Difference between revisions of "Os06g0157700"
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| − | Japanese scholars indicate, RICE FLOWERING LOCUS T1 (RFT1), and Heading date 3a (Hd3a) homology is the main activating factor of a long day under the conditions. (Ogiso-Tanaka et al. 2013) | + | Japanese scholars indicate, RICE FLOWERING LOCUS T1 (RFT1), and Heading date 3a (Hd3a) homology is the main activating factor of a long day under the conditions. (Ogiso-Tanaka et al., 2013) |
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==Labs working on this gene== | ==Labs working on this gene== | ||
^Rice Genome Research Program (RGP), National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305, Japan | ^Rice Genome Research Program (RGP), National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305, Japan | ||
Revision as of 16:52, 10 May 2014
Please input one-sentence summary here.
Contents
Annotated Information
Function
Please input function information here. The rice photoperiod sensitivity gene Hd3 was originally detected as a heading date-related quantitative trait locus localized on chromosome 6 of rice. But the effect is small, it is a minor QTL located on chromosome 6 between RFLP markers R1952-C1032, and isolated with the four markers contain R2749, R1962, R2967 and C764 (Yamamoto et al., 1997). Furthermore, it was found the site of Hd3 was composed of two sub-sites Hd3a and Hd3b, both sites had additive effects. In the short daylight, Hd3a locus alleles from Kasalath promoted the heading; however, in the long sunshine or large fields, Hd3b locus alleles from Kasalath delayed heading. Hd3a and molecular markers B174 were separated as well as Hd3b and molecular markers R1952 did, the genetic distance is about 1.6cM (Monna et al., 2002)
Expression
Please input expression information here. The full length of Hd3a cDNA is 847bp contains four exons encoding 178 amino acid protein products. Sequence analysis showed: Kasalath and Nipponbare allele coding region has a single base substitution, and a 2-synonymous nucleotide substitutions. This codon in Nipponbare is proline, while aspartic acid in Kasalath. And both alleles are functional, however, Hd3a in Kasalath promotes more powerful. The expression patterns of Hd1 and Hd3a were 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 low levels in the daytime. In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions. Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length. This result suggests that suppression of Hd3a expression is a principle cause of late heading under low temperature and long-day conditions. (Luan et al., 2009)
Evolution
Please input evolution information here. A previous study revealed that the Kasalath allele of Hd3a promotes heading under short-day conditions. The rice Heading date 1 (Hd1) gene, a homolog of CONSTANS (CO), has been shown to promote heading under short-day conditions. Besides, the amount of Hd3a mRNA is up-regulated by Hd1 under short-day conditions, suggesting that Hd3a promotes heading under the control of Hd1. These results indicate that Hd3a encodes a protein closely related to Arabidopsis FT and that the function and regulatory relationship with Hd1 and CO, respectively. Furthermore, Hd3a and FT are conserved between rice and Arabidopsis. (Kojima et al., 2002)
Homology
Japanese scholars indicate, RICE FLOWERING LOCUS T1 (RFT1), and Heading date 3a (Hd3a) homology is the main activating factor of a long day under the conditions. (Ogiso-Tanaka et al., 2013)
Labs working on this gene
^Rice Genome Research Program (RGP), National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305, Japan
^Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305, Japan
^Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan
^Bio-oriented Technology Research Advancement Institution, Omiya, Saitama 331-8537, Japan,Bio-oriented Technology Research Advancement Institution, Omiya, Saitama 331-8537, Japan
^Department of Molecular Genetics, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
^Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, People’s Republic of China
^State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, People’s Republic of China
^State Key Laboratory of Plant Physiology and Biochemistry, National Center for the Evaluation of Agricultural Wild Plants (Rice), Laboratory of Crop Heterosis and Utilization of the Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, People’s Republic of China
^Chemistry and Life Science College, Tianjin Normal University, Tianjin, People’s Republic of China
^Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, 305-0854 Japan
^Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
^Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation, Kawaguchi, Saitama, 332-0012 Japan
^Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
^Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai Tsukuba, Ibaraki, Japan
References
Please input cited references here. M. Yano;Y. Harushima;Y. Nagamura;N. Kurata;Y. Minobe and T. Sasaki. Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theoretical and Applied Genetics, 1997, 95(7): 1025-1032
L. Monna;H. Lin;S. Kojima;T. Sasaki;M. Yano. Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice. Theoretical and Applied Genetics, 2002, 104(5): 772-778
Weijiang Luan;Huizhe Chen;Yaping Fu;Huamin Si;Wen Peng;Susheng Song;Wenzhen Liu;Guocheng Hu;Zongxiu Sun;Daoxin Xie;Chuanqing Sun. The Effect of the Crosstalk between Photoperiod and Temperature on the Heading-Date in Rice. PLoS ONE, 2009, 4(6): e5891
Shoko Kojima;Yuji Takahashi;Yasushi Kobayashi;Lisa Monna;Takuji Sasaki;Takashi Araki;Masahiro Yano. Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant and Cell Physiology, 2002, 43(10): 1096-1105
Eri Ogiso-Tanaka;Kazuki Matsubara;Shin-ichi Yamamoto;Yasunori Nonoue;Jianzhong Wu;Hiroko Fujisawa;Harumi Ishikubo;Tsuyoshi Tanaka;Tsuyu Ando;Takashi Matsumoto;Masahiro Yano. Natural Variation of the RICE FLOWERING LOCUS T 1 Contributes to Flowering Time Divergence in Rice. PLoS ONE, 2013, 8(10): e75959
Structured Information
| Gene Name |
Os06g0157700 |
|---|---|
| Description |
Similar to SP3D |
| Version |
NM_001063395.1 GI:115466521 GeneID:4340185 |
| Length |
2449 bp |
| Definition |
Oryza sativa Japonica Group Os06g0157700, 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 6:2939005..2941453 |
| Sequence Coding Region |
2939157..2939363,2939526..2939587,2939721..2939761,2941069..2941298 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008399:2939005..2941453 source=RiceChromosome06 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008399:2939005..2941453 source=RiceChromosome06 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggccggaagtggcagggacagggaccctcttgtggttggtagggttgtgggtgatgtgctggacgcgttcgtccggagcaccaacctcaaggtcacctatggctccaagaccgtgtccaatggctgcgagctcaagccgtccatggtcacccaccagcctagggtcgaggtcggcggcaatgacatgaggacattctacacccttgtgatggtagacccagatgcaccaagcccaagtgaccctaaccttagggagtatctacattggttggtcactgatattcctggtactactgcagcgtcatttgggcaagaggtgatgtgctacgagagcccaaggccaaccatggggatccaccggctggtgttcgtgctgttccagcagctggggcgtcagacagtgtacgcgcccgggtggcgtcagaacttcaacaccaaggacttcgccgagctctacaacctcggctcgccggtcgccgccgtctacttcaactgccagcgcgaggcaggctccggcggcaggagggtctacccctag</cdnaseq> |
| Protein Sequence |
<aaseq>MAGSGRDRDPLVVGRVVGDVLDAFVRSTNLKVTYGSKTVSNGCE LKPSMVTHQPRVEVGGNDMRTFYTLVMVDPDAPSPSDPNLREYLHWLVTDIPGTTAAS FGQEVMCYESPRPTMGIHRLVFVLFQQLGRQTVYAPGWRQNFNTKDFAELYNLGSPVA AVYFNCQREAGSGGRRVYP</aaseq> |
| Gene Sequence |
<dnaseqindica>153..359#522..583#717..757#2065..2294#tgcaccacacacagttcagctagcagatcacctagctagatagctgcctctatcacagtatatttgctccctgcaacttgctgctgctgcaatagctagcagctgcagctagtaagcaaaactataaaccttcagggttttttgcaagatcgatggccggaagtggcagggacagggaccctcttgtggttggtagggttgtgggtgatgtgctggacgcgttcgtccggagcaccaacctcaaggtcacctatggctccaagaccgtgtccaatggctgcgagctcaagccgtccatggtcacccaccagcctagggtcgaggtcggcggcaatgacatgaggacattctacacccttgtatgtgagctctaccatgtgtcgtagttggtgcagagaccagaagttatactttctttcattattatattatagaaaaatttgtttggtacttaacccaagatgactttaaaatgcattaatttgatgtttgtcatggttttttgtggtgtgtacctgaaggtgatggtagacccagatgcaccaagcccaagtgaccctaaccttagggagtatctacattggtaagcacactaatgttaagctagcgcacttgttttcatgcaatgatcaaaataatcactgctagctgatttacatacataaccacatcttgactgcatgatgggttgatcatcttaatttgtttgtccacaggttggtcactgatattcctggtactactgcagcgtcatttggtcagtattaaacgatcaaatggtttagattgatttgatttcccacttaaatacattgcagtataaaactaacagaggtaaattgtctttccatactattgtttgggggggggggggcagggggcagtgagttgttgagcattttccctcactcgcgagcccccagtttgccgcattaattccccatcatccttcaccaccacaaaaaaaaaagtgatttggagaaggatacgctcctccaaataatttttaacaagttcaccaccacaacgaggcaccgacaaccgccatgagtccacgcaccctgcagctagtcgtgccaccagcaccacagttagccacaccgcgagcaatccacgccatcacttgccgctgtgagtccacgatcacacgcctcgatcagccagctgccatgatatgtcggcttgggcttggattctgcaacataccatgtccccatcgatggcaccacactctaattcgccaacacaacactgaagggatcggatcgggagggctagctcactcaagatagtgacgggatgattcgatgggaattccatggggaacaaagcacaaaatcattaaaatgtccttttcaattccatggcaaattcctaaagcaatactctctctccattctataatgtaggttgcacactcatttcaagattcaactttcaaaacatttgactaacgatttgtataatataaattgaattttatttgatagaaataatattattggattgatatttcaatatactttcatatggttataattttgttactacaaactttatagtatattagaaattataaataaaaaattagttttgtagaccgtacatgccaagtttgaccataccatattatgaaaaagagggagtagtaaccttgtttatatttgcaatatatactccctccgtttctaaatatctgacgctgttgactttttaaacatgtttgaccgttcgtcttattaaaaaataagtaattattaattcttttcctatcatttgatttattgttaaatatatttttatgcagacatatagttttacatatttcataaaagtttttgaataagaagaatgatcgtcaaatatttagaaacgaggggagtatattgctagtaaattttactgtaaagtcatgtttcttcatgtgtcttttttagaacatttcttcttcatgtgttccaatcaattttttcgatctccaccaccactaccacagttgtatgtgtagtagctagctgttgcacatgctcatgttaatctgaatctgtccatggttttttgcagggcaagaggtgatgtgctacgagagcccaaggccaaccatggggatccaccggctggtgttcgtgctgttccagcagctggggcgtcagacagtgtacgcgcccgggtggcgtcagaacttcaacaccaaggacttcgccgagctctacaacctcggctcgccggtcgccgccgtctacttcaactgccagcgcgaggcaggctccggcggcaggagggtctacccctagctaacgatgatcccgatcgatctgctgcatgctcactatcatcatccagcatgctatacattgcaggttcagacaattgaaatgattctcgacacacaacatatatatgatggtgtaattaattatgcaattaaatagctgagcaaggctaaggt</dnaseqindica> |
| External Link(s) |
