikelet numbers per panicle; this occurs independently of the control of flowering time.
  • Flowering genes downstream of OsPRR1 such as OsGI and Hd1 were down regulated in the A654 mutant.
  • Together, these results suggest that overexpression of OsLF might repress expression of OsGI and Hd1 by competing with OsPRR1 in interacting with OsPIL13 and OsPIL15 and thus induce late flowering.
  • A single NB strongly suppressed the mRNA of Hd3a, a homolog of Arabidopsis thaliana FLOWERING LOCUS T (FT), whereas the mRNAs of OsGI and Hd1 were not affected.
  • Since the photoperiod-insensitive allele of Hd1 confers a long vegetative phase, it is a good candidate for breeding rice varieties with high yielding potential for low latitudes.
  • The RNA levels of Heading date 3a (Hd3a), encoding a floral activator, are highly correlated with flowering time, and there is a high degree of polymorphism in the Heading date 1 (Hd1) protein, which is a major regulator of Hd3a expression.
  • Functional and nonfunctional alleles of Hd1 are associated with early and late flowering, respectively, suggesting that Hd1 is a major determinant of variation in flowering time of cultivated rice.
  • We also found that the type of Hd3a promoter and the level of EHd1 expression contribute to the diversity in flowering time and Hd3a expression level.
  • Variations in Hd1 proteins, Hd3a promoters, and EHd1 expression levels contribute to diversity of flowering time in cultivated rice.
  • Map-based cloning revealed that the rice flowering-time quantitative trait locus (QTL) Heading date 16 (Hd16) encodes a casein kinase-I protein.
  • Heading date 1 (Hd1), a regulator of the florigen gene Hd3a, is one of the main factors used to generate diversity in flowering.
  • Loss-of-function alleles of Hd1 are common in cultivated rice and cause the diversity of flowering time.
  • In contrast with Hd3a, which has been highly conserved, Hd1 may have undergone human selection to diversify the flowering times of rice during domestication or the early stage of the cultivation period.
  • Heading date 1 (Hd1), an ortholog of Arabidopsis CONSTANS, is a possible target of human selection during domestication to diversify flowering times of cultivated rice.
  • We further revealed that Hd1 and/or EHd1 caused up-regulation of Terminal Flower 1-like genes and precocious expression of panicle formation-related genes at shoot apical meristems during panicle development.
  • The comparison of the nucleotide sequences suggested that Ef1 is the same as Early heading date 1 (EHd1).
  • The quantitative real-time PCR assay revealed that DTH8 could down-regulate the transcriptions of EHd1 (for Early heading date1) and Hd3a (for Heading date3a; a rice ortholog of FLOWERING LOCUS T) under long-day conditions.
  • The Early heading date 1 (EHd1) which promotes the RFT1, was up-regulated by DTH3 in both LD and SD conditions.
  • Heading date gene, dth3 controlled late flowering in O. Glaberrima Steud. by down-regulating EHd1.
  • By using near-isogenic lines with functional or deficient alleles of several rice flowering-time genes, we observed significant digenetic interactions between Hd16 and four other flowering-time genes (Ghd7, Hd1, DTH8 and Hd2).
  • These results demonstrate that Hd16 acts as an inhibitor in the rice flowering pathway by enhancing the photoperiod response as a result of the phosphorylation of Ghd7.
  • Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response.
  • Characterization and detection of epistatic interactions of 3 QTLs, Hd1 , Hd2 , and Hd3, controlling heading date in rice using nearly isogenic lines.
  • We grew four rice lines having different flowering time genotypes (Hd1 eHd1, Hd1 EHd1, Hd1 eHd1 and Hd1 EHd1) under distinct photoperiod conditions.
  • In addition, expression of the Hd3a and Rice Flowering-locus T 1 (RFT1) florigen genes was up-regulated in leaves of the Hd1 EHd1 line at the time of the floral transition.
  • They were used to analyze the effects of Hd1 on heading date, plant height and yield traits.
  • Pleiotropism of the photoperiod-insensitive allele of Hd1 on heading date, plant height and yield traits in rice.
  • We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (EHd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice.
  • In rice, OsGI, Hd1 and Hd3a were identified as orthologs of GI, CO and FT, respectively, and are also important regulators of flowering.
  • Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS.
  • Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.
  • Under SD conditions, flowering is promoted through the activation of FT-like genes (rice florigens) by Heading date 1 (Hd1, a rice CONSTANS homolog) and Early heading date 1 (EHd1, with no ortholog in the Arabidopsis genome).
  • On the other hand, under long-day (LD) conditions, flowering is delayed by the repressive function of Hd1 on FT-like genes and by downregulation of EHd1 by the flowering repressor Ghd7 - a unique pathway in rice.
  • We report here that an early heading date 3 (ehd3) mutant flowered later than wild-type plants, particularly under LD conditions, regardless of the Hd1-deficient background.
  • Furthermore, Ehd3 ghd7 plants flowered earlier and show higher EHd1 transcript levels than ehd3 ghd7 plants, suggesting a Ghd7-independent role of Ehd3 in the upregulation of EHd1.
  • In rice, a short-day plant (SDP), the CO ortholog Heading date 1 (Hd1) regulates FT ortholog Hd3a, but regulation of Hd3a by Hd1 differs from that in Arabidopsis.
  • Phytochrome B regulates Heading date 1 (Hd1)-mediated expression of rice florigen Hd3a and critical day length in rice.
  • The non-functional Hd1 alleles found in cultivated rice may be selected during domestication, because they were not found or very rare in wild ancestral rice.
  • 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.
  • The present study was carried out in rice to examine to what extent these three developmental components are modified by the three flowering time genes, Se1 (= Hd1), Ef1 and e1 (= m-Ef1), which are known to contribute to flowering time in temperate and tropical regions of rice cultivation.
  • The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime.
  • In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions.
  • Since the two genes Se1 (= Hd1) and Ef1 (= EHd1) are known to up-regulate the rice homolog of Arabidopsis FT, it is suggested that the detected epistasis may respond to diverse environments by modulating the CO/FT system conserved in flowering plants.
  • We propose that both positive (OsMADS50 and EHd1) and negative (Hd1, phyB and Ghd7) regulators of RFT1 form a gene network that regulates LD flowering in rice.
  • Among these regulators, EHd1, a rice-specific floral inducer, integrates multiple pathways to regulate RFT1, leading to flowering under appropriate photoperiod conditions.
  • 3-kb region covering heading date gene Hd1 were developed from the indica rice cross Zhenshan97 (ZS97)/Milyang 46 (MY46).
  • EHd1 and Hd3a can also be down-regulated by the photoperiodic flowering genes Ghd7 and Hd1 (a rice ortholog of CONSTANS).
  • 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.
  • Ehd2, a rice ortholog of the maize INDETERMINATE1 gene, promotes flowering by up-regulating EHd1.
  • First, overexpression of Hd1 causes a delay in flowering under SD conditions and this effect requires phyB, suggesting that light modulates Hd1 control of Hd3a transcription.
  • We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a).
  • All 12 temperate japonica breeding lines adapted to the tropics possessed the loss-of-function alleles of Hd1 with no change of other flowering genes compared to common Korean temperate japonica varieties.
  • The lines carrying Hd1 alone show reduced plant height with fewer primary and secondary branches in panicles.

Literature:

Gene Resources:

Sequences:

cDNA Sequence
  • >LOC_Os06g16370.1
    CTTCCAAAAAACACTCACAAAATTCCACAAGAGCCATGCGAGGTAGAGGAACAGGAGAAGACGCATACACACACGACACATAGAGAGAGAGGACAAACACAATAGCTTGGATCGATAGACTTGTCCATGTGGTGCAAGCTAAAGCTACTACTACCACAAGCAAGGCTACTTCGTTCATGAATTATAATTTTGGTGGCAACGTGTTCGACCAGGAGGTTGGAGTTGGAGGCGAAGGAGGAGGAGGAGGAGAGGGGAGCGGCTGCCCATGGGCGCGGCCGTGCGACGGGTGCCGCGCGGCGCCGAGCGTGGTGTACTGCCGCGCGGACGCGGCGTACCTGTGCGCGTCGTGCGACGCGCGGGTGCACGCGGCCAACCGCGTGGCGTCCCGCCACGAGCGCGTGCGGGTGTGCGAGGCCTGCGAGCGCGCCCCGGCCGCGCTCGCGTGCCGCGCCGACGCCGCCGCGCTGTGCGTGGCGTGCGACGTGCAGGTGCACTCCGCGAACCCGCTCCCGGCCATCACCATCCCGGCCACCTCCGTCCTCGCTGAGGCGGTGGTGGCCACCGCCACCGTCCTCGGCGACAAGGACGAGGAGGTGGACTCTTGGCTTCTCCTCTCCAAAGATTCCGACAACAACAACAACAATAACAACAACAACGACAACGACAATAACGACAACAACAACAGCAACAGCAGCAACAACGGCATGTATTTTGGTGAAGTCGATGAGTACTTTGATCTTGTCGGGTACAATTCGTACTACGACAACCGCATCGAAAACAACCAAGATCGGCAGTATGGGATGCATGAACAGCAAGAGCAGCAGCAGCAGCAGCAGGAGATGCAAAAGGAGTTTGCAGAGAAGGAAGGGAGCGAGTGTGTGGTACCTTCACAGATCACAATGCTGAGTGAGCAGCAGCATAGTGGTTATGGAGTTGTGGGAGCAGACCAGGCCGCCTCCATGACCGCCGGCGTCAGTGCTTACACAGATTCCATCAGCAACAGCATATCTTTCTCATCAATGGAGGCGGGTATAGTACCAGACAGCACGGTGATAGATATGCCAAATTCCAGAATCCTGACACCTGCTGGAGCAATCAATCTCTTCTCAGGTCCCTCGCTTCAGATGTCCCTTCACTTCAGCTCCATGGACAGGGAGGCCAGGGTGCTCAGGTACAGGGAGAAGAAGAAGGCCAGGAAGTTTGAGAAGACAATACGTTATGAAACAAGAAAGGCGTATGCAGAGGCACGACCCCGGATCAAGGGCCGTTTCGCCAAGAGATCAGATGTGCAGATCGAAGTGGACCAGATGTTCTCCACTGCAGCTCTATCTGACGGTAGCTATGGTACTGTTCCATGGTTCTGATGGGACTCATGAGACGCTATCTTATAGGCATATATATGGGGACTTACTGAGTAGCAATAACATCGATCCAGTGGGAGTAGTTCTAGACAATCTGTGTTATGAATAATAGTGTGTTGTTTGCGACTTAAAATTGATCAAGTACCTTAGCTTTTTAAAGTTTTGCTTTGTAATTTCCGGATAGCAGATATATATTGTTGGTACTTGCTCAGTAGCTTTAAGTTTTTGAAGTAAGCAAAGAGCAGTGATGAGATGAAATGAGTATGTGTATAACTGTATATAGATAA
CDS Sequence
  • >LOC_Os06g16370.1
    ATGAATTATAATTTTGGTGGCAACGTGTTCGACCAGGAGGTTGGAGTTGGAGGCGAAGGAGGAGGAGGAGGAGAGGGGAGCGGCTGCCCATGGGCGCGGCCGTGCGACGGGTGCCGCGCGGCGCCGAGCGTGGTGTACTGCCGCGCGGACGCGGCGTACCTGTGCGCGTCGTGCGACGCGCGGGTGCACGCGGCCAACCGCGTGGCGTCCCGCCACGAGCGCGTGCGGGTGTGCGAGGCCTGCGAGCGCGCCCCGGCCGCGCTCGCGTGCCGCGCCGACGCCGCCGCGCTGTGCGTGGCGTGCGACGTGCAGGTGCACTCCGCGAACCCGCTCCCGGCCATCACCATCCCGGCCACCTCCGTCCTCGCTGAGGCGGTGGTGGCCACCGCCACCGTCCTCGGCGACAAGGACGAGGAGGTGGACTCTTGGCTTCTCCTCTCCAAAGATTCCGACAACAACAACAACAATAACAACAACAACGACAACGACAATAACGACAACAACAACAGCAACAGCAGCAACAACGGCATGTATTTTGGTGAAGTCGATGAGTACTTTGATCTTGTCGGGTACAATTCGTACTACGACAACCGCATCGAAAACAACCAAGATCGGCAGTATGGGATGCATGAACAGCAAGAGCAGCAGCAGCAGCAGCAGGAGATGCAAAAGGAGTTTGCAGAGAAGGAAGGGAGCGAGTGTGTGGTACCTTCACAGATCACAATGCTGAGTGAGCAGCAGCATAGTGGTTATGGAGTTGTGGGAGCAGACCAGGCCGCCTCCATGACCGCCGGCGTCAGTGCTTACACAGATTCCATCAGCAACAGCATATCTTTCTCATCAATGGAGGCGGGTATAGTACCAGACAGCACGGTGATAGATATGCCAAATTCCAGAATCCTGACACCTGCTGGAGCAATCAATCTCTTCTCAGGTCCCTCGCTTCAGATGTCCCTTCACTTCAGCTCCATGGACAGGGAGGCCAGGGTGCTCAGGTACAGGGAGAAGAAGAAGGCCAGGAAGTTTGAGAAGACAATACGTTATGAAACAAGAAAGGCGTATGCAGAGGCACGACCCCGGATCAAGGGCCGTTTCGCCAAGAGATCAGATGTGCAGATCGAAGTGGACCAGATGTTCTCCACTGCAGCTCTATCTGACGGTAGCTATGGTACTGTTCCATGGTTCTGA
Protein Sequence
  • >LOC_Os06g16370.1
    MNYNFGGNVFDQEVGVGGEGGGGGEGSGCPWARPCDGCRAAPSVVYCRADAAYLCASCDARVHAANRVASRHERVRVCEACERAPAALACRADAAALCVACDVQVHSANPLPAITIPATSVLAEAVVATATVLGDKDEEVDSWLLLSKDSDNNNNNNNNNDNDNNDNNNSNSSNNGMYFGEVDEYFDLVGYNSYYDNRIENNQDRQYGMHEQQEQQQQQQEMQKEFAEKEGSECVVPSQITMLSEQQHSGYGVVGADQAASMTAGVSAYTDSISNSISFSSMEAGIVPDSTVIDMPNSRILTPAGAINLFSGPSLQMSLHFSSMDREARVLRYREKKKARKFEKTIRYETRKAYAEARPRIKGRFAKRSDVQIEVDQMFSTAALSDGSYGTVPWF*