Difference between revisions of "Os06g0142600"
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===Function=== | ===Function=== | ||
Heading date 17 (Hd17) is a gene that encodes a homolog of Arabidopsis EARLY FLOWERING 3 (ELF3),which plays important roles in maintaining circadian rhythms, and that the QTL lies within the pathway responsible for rice’s | Heading date 17 (Hd17) is a gene that encodes a homolog of Arabidopsis EARLY FLOWERING 3 (ELF3),which plays important roles in maintaining circadian rhythms, and that the QTL lies within the pathway responsible for rice’s | ||
| − | photoperiodic flowering through the modulation of the transcription level of a flowering repressor, Grain number, plant height and heading date7(Ghd7). Natural variation in Hd17 may change the transcription level of a flowering repressor, Grain number, plant height and heading date 7 (Ghd7), suggesting that Hd17 is part of rice’s photoperiodic flowering pathway | + | photoperiodic flowering through the modulation of the transcription level of a flowering repressor, Grain number, plant height and heading date7(Ghd7). Natural variation in Hd17 may change the transcription level of a flowering repressor, Grain number, plant height and heading date 7 (Ghd7), suggesting that Hd17 is part of rice’s photoperiodic flowering pathway<ref name="ref1" />.The QTL mapped on chromosome 6 was designated as Hd17. Both Hd16and Hd17 are involved in photoperiod response, as revealed by observation of heading date in near-isogenic lines (NILs) under SD and LD conditions<ref name="ref3" />. |
===Expression=== | ===Expression=== | ||
Os06g1042600 is the Hd17 gene, and that the SNP in Os06g0142600 caused the flowering time difference between | Os06g1042600 is the Hd17 gene, and that the SNP in Os06g0142600 caused the flowering time difference between | ||
| − | ‘Nipponbare’ and NIL-Hd17. Nevertheless, the nucleotide change in Hd17 does not appear to affect its transcription level.The nucleotide change in Hd17 did not seem to affect Hd1 expression; however, its effect on flowering time disappeared in a background with a defective Hd1 allele[1].Hd17 promotes flowering under long and short day conditions by negatively regulating the flowering repressor Ghd7, and consequently upregulating levels of Ehd1 and FT-like gene expression | + | ‘Nipponbare’ and NIL-Hd17. Nevertheless, the nucleotide change in Hd17 does not appear to affect its transcription level.The nucleotide change in Hd17 did not seem to affect Hd1 expression; however, its effect on flowering time disappeared in a background with a defective Hd1 allele[1].Hd17 promotes flowering under long and short day conditions by negatively regulating the flowering repressor Ghd7, and consequently upregulating levels of Ehd1 and FT-like gene expression<ref name="ref2" />. |
===Evolution=== | ===Evolution=== | ||
| − | Genes which have been isolated as key regulators of the photoperiodic regulation of flowering are well conserved between rice and Arabidopsis | + | Genes which have been isolated as key regulators of the photoperiodic regulation of flowering are well conserved between rice and Arabidopsis<ref name="ref4" />.Natural variation in heading date and photoperiod sensitivity has played pivotal roles in a wide range of regional adaptations in many crop plants<ref name="ref5" />. |
==Labs working on this gene== | ==Labs working on this gene== | ||
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==References== | ==References== | ||
| − | + | <references> | |
| − | + | <ref name="ref1"> | |
| − | + | Costa, L. M. From Biological Warfare to the Brighter Side of Rice Research. Plant Cell Physiol 53, no. 4 (2012): 603-5.</ref> | |
| − | + | <ref name="ref2"> | |
| − | + | Matsubara, K., E. Ogiso-Tanaka, K. Hori, K. Ebana, T. Ando and M. Yano. Natural Variation in Hd17, a Homolog of Arabidopsis Elf3 That Is Involved in Rice Photoperiodic Flowering. Plant and Cell Physiology 53, no. 4 (2012): 709-716.</ref> | |
| − | + | <ref name="ref3"> | |
| − | + | Kazuki M, Kiyosumi H, Eri O T, Masahiro Y. Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice. (2014).</ref> | |
| − | + | <ref name="ref4"> | |
| − | + | Guo, Liang, Zhen-hua Zhang and Jie-yun Zhuang. "Quantitative Trait Loci for Heading Date and Their Relationship with Genetic Control of Yield Traits in Rice (Oryza Sativa)." Rice Science 20, no. 1 (2013): 1-12.</ref> | |
| − | + | <ref name="ref5"> | |
| + | Kwon, C. T., S. C. Yoo, B. H. Koo, S. H. Cho, J. W. Park, Z. Zhang, J. Li, Z. Li and N. C. Paek. "Natural Variation in Early Flowering1 Contributes to Early Flowering in Japonica Rice under Long Days." Plant Cell Environ 37, no. 1 (2014): 101-12.</ref> | ||
| + | </references> | ||
==Structured Information== | ==Structured Information== | ||
{{JaponicaGene| | {{JaponicaGene| | ||
Revision as of 15:00, 31 May 2014
Please input one-sentence summary here.
Contents
Annotated Information
Function
Heading date 17 (Hd17) is a gene that encodes a homolog of Arabidopsis EARLY FLOWERING 3 (ELF3),which plays important roles in maintaining circadian rhythms, and that the QTL lies within the pathway responsible for rice’s photoperiodic flowering through the modulation of the transcription level of a flowering repressor, Grain number, plant height and heading date7(Ghd7). Natural variation in Hd17 may change the transcription level of a flowering repressor, Grain number, plant height and heading date 7 (Ghd7), suggesting that Hd17 is part of rice’s photoperiodic flowering pathway[1].The QTL mapped on chromosome 6 was designated as Hd17. Both Hd16and Hd17 are involved in photoperiod response, as revealed by observation of heading date in near-isogenic lines (NILs) under SD and LD conditions[2].
Expression
Os06g1042600 is the Hd17 gene, and that the SNP in Os06g0142600 caused the flowering time difference between ‘Nipponbare’ and NIL-Hd17. Nevertheless, the nucleotide change in Hd17 does not appear to affect its transcription level.The nucleotide change in Hd17 did not seem to affect Hd1 expression; however, its effect on flowering time disappeared in a background with a defective Hd1 allele[1].Hd17 promotes flowering under long and short day conditions by negatively regulating the flowering repressor Ghd7, and consequently upregulating levels of Ehd1 and FT-like gene expression[3].
Evolution
Genes which have been isolated as key regulators of the photoperiodic regulation of flowering are well conserved between rice and Arabidopsis[4].Natural variation in heading date and photoperiod sensitivity has played pivotal roles in a wide range of regional adaptations in many crop plants[5].
Labs working on this gene
1.National Institute of Crop Science, Tsukuba, Ibaraki, 305-8518 Japan.
2.Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan.
3.National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
4.Chinese National Center for Rice Improvement / State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
5.Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
6.Key Lab of Crop Heterosis and Utilization of Ministry of Education, and Beijing Key Lab of Crop Genetic Improvement, China Agriculture University, Beijing 100093, China.
7.Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang 232-916, Republic of Korea.
References
- ↑ Costa, L. M. From Biological Warfare to the Brighter Side of Rice Research. Plant Cell Physiol 53, no. 4 (2012): 603-5.
- ↑ Kazuki M, Kiyosumi H, Eri O T, Masahiro Y. Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice. (2014).
- ↑ Matsubara, K., E. Ogiso-Tanaka, K. Hori, K. Ebana, T. Ando and M. Yano. Natural Variation in Hd17, a Homolog of Arabidopsis Elf3 That Is Involved in Rice Photoperiodic Flowering. Plant and Cell Physiology 53, no. 4 (2012): 709-716.
- ↑ Guo, Liang, Zhen-hua Zhang and Jie-yun Zhuang. "Quantitative Trait Loci for Heading Date and Their Relationship with Genetic Control of Yield Traits in Rice (Oryza Sativa)." Rice Science 20, no. 1 (2013): 1-12.
- ↑ Kwon, C. T., S. C. Yoo, B. H. Koo, S. H. Cho, J. W. Park, Z. Zhang, J. Li, Z. Li and N. C. Paek. "Natural Variation in Early Flowering1 Contributes to Early Flowering in Japonica Rice under Long Days." Plant Cell Environ 37, no. 1 (2014): 101-12.
Structured Information
| Gene Name |
Os06g0142600 |
|---|---|
| Description |
Conserved hypothetical protein |
| Version |
NM_001063305.2 GI:297605157 GeneID:4340087 |
| Length |
5003 bp |
| Definition |
Oryza sativa Japonica Group Os06g0142600, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 6:2233133..2238135 |
| Sequence Coding Region |
2235411..2236400,2237799..2238059 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008399:2233133..2238135 source=RiceChromosome06 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008399:2233133..2238135 source=RiceChromosome06 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggcgacgaggggaggaggcggaggaggaggagggaaggaggcgaaggggaaggtgatgggcccgctgttcccgcggctccacgtcaacgacgcggccaagggcggaggcccgcgggcgccgccccggaacaagatggcgctctacgagcagttcaccgtgccctcgcatcgcttcagcggcggaggaggcggcggcggagtaggaggcagccccgcgcactcgacgtcggcggcgagccagagccagagccagagccaggtttatggacgtgacagttctctgttccagccgttcaatgtgccttccaatcgacctggccattctactgaaaagatcaattcagataagatcaacaagaagattagtggttcaagaaaagaactggggatgttatcctctcagactaagggcatggatatttatgcttcaagatcaactgctgaggcaccacaaagaagagcagaaaatacaataaagagttcttcgggaaagagattggccgatgatgatgaatttatggttccttctgtcttcaattccagatttcctcaatatagtactcaagagaatgcaggggttcaagaccaatcaacaccccttgttgctgcaaatccacacaaaagcccttcaacagtgtccaaatcatccacaaagtgttataacactgttagcaagaaattggagagaatccatgtttctgatgtgaaatcaaggacccctttgaaagacaaggagatggaagcagcacagacatccaaaaacgtggaagttgaaaaaagttcatcctttcatgcttccaaagatatgtttgaaagcaggcatgctaaagtatatcctaagatggataagacgggcattataaatgattctgatgagccacatggtggaaatagtgggcatcaagcgacaagcagaaatggaggttccatgaaatttcagaaccctccaatgagaagaaatgaaatttcctctaatccatcttctgaaaatactgataggcattataatttaccgcaaggaggcatagaggaaacaggtacaaagagaaaaaggttgctagaacaacacgatgcagagaaaagtgatgatgtgtcaaggttgctagaacaacacgatgcagagaacattgatgatgtgtctgattcctcggtggagtgtataactggttgggagatttctccagataaaattgttggagccattggtacaaagcatttctggaaagcaagacgtgctattatgaagtaa</cdnaseq> |
| Protein Sequence |
<aaseq>MATRGGGGGGGGKEAKGKVMGPLFPRLHVNDAAKGGGPRAPPRN KMALYEQFTVPSHRFSGGGGGGGVGGSPAHSTSAASQSQSQSQVYGRDSSLFQPFNVP SNRPGHSTEKINSDKINKKISGSRKELGMLSSQTKGMDIYASRSTAEAPQRRAENTIK SSSGKRLADDDEFMVPSVFNSRFPQYSTQENAGVQDQSTPLVAANPHKSPSTVSKSST KCYNTVSKKLERIHVSDVKSRTPLKDKEMEAAQTSKNVEVEKSSSFHASKDMFESRHA KVYPKMDKTGIINDSDEPHGGNSGHQATSRNGGSMKFQNPPMRRNEISSNPSSENTDR HYNLPQGGIEETGTKRKRLLEQHDAEKSDDVSRLLEQHDAENIDDVSDSSVECITGWE ISPDKIVGAIGTKHFWKARRAIMK</aaseq> |
| Gene Sequence |
<dnaseqindica>1736..2725#77..337#atggccacaaaaaccggcgacctcctccaccccgccatggcctgacgcccccgagaagctgctgcggcgggaggcgatggcgacgaggggaggaggcggaggaggaggagggaaggaggcgaaggggaaggtgatgggcccgctgttcccgcggctccacgtcaacgacgcggccaagggcggaggcccgcgggcgccgccccggaacaagatggcgctctacgagcagttcaccgtgccctcgcatcgcttcagcggcggaggaggcggcggcggagtaggaggcagccccgcgcactcgacgtcggcggcgagccagagccagagccagagccaggtgactcgacgtcctgcccgtatgatcgattcgattgggggtagtgtgtgcgactgctaaattggtactagtaggcgacaattctgtgcaaatggagctaaacgccttgcaaatcgaatcgaattagaagcctaaattggtaggcaataattctgtgcaatggagctaaacttccttgcaaatcgaatagaactaaaagctgggaagataatttcgaggcacaaatggtgccctcgacgtcgacgagctaggtcagagggggcgtttcacgccttaccctttgtagttatctcggttgggatagatgaattgatgggcgaatttagtgcaacggagctaaacacatggaaaaattggataagattaaggccgagaagcccagtttgaggcacaaatgccatgttccttttgtgctgattaatctatcatgccgtcgacatgtgattcaattacttgcaaatatagtcatacaattgtggtaggagtaacatgcttgcacgttgtcatagtgtcattattgatctttctccgtgctgataactcacttgtgttgaaggcgaaagagcagaacaaaaccattatatgcagtttacatcagctcttccggtaaagttttggagacggggcataagttccttgcaaacaatatcggatattatagcttattgcaaattgtatatggccagatatgctatgattgtgtttgctgaggtctggtgtttgtaatatacaaacaaaaaggtccacatgtgaaactgcatgtagcgcaggtggcaaagagtagccgtagtgctgctcaacgtactgtgttctattctccctgacgtgctcaccttccttaaatcattgacactaggttcctccttagtgtcttgcatttttgcctgccgaaaaaaaaaggtccacgtgaaagggaatgataaaaatggtggttgatatgctttgattgtcaggcacacgttcaacctgtatgtgataaatatcaacggttttctaatactgttttcagcaaggatttaggagtggaaaatattctttagaacaaatctgcaatagcctcccacaacacatccaactaccttttgataatgggatagttatagacatgaagtgcgaatggcaaaagtccaagtcatagatttccaaatgaagaaatgtgaacaaaataagaaagaaagaagtccatttgcagtattatgtctcttttgcccttctttgggtcgaaaataaaataaaaaatcgagatcttaccatgagatacttaatctcccaccactttttctaattcaacatggaagttcttggatagtttaaatacgcttcctaccaattagcgtggaatcctcgcaatttttcactaaatctagtagtactgaaatggattttattttcttccaggtttatggacgtgacagttctctgttccagccgttcaatgtgccttccaatcgacctggccattctactgaaaagatcaattcagataagatcaacaagaagattagtggttcaagaaaagaactggggatgttatcctctcagactaagggcatggatatttatgcttcaagatcaactgctgaggcaccacaaagaagagcagaaaatacaataaagagttcttcgggaaagagattggccgatgatgatgaatttatggttccttctgtcttcaattccagatttcctcaatatagtactcaagagaatgcaggggttcaagaccaatcaacaccccttgttgctgcaaatccacacaaaagcccttcaacagtgtccaaatcatccacaaagtgttataacactgttagcaagaaattggagagaatccatgtttctgatgtgaaatcaaggacccctttgaaagacaaggagatggaagcagcacagacatccaaaaacgtggaagttgaaaaaagttcatcctttcatgcttccaaagatatgtttgaaagcaggcatgctaaagtatatcctaagatggataagacgggcattataaatgattctgatgagccacatggtggaaatagtgggcatcaagcgacaagcagaaatggaggttccatgaaatttcagaaccctccaatgagaagaaatgaaatttcctctaatccatcttctgaaaatactgataggcattataatttaccgcaaggaggcatagaggaaacaggtacaaagagaaaaaggttgctagaacaacacgatgcagagaaaagtgatgatgtgtcaaggttgctagaacaacacgatgcagagaacattgatgatgtgtctgattcctcggtggagtgtataactggttgggagatttctccagataaaattgttggagccattggtacaaagcatttctggaaagcaagacgtgctattatgaagtaagtaaaactatccttttgagcttagtttggcccactcaaactagacttgtttgcagctctaattacgtataggtagctttgatgaataaaatttgttttgtttcccttgctttactgttatttgctcttaatttgcggttgatcttaatcatcttagacagaaaaacatgatgactatctcgtttgtttttggtttatttcatatttgaatgccaatagatgtcagctccagatgatatttcaaatacctcatgcatggaaactgtgcatacttatgccaaattttgggcttacaagtcagcatgtctacaaatttctttggcagaattaatatatatctagttcaacatttgctgatttgtaattggattagttgtctgcagaatgccggcatgttttattttcctttcaactaggtcaatcagttttgttgttgtctgttgttcttgtccacctacacctgtactactgaaatgttctcttttggagatgtcaatgaaaattttaatctatagtggtttcaattttattttcattttagtcaagaagaatggcataatctcatttaaaaagattgtaaaagtgtccctgttaaagtgatattgtaggtattgctttaccaagctactgtatgattccctttattgttttacactctaatcttctttaaactctatgcagtcaacagagggtgtttgctgtccaggtttttgagctgcataagttggtaaaagtgagtctagcaaatttctcttccttctagccactcttaagcaggttaattcgtggataggattttgtccataatctgtttataacccacacttgtatttgacttacaatcaggtgcagaagttgattgcagcatcgccacatgtacttattgaaagtgatccttgccttggcaatgccttgttgggtagcaagaacaagctggtggaagaaaacctgaaagcacaacctcttttagtcgcaaccatcgatgacgtggagccaagtctacagcaaccggaggtatcaaaagaaaacactgaagacagcccaccctcccctcatgatactgggcttggcagtggtcaacgtgatcaagctgcaacaaatggcgtctctaaaagcaatcgtcgagctacacctgttgcttctgataacaaacaaaataactggggcgttcaacttcaaccacctcaaaatcaatggcttgtccctgtcatgtctcctttggaaggccttgtctataagccttattctggtccgtgccctccagctggtagcatattggccccgttttatgccaactgtactcctttgagtcttccatcaacagctggagatttcatgaactcggcatacggtgttcctatgcctcatcagccacaacatatgggtgctcctggccctccttccatgcctatgaactacttcccgcctttcagcataccagtgatgaacccaactgcaccggcacctgtagtcgaacaagggagacatccttcgatgccacagccttatgggaactttgagcagcagtcgtggatctcatgtaacatgtcacatccaagtggcatttggagatttcatgcctcaagagatagcgaggcacaggccagcagcgctagcagtccttttgacaggttccaatgcagtggaagtggtcctgtatccgccttccccacagtatcagctcagaacaaccagcctcagccctcatatagcagccgggacaaccagaccaatgttatcaaggttgttccacataattcacgaactgcttcagagtcagcagcacggattttccggtcaatacaaatggaacggcaacgagatgattgatagccatgagaactggcaattttatgctggatgcatttgatgacttggtaaatgtagagaagaggtttgccagattatggtgacccctatatttatcctgaccgtttatagacagatgatgatactgtatattctcaagggcgggctccgtcagggtgatgtcgccccttcgtcaatttgtaatgtattttgtacagtaggacaggacagtatctgtttaactttaacgctatgtaaagccattgctggtcagttaagcagaataatactaaagctaatgagctggggaaaagaccccgctctttttatctctttcttttgtgaaccctgattacgagttaaggccccgcgccatttgtggggatttgctcttataagtgtgtgatctatattgcaaacagaatggagatatatgatttttggatatatgtaatgtgtgccagtatttt</dnaseqindica> 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