Gene Details:

Functional Descriptions:

  • Rice is a short-day plant, and we found that mutation in either phyB or PHYC caused moderate early flowering under the long-day photoperiod, while monogenic phyA mutation had little effect on the flowering time.
  • The phyA mutation, however, in combination with phyB or PHYC mutation caused dramatic early flowering.
  • ACO1 expression was controlled mainly by phyA and phyB, and a histochemical analysis showed that ACO1 expression was localized to the basal parts of leaf sheaths of phyAphyBPHYC seedlings, similar to mature wild-type plants at the heading stage, when internode elongation was greatly promoted.
  • Seedlings of phyB and phyB PHYC mutants exhibited a partial loss of sensitivity to continuous red light (Rc) but still showed significant deetiolation responses.
  • In addition, the transcription levels of several ethylene- or gibberellin (GA)-related genes were changed in phyAphyBPHYC mutants, and measurement of the plant hormone levels indicated low ethylene production and bioactive GA levels in the phyAphyBPHYC mutants.
  • Distinct metabolic profiles between phyA phyB PHYC triple mutants and the wild type (WT), as well as those between young and mature leaf blades, could be clearly observed by principal component analysis (PCA).
  • The metabolite profiles indicated high accumulation of amino acids, organic acids, sugars, sugar phosphates, and nucleotides in the leaf blades of phyA phyB PHYC triple mutants, especially in the young leaves, compared with those in the WT.
  • Although phyAphyBPHYC phytochrome-null mutants in rice (Oryza sativa) have morphological changes and exhibit internode elongation, even as seedlings, it is unknown how phytochromes contribute to the control of internode elongation.
  • A gene for 1-aminocyclopropane-1-carboxylate oxidase (ACO1), which is an ethylene biosynthesis gene contributing to internode elongation, was up-regulated in phyAphyBPHYC seedlings.
  • We demonstrate that ethylene induced internode elongation and ACO1 expression in phyAphyBPHYC seedlings but not in the wild type and that the presence of bioactive GAs was necessary for these effects.
  • RESULTS: A rice mutant, late heading date 3 (LHD3), was characterized, and the gene LHD3 was identified with a map-based cloning strategy.
  • Compared with wild-type plants, the LHD3 mutant exhibited delayed flowering under both LD (long-day) and SD (short-day) conditions, and delayed flowering time was positively associated with the day length via the Ehd1 pathway.
  • In addition, LHD3 showed a pale-green-leaf phenotype and a slower chlorophyll synthesis rate during the greening process.
  • The transcription patterns of many key genes involved in photoperiod-mediated flowering and chlorophyll synthesis were altered in LHD3.

Literature:

Gene Resources:

Sequences:

cDNA Sequence
  • >LOC_Os03g54084.1
    GGAGATATTATCTTGGGCTGCCTTGCCGTGCAGTGTGGCTCGCTGTCCCACTCAGGTGCGGCGCTATTCCAATCCGTGCTTATCCCCGGCAGAATCCAATCCCCCTCGCGGCTTTTCTCCAAAAGCGCTCCGCCTTCTCGCCTATTTCGCTCGCTGCCGCGGCCATGATTCCCCGCTGATACCTCCGCGCGCCCATTTGGTTCCTCCTCGCCGAATCCCCCTTCGCAGCCGGTGGTTCTAGTTGAGGAGGAGGAGGAGGGGATTTGGTTGGGGGCGAGGGGGAGGAGGGGGTTGTGGAGATGTCGTCGTCGCGGTCGAACAACCGGGCGACGTGCTCGCGGAGCAGCTCGGCGCGGTCCAAGCACAGCGCGCGGGTGGTGGCGCAGACGCCGATGGACGCGCAGCTGCACGCGGAGTTCGAGGGGTCGCAGCGCCACTTCGACTACTCGTCGTCGGTGGGCGCGGCCAATCGGTCGGGCGCCACCACCAGCAACGTCTCCGCCTACCTCCAGAACATGCAGCGCGGCCGCTTCGTCCAGCCCTTCGGGTGCCTGCTCGCCGTCCACCCGGAGACGTTCGCGCTGCTCGCCTACAGCGAGAACGCCGCCGAGATGCTCGACCTCACGCCGCACGCCGTGCCCACCATTGACCAGCGCGAGGCGCTCGCCGTCGGCACCGACGTGCGCACGCTCTTCCGCTCGCACAGCTTCGTCGCGCTGCAGAAGGCCGCCACCTTCGGGGACGTCAACCTGCTCAACCCCATCCTCGTCCACGCCAGGACCTCCGGGAAGCCCTTCTACGCCATCATGCACCGCATCGACGTCGGCCTCGTCATCGACCTCGAGCCGGTCAACCCCGTCGACCTGCCCGTCACCGCCACAGGCGCGATCAAGTCGTACAAGCTCGCTGCCAGGGCCATCGCCAGGCTGCAGTCCCTGCCCAGTGGGAACCTCTCCCTGCTGTGCGACGTGCTGGTCCGCGAGGTGAGCGAGCTCACTGGCTATGACAGGGTGATGGCGTACAAGTTCCATGAGGATGAGCATGGTGAGGTGATTGCTGAGTGCAAGAGATCTGATTTGGAGCCGTATCTTGGCCTGCACTACCCAGCCACTGACATTCCTCAGGCATCCAGGTTTTTGTTCATGAAGAACAAAGTGCGGATGATATGCGATTGCTCCGCAACGCCTGTGAAGATCATCCAAGATGACAGCCTAACACAACCTATAAGCATATGCGGATCTACTCTCAGGGCACCCCATGGTTGCCATGCACAGTACATGGCAAGCATGGGCTCCGTTGCATCACTTGTGATGTCGGTCACTATAAATGAGGATGAGGATGATGATGGAGACACTGGGAGTGACCAGCAGCCGAAAGGGAGGAAGCTGTGGGGGTTGATGGTCTGCCATCACACAAGCCCGAGGTTTGTCCCTTTCCCGCTTAGGTATGCTTGCGAGTTTCTCTTGCAAGTATTTGGGATACAGATCAACAAGGAGGTGGAACTGGCTGCTCAGGCAAAGGAGAGGCACATCCTCCGCACGCAGACTCTTCTCTGTGATATGCTCCTTCGAGATGCTCCTGTTGGGATATTTACCCAATCACCTAACGTAATGGATCTAGTGAAATGTGATGGTGCAGCATTGTATTACCAAAACCAGCTTTGGGTGCTAGGATCAACGCCCTCTGAAGCAGAGATAAAAAACATTGTTGCTTGGTTGCAGGAGTACCATGACGGTTCTACTGGATTGAGTACCGACAGCTTAGTTGAAGCAGGTTATCCTGGCGCTGCTGCACTTGGTGATGTTGTGTGTGGCATGGCAGCTATAAAGATCTCTTCAAAAGATTTCATCTTCTGGTTCCGATCCCACACGGCAAAGGAGATTAAATGGGGAGGAGCTAAGCATGAACCAATTGATGCAGATGACAATGGTAGGAAGATGCATCCACGATCTTCATTCAAAGCCTTCTTGGAGGTAGTTAAATGGAGGAGTGTTCCTTGGGAGGATGTTGAAATGGATGCTATCCATTCTCTGCAGCTAATATTACGTGGCTCCTTGCAAGATGAAGATGCCAACAAGAACAACAATGCAAAGTCCATTGTTACAGCTCCATCTGATGATATGAAGAAGATTCAGGGGCTCCTTGAACTGAGAACCGTTACAAACGAGATGGTGCGCCTAATTGAGACAGCAACTGCGCCTATCTTGGCTGTTGACATCACTGGGAGCATAAACGGATGGAATAATAAGGCTGCAGAACTCACTGGATTACCTGTCATGGAAGCCATAGGGAAGCCTCTGGTCGATCTCGTCATCGATGATTCTGTTGAAGTGGTTAAGCAAATTTTAAATTCAGCTTTACAAGGAATAGAAGAGCAAAATCTGCAAATTAAGCTTAAAACATTTAATCACCAGGAAAATAATGGACCTGTAATTTTGATGGTTAACGCCTGCTGCAGTCGTGACCTTTCAGAGAAAGTTGTGGGGGTTTGCTTTGTAGCACAAGATATGACAGGGCAGAACATTATCATGGATAAGTACACTCGGATACAAGGGGACTATGTTGCTATAGTAAAGAACCCTTCGGAGCTCATCCCCCCTATATTTATGATCAATGATCTTGGTTCCTGCTTAGAGTGGAATGAAGCTATGCAAAAAATTACTGGTATAAAGAGGGAAGATGCAGTAGATAAATTGCTAATCGGGGAAGTTTTCACCCACCATGAGTATGGCTGTAGGGTGAAAGACCATGGTACTCTGACCAAACTTAGCATATTAATGAACACAGTGATATCTGGTCAAGATCCTGAGAAGCTTCTTTTTGGTTTCTTCAACACCGATGGCAAGTACATAGAGTCACTGATGACAGCAACCAAGAGGACAGATGCTGAGGGTAAGATCACTGGCGCCCTTTGCTTTCTTCATGTGGCCAGCCCAGAGCTTCAACATGCTCTGCAGGTGCAGAAGATGTCTGAACAAGCTGCTATGAACAGCTTTAAGGAACTGACATACATACGTCAAGAATTAAGGAACCCACTCAATGGCATGCAATTTACTCGAAATTTGTTGGAACCTTCTGACTTGACTGAGGAGCAGAGGAAACTTCTAGCATCAAATGTCCTCTGTCAAGAACAGCTGAAAAAGATTTTACATGACACTGATCTAGAAAGCATTGAACAGTGCTACACGGAGATGAGCACCGTAGATTTCAACCTGGAGGAAGCCCTGAATACAGTCCTAATGCAAGCCATGCCCCAGAGCAAGGAGAAACAAATTTCCATTGACCGTGATTGGCCTGCAGAAGTATCATGTATGCACCTCTGCGGGGACAATTTAAGGCTTCAACAAGTCCTAGCAGACTTCCTGGCATGCATGCTTCAATTTACACAGCCAGCTGAAGGGCCTATTGTGCTCCAAGTCATCCCCAGGATGGAAAATATTGGATCTGGAATGCAGATTGCTCATCTAGAGTTCAGGCTTGTCCATCCAGCTCCGGGCGTTCCAGAGGCTCTGATACAAGAGATGTTCCGCCACAGCCCAGGTGCATCTCGAGAGGGCCTTGGCCTTTACATAAGCCAGAAGCTCGTGAAGACGATGAGCGGCACGGTTCAGTACCTCCGGGAATCAGAGAGCTCGTCGTTCATCGTCCTGGTAGAGTTCCCGGTCGCCCAGCTCAGCACCAAGAGGTGCAAGGCTTCCACGAGTAAATTCTGAACTTAGGGCTATGGCCAAAATTCTTGTGGGTGCTGTATTGTTGTTGTTGCTGCTGCTGCTATTAGCAGATCAGGCAGTCTGAGGAGTACGTTAGCTGAAGATGTATCAGATGTGTGTAGCTTGTGAAAGTGAAGGTAGTGGTTGGATAGATGTATTTGTCACGTTGATGTCTGGAGAGCTAGTGAGCGAGCTACTAGGTGTTAGTGTAATTTAACCGGCAAATGTATGAACGAATTATGAATAAAATCTTCACTTGTGTTGTCATGAATAAAATCTTCACTTGTGCTGTCA
CDS Sequence
  • >LOC_Os03g54084.1
    ATGTCGTCGTCGCGGTCGAACAACCGGGCGACGTGCTCGCGGAGCAGCTCGGCGCGGTCCAAGCACAGCGCGCGGGTGGTGGCGCAGACGCCGATGGACGCGCAGCTGCACGCGGAGTTCGAGGGGTCGCAGCGCCACTTCGACTACTCGTCGTCGGTGGGCGCGGCCAATCGGTCGGGCGCCACCACCAGCAACGTCTCCGCCTACCTCCAGAACATGCAGCGCGGCCGCTTCGTCCAGCCCTTCGGGTGCCTGCTCGCCGTCCACCCGGAGACGTTCGCGCTGCTCGCCTACAGCGAGAACGCCGCCGAGATGCTCGACCTCACGCCGCACGCCGTGCCCACCATTGACCAGCGCGAGGCGCTCGCCGTCGGCACCGACGTGCGCACGCTCTTCCGCTCGCACAGCTTCGTCGCGCTGCAGAAGGCCGCCACCTTCGGGGACGTCAACCTGCTCAACCCCATCCTCGTCCACGCCAGGACCTCCGGGAAGCCCTTCTACGCCATCATGCACCGCATCGACGTCGGCCTCGTCATCGACCTCGAGCCGGTCAACCCCGTCGACCTGCCCGTCACCGCCACAGGCGCGATCAAGTCGTACAAGCTCGCTGCCAGGGCCATCGCCAGGCTGCAGTCCCTGCCCAGTGGGAACCTCTCCCTGCTGTGCGACGTGCTGGTCCGCGAGGTGAGCGAGCTCACTGGCTATGACAGGGTGATGGCGTACAAGTTCCATGAGGATGAGCATGGTGAGGTGATTGCTGAGTGCAAGAGATCTGATTTGGAGCCGTATCTTGGCCTGCACTACCCAGCCACTGACATTCCTCAGGCATCCAGGTTTTTGTTCATGAAGAACAAAGTGCGGATGATATGCGATTGCTCCGCAACGCCTGTGAAGATCATCCAAGATGACAGCCTAACACAACCTATAAGCATATGCGGATCTACTCTCAGGGCACCCCATGGTTGCCATGCACAGTACATGGCAAGCATGGGCTCCGTTGCATCACTTGTGATGTCGGTCACTATAAATGAGGATGAGGATGATGATGGAGACACTGGGAGTGACCAGCAGCCGAAAGGGAGGAAGCTGTGGGGGTTGATGGTCTGCCATCACACAAGCCCGAGGTTTGTCCCTTTCCCGCTTAGGTATGCTTGCGAGTTTCTCTTGCAAGTATTTGGGATACAGATCAACAAGGAGGTGGAACTGGCTGCTCAGGCAAAGGAGAGGCACATCCTCCGCACGCAGACTCTTCTCTGTGATATGCTCCTTCGAGATGCTCCTGTTGGGATATTTACCCAATCACCTAACGTAATGGATCTAGTGAAATGTGATGGTGCAGCATTGTATTACCAAAACCAGCTTTGGGTGCTAGGATCAACGCCCTCTGAAGCAGAGATAAAAAACATTGTTGCTTGGTTGCAGGAGTACCATGACGGTTCTACTGGATTGAGTACCGACAGCTTAGTTGAAGCAGGTTATCCTGGCGCTGCTGCACTTGGTGATGTTGTGTGTGGCATGGCAGCTATAAAGATCTCTTCAAAAGATTTCATCTTCTGGTTCCGATCCCACACGGCAAAGGAGATTAAATGGGGAGGAGCTAAGCATGAACCAATTGATGCAGATGACAATGGTAGGAAGATGCATCCACGATCTTCATTCAAAGCCTTCTTGGAGGTAGTTAAATGGAGGAGTGTTCCTTGGGAGGATGTTGAAATGGATGCTATCCATTCTCTGCAGCTAATATTACGTGGCTCCTTGCAAGATGAAGATGCCAACAAGAACAACAATGCAAAGTCCATTGTTACAGCTCCATCTGATGATATGAAGAAGATTCAGGGGCTCCTTGAACTGAGAACCGTTACAAACGAGATGGTGCGCCTAATTGAGACAGCAACTGCGCCTATCTTGGCTGTTGACATCACTGGGAGCATAAACGGATGGAATAATAAGGCTGCAGAACTCACTGGATTACCTGTCATGGAAGCCATAGGGAAGCCTCTGGTCGATCTCGTCATCGATGATTCTGTTGAAGTGGTTAAGCAAATTTTAAATTCAGCTTTACAAGGAATAGAAGAGCAAAATCTGCAAATTAAGCTTAAAACATTTAATCACCAGGAAAATAATGGACCTGTAATTTTGATGGTTAACGCCTGCTGCAGTCGTGACCTTTCAGAGAAAGTTGTGGGGGTTTGCTTTGTAGCACAAGATATGACAGGGCAGAACATTATCATGGATAAGTACACTCGGATACAAGGGGACTATGTTGCTATAGTAAAGAACCCTTCGGAGCTCATCCCCCCTATATTTATGATCAATGATCTTGGTTCCTGCTTAGAGTGGAATGAAGCTATGCAAAAAATTACTGGTATAAAGAGGGAAGATGCAGTAGATAAATTGCTAATCGGGGAAGTTTTCACCCACCATGAGTATGGCTGTAGGGTGAAAGACCATGGTACTCTGACCAAACTTAGCATATTAATGAACACAGTGATATCTGGTCAAGATCCTGAGAAGCTTCTTTTTGGTTTCTTCAACACCGATGGCAAGTACATAGAGTCACTGATGACAGCAACCAAGAGGACAGATGCTGAGGGTAAGATCACTGGCGCCCTTTGCTTTCTTCATGTGGCCAGCCCAGAGCTTCAACATGCTCTGCAGGTGCAGAAGATGTCTGAACAAGCTGCTATGAACAGCTTTAAGGAACTGACATACATACGTCAAGAATTAAGGAACCCACTCAATGGCATGCAATTTACTCGAAATTTGTTGGAACCTTCTGACTTGACTGAGGAGCAGAGGAAACTTCTAGCATCAAATGTCCTCTGTCAAGAACAGCTGAAAAAGATTTTACATGACACTGATCTAGAAAGCATTGAACAGTGCTACACGGAGATGAGCACCGTAGATTTCAACCTGGAGGAAGCCCTGAATACAGTCCTAATGCAAGCCATGCCCCAGAGCAAGGAGAAACAAATTTCCATTGACCGTGATTGGCCTGCAGAAGTATCATGTATGCACCTCTGCGGGGACAATTTAAGGCTTCAACAAGTCCTAGCAGACTTCCTGGCATGCATGCTTCAATTTACACAGCCAGCTGAAGGGCCTATTGTGCTCCAAGTCATCCCCAGGATGGAAAATATTGGATCTGGAATGCAGATTGCTCATCTAGAGTTCAGGCTTGTCCATCCAGCTCCGGGCGTTCCAGAGGCTCTGATACAAGAGATGTTCCGCCACAGCCCAGGTGCATCTCGAGAGGGCCTTGGCCTTTACATAAGCCAGAAGCTCGTGAAGACGATGAGCGGCACGGTTCAGTACCTCCGGGAATCAGAGAGCTCGTCGTTCATCGTCCTGGTAGAGTTCCCGGTCGCCCAGCTCAGCACCAAGAGGTGCAAGGCTTCCACGAGTAAATTCTGA
Protein Sequence
  • >LOC_Os03g54084.1
    MSSSRSNNRATCSRSSSARSKHSARVVAQTPMDAQLHAEFEGSQRHFDYSSSVGAANRSGATTSNVSAYLQNMQRGRFVQPFGCLLAVHPETFALLAYSENAAEMLDLTPHAVPTIDQREALAVGTDVRTLFRSHSFVALQKAATFGDVNLLNPILVHARTSGKPFYAIMHRIDVGLVIDLEPVNPVDLPVTATGAIKSYKLAARAIARLQSLPSGNLSLLCDVLVREVSELTGYDRVMAYKFHEDEHGEVIAECKRSDLEPYLGLHYPATDIPQASRFLFMKNKVRMICDCSATPVKIIQDDSLTQPISICGSTLRAPHGCHAQYMASMGSVASLVMSVTINEDEDDDGDTGSDQQPKGRKLWGLMVCHHTSPRFVPFPLRYACEFLLQVFGIQINKEVELAAQAKERHILRTQTLLCDMLLRDAPVGIFTQSPNVMDLVKCDGAALYYQNQLWVLGSTPSEAEIKNIVAWLQEYHDGSTGLSTDSLVEAGYPGAAALGDVVCGMAAIKISSKDFIFWFRSHTAKEIKWGGAKHEPIDADDNGRKMHPRSSFKAFLEVVKWRSVPWEDVEMDAIHSLQLILRGSLQDEDANKNNNAKSIVTAPSDDMKKIQGLLELRTVTNEMVRLIETATAPILAVDITGSINGWNNKAAELTGLPVMEAIGKPLVDLVIDDSVEVVKQILNSALQGIEEQNLQIKLKTFNHQENNGPVILMVNACCSRDLSEKVVGVCFVAQDMTGQNIIMDKYTRIQGDYVAIVKNPSELIPPIFMINDLGSCLEWNEAMQKITGIKREDAVDKLLIGEVFTHHEYGCRVKDHGTLTKLSILMNTVISGQDPEKLLFGFFNTDGKYIESLMTATKRTDAEGKITGALCFLHVASPELQHALQVQKMSEQAAMNSFKELTYIRQELRNPLNGMQFTRNLLEPSDLTEEQRKLLASNVLCQEQLKKILHDTDLESIEQCYTEMSTVDFNLEEALNTVLMQAMPQSKEKQISIDRDWPAEVSCMHLCGDNLRLQQVLADFLACMLQFTQPAEGPIVLQVIPRMENIGSGMQIAHLEFRLVHPAPGVPEALIQEMFRHSPGASREGLGLYISQKLVKTMSGTVQYLRESESSSFIVLVEFPVAQLSTKRCKASTSKF*