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| − | The rice Os03g0188400 is described as basic helix-loop-helix dimerisation region bHLH domain containing protein and it belongs to Oryza sativa Japonica Group.
| + | The rice '''Os03g0188400''' was reported as '''''OsbHLH044''''' in 2006 <ref name="ref1" /> by researchers from the China. It is a member of bHLH transcription factor gene family. |
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| − | ==Function== | + | ==Annotated Information== |
| − | Previous studies have contributed to the development of over 6000 DNA markers3-5 (http://rgp.dna.affrc.go.jp/; http://www.gramene.org) that provide genome coverage of approximately one marker every 0.25 cM, or every 75-100 kb. Most are expressed sequence tags (ESTs) that are widely used as the basis for physical map construction, sequence assembly and comparative genome analysis, but polymorphism detection within the cultivated rice gene pool is inefficient.
| + | ===Gene Symbol=== |
| | + | *'''''Os03g0188400''''' '''''<=>''''' '''''OsbHLH044''''' |
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| − | 1. Os03g0188400 - Cytokinin-inducible type-A response regulator OsRR6 overexpression effect on rice leaves
| + | ===Function=== |
| − | 2. Os03g0188400 - Abscisic acid and gibberellin effect on calluses (dye-swap)
| + | * The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes. |
| − | 3. Os03g0188400 - Abscisic acid and gibberellin effect on calluses
| + | * rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs. |
| − | 4. Os03g0188400 - Silent Information Regulator 2-related gene OsSRT1 knockdown effect on rice leaves
| + | * bHLHs represent key regulatory components in transcriptional networks controlling a number of biological processes. |
| − | 5. Os03g0188400 - Lipopolysaccharide and chitin oligosaccharide effect on rice cells
| + | * Plant bHLHs have been reported to function in light signaling, hormone signaling, wound and drought stress responses, symbiotic ammonium transport, shoot branching, root, fruit and flower development, et al. <ref name="ref1" /> <ref name="ref2" /> <ref name="ref3" /> |
| − | 6. Os03g0188400 - Benzothiadiazole effect on Oryza sativa leaves
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| − | == Expression == | + | ===Expression=== |
| − | It is necessary to reexamine the predicted genes with use of experimental data and systematically analyze the alternatively spliced transcripts in the rice genome.
| + | * Similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs. |
| − | ESTs are regarded as direct evidence of gene expression. With suitable algorithms and well-curated ESTs, the inherent errors in EST information can be effectively reduced in gene/isoform annotations.
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| − | EST sequences:
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| − | 1.Accession: D40346.1
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| − | Description:RICS2264A Rice shoot Oryza sativa (japonica cultivar-group) cDNA, mRNA sequence
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| − | Library ID:193
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| − | End:569497
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| − | Tissue:stem
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| − | 2.Accession:BF145188.1
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| − | Description:EI35K24 Normalized rice cDNA library Oryza sativa cDNA clone EI35K24 similar to Pathogen induced defense- responsive sequence, mRNA sequence
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| − | Clone:EI35K24
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| − | Library ID:6983
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| − | GI:40385992
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| − | Tissue:mixed
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| − | 3.Accession:CF993041.1
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| − | Description:22185rsicee_7682.y1 Oryza sativa cv. LYP9 tillering whole plant cDNA library Oryza sativa (indica cultivar-group) cDNA 5', mRNA sequence
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| − | Library ID:14617
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| − | GI:58594733
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| − | End:5'
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| − | Tissue:whole plant
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| − | 4.Accession:CK011973.1
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| − | Description:24659rsicef_0866.y1 Oryza sativa cv. PA64s panicle sterile cDNA library Oryza sativa (indica cultivar-group) cDNA 5', mRNA sequence
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| − | Library ID:14618
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| − | GI:58601445
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| − | End:5'
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| − | Tissue:panicle
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| − | 5.Accession:BX901684
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| − | Description:BX901684 Oryza sativa library (Han B) Oryza sativa cDNA clone p726b05p5, mRNA sequence
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| − | Library ID:15105
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| − | Clone:p726b05p5
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| − | GI:40491772
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| − | Tissue:unspecified_tissue
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| | ===Evolution=== | | ===Evolution=== |
| − | The O. sativa rice accessions show differentiation into five groups: aromatic, aus, indica, temperate japonica, and tropical japonica. This deep genetic structure is, in part, a legacy of structure in ancestral rice populations. Within Oryza sativa, there is an ancient and well-established divergence between the two major subspecies, indica and japonica. There is a hypothesis that indica and japonica are derived from independent domestication events from an ancestral rice that had allelic already differentiated into (at least) two gene pools (Caiand Morishima 2002; Ma and Bennetzen 2004; Yamariumunder the SMMwas assessed to determine whether naka et al. 2004). The differences between the indica and japonica subspecies are very apparent at all levels of analysis. Differences between nonsticky (indica) and sticky (japonica) rice are documented in Chinese literature as early as 100 AD (Matsuo et al. 1997). Japonica is typically found in temperate East Asia, upland areas of Southeast Asia, and high elevations in South Asia. Recent studies trace the molecular evolution of event that led to the evolution of modern maize (Matmaize offer several points of comparison that help illumi- suoka et al. 2002). Phylogenetic analysis and FST values demonstrate a close evolutionary relationship between the aromatic, temperate japonica, and tropical japonica subpopulations, which comprise the Japonica varietal group, while the indica and aus subpopulations have a distinct ancestry and are recognized as members of the Indica varietal group. The deep genetic structure in rice may also result from autogamous breeding system. While both breeding system and domestication history have had large effects on the structuring of diversity in rice, the independent population histories of the groups have also formed the gene pools. Recently, a second mutation in the BADH2 gene, badh2.2, was found to be associated with fragrance within a limited set of germplasm from China. Evidence that there may be additional mutations in the pathway leading to 2AP synthesis comes from a rigorous study involving a diverse panel of fragrant germplasm that identified several accessions, mostly from Southeast Asia, that had elevated levels of 2AP but did not carry the badh2.1 allele. Studies demonstrated that the Group V accessions, both fragrant and nonfragrant, cluster with the ancestral Japonica accessions both across the BADH2 gene and across the entire 5.3-Mb region of chromosome 8 surveyed. | + | * The studies of researchers indicate that the ancient bHLH gene family has likely expanded considerably during flowering plant evolution to include many relatively young members, allowing both the conservation and divergence of gene function. |
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| | + | You can also add sub-section(s) at will. |
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| | ==Labs working on this gene== | | ==Labs working on this gene== |
| − | Plant Breeding Department, Cornell University, Ithaca, New York
| + | * Shanghai Jiao Tong University-Shanghai Institutes for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, 200240 |
| − | Department of Agriculture-Agricultural Research Service Dale Bumpers
| + | * School of Life Science, Shanghai University, Shanghai, People’s Republic of China, 200444 |
| − | National Rice Research Center, Stuttgart, Arizona
| + | * School of Life Science, Xiamen University, Xiamen, People’s Republic of China, 361005 |
| − | Cornell University, Department of Plant Breeding and Genetics, Ithaca, NY 14853;
| + | * Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China, 200032 |
| − | Grain Quality Nutrition and Postharvest Centre, International Rice Research Institute, Los Ban˜ os, Philippines
| + | * Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 |
| − | Plant Breeding Dept, Cornell University, Ithaca
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| − | Cold Spring Harbor Lab,
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| − | International Rice Research Institute, P.O. Box 933, Manila
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| − | National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University
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| − | Institute of the Society for Tecno-innovation of Agriculture, Forestry and Fisheries (STAFF)
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| − | Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan, Applied Genomics Laboratory, Department of Molecular Genetics, National Institute of Agrobiological Sciences
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| − | USDA Center for Agricultural Bioinformatics, Theory Center, Cornell University, Ithaca,
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| | ==References== | | ==References== |
| − | Garris A J, Tai T H, Coburn J, et al. Genetic structure and diversity in Oryza sativa L[J]. Genetics, 2005, 169(3): 1631-1638.
| + | <references> |
| − | | + | * <ref name="ref1"> |
| − | Michael J. K, Mariafe N. C, Melissa A. F, et al. The origin and evolution of fragrance in rice (Oryza sativa L.), PNAS ,2009, 106 (34): 14444–14449.
| + | Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, Guo J, Liang W, Chen L, Yin J, |
| − | | + | Ma H, Wang J, Zhang D. Genome-wide analysis of basic/helix-loop-helix |
| − | Susan R. M, Leonid T, Yunbi X, et al. Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.) [J]. DNA Research,2002, 199–207.
| + | transcription factor family in rice and Arabidopsis. Plant Physiol. 2006 |
| | + | Aug;141(4):1167-84. PubMed PMID: 16896230; PubMed Central PMCID: PMC1533929. |
| | + | </ref> |
| | + | * <ref name="ref2"> |
| | + | Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martínez-García JF, |
| | + | Bilbao-Castro JR, Robertson DL. Genome-wide classification and evolutionary |
| | + | analysis of the bHLH family of transcription factors in Arabidopsis, poplar, |
| | + | rice, moss, and algae. Plant Physiol. 2010 Jul;153(3):1398-412. doi: |
| | + | 10.1104/pp.110.153593. PubMed PMID: 20472752; PubMed Central PMCID: PMC2899937. |
| | + | </ref> |
| | + | * <ref name="ref3"> |
| | + | Feller A, Machemer K, Braun EL, Grotewold E. Evolutionary and comparative |
| | + | analysis of MYB and bHLH plant transcription factors. Plant J. 2011 |
| | + | Apr;66(1):94-116. doi: 10.1111/j.1365-313X.2010.04459.x. Review. PubMed PMID: |
| | + | 21443626. |
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| − | http://www.metalife.com/UniGene/Os%2031303_1838177
| + | </ref> |
| | + | </references> |
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| | ==Structured Information== | | ==Structured Information== |
| − | {{JaponicaGene|
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| − | GeneName = Os03g0188400|
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| − | Description = Basic helix-loop-helix dimerisation region bHLH domain containing protein|
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| − | Version = NM_001055752.1 GI:115451232 GeneID:4331887|
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| − | Length = 1580 bp|
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| − | Definition = Oryza sativa Japonica Group Os03g0188400, complete gene.|
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| − | Source = Oryza sativa Japonica Group
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| − | ORGANISM Oryza sativa Japonica Group
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| − | Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
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| − | Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
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| − | clade; Ehrhartoideae; Oryzeae; Oryza.
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| − | |
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| − | Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
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| − | AP = Chromosome 3:4607271..4608850|
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| − | CDS = 4607376..4607801,4607897..4608355,4608529..4608633|
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| − | GCID = <gbrowseImage1>
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| − | name=NC_008396:4607271..4608850
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| − | source=RiceChromosome03
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| − | preset=GeneLocation
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| − | </gbrowseImage1>|
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| − | GSID = <gbrowseImage2>
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| − | name=NC_008396:4607271..4608850
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| − | source=RiceChromosome03
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| − | preset=GeneLocation
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| − | </gbrowseImage2>|
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| − | CDNA = <cdnaseq>atggcgttagaggccgtggtgtttccgcagggccatttcggctacgggtgcggaagggactcgccggcgtacgggatgccgtggtgcgacgtcctggctgctgccggcggcggcggcggcttcggtgagttttacggagtggacgagtgggatgaccagctgcaggtcgcctccgtggatgagtgggaggtggcatccaaggataactcggatgcttccacggagggcaaggcggcggcggcggagcgggcggagccggtggccgccgggaggaggaaacggaggcggacgaaggtcgtcaagaacaaggaggagatcgagtgccagcggatgacccacattgccgtcgagcgcaaccgccgccgccagatgaacgagtacctcgccgtgctccgctccctcatgccggcgtcctactcgcagaggggtgatcaagcatcgatcgtcggaggagcaatcaactacgtgaaggagctggagcagctactgcagtcgctggaagtccaaaagagcctcaagaaccgcagcggcgccatggacgccgccggcgattcccctttcgccggcttcttcagcttcccacagtactccacgtcgcctcgcactggctgcagcgccgccgccagcgccgggagctccggcagtgcgagcagcgtcgtcatggacgacacggcgggctccgcggagagcggccggcagtcggcggccatcgccgacatcgaggtgaccatggtggaagggcacgcgagcctcaaggtgctcgcgcggcggcgaccgaagcagctgctgaagctggtcgtcgggctgcagcagctgcgcatcccgccgctgcatctcaacgtgaccaccgtcgacgccatggtcctctactccttcagcctcaaggtggaggatgattccaagctgggctctgtggaagacattgccaccgctgtgcatcagatcctgggcagcattcagcagcaggaggccgtcctctccatcagctga</cdnaseq>|
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| − | AA = <aaseq>MALEAVVFPQGHFGYGCGRDSPAYGMPWCDVLAAAGGGGGFGEF YGVDEWDDQLQVASVDEWEVASKDNSDASTEGKAAAAERAEPVAAGRRKRRRTKVVKN KEEIECQRMTHIAVERNRRRQMNEYLAVLRSLMPASYSQRGDQASIVGGAINYVKELE QLLQSLEVQKSLKNRSGAMDAAGDSPFAGFFSFPQYSTSPRTGCSAAASAGSSGSASS VVMDDTAGSAESGRQSAAIADIEVTMVEGHASLKVLARRRPKQLLKLVVGLQQLRIPP LHLNVTTVDAMVLYSFSLKVEDDSKLGSVEDIATAVHQILGSIQQQEAVLSIS</aaseq>|
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| − | DNA = <dnaseqindica>106..531#627..1085#1259..1363#aactcactctttaattcgcctccccctgaatcgtgtgcgtatcgtatcgtggcgtcgtcagttcgcgaaaaaaaacgcccgttcgttttgccgggtgcgtgcaggatggcgttagaggccgtggtgtttccgcagggccatttcggctacgggtgcggaagggactcgccggcgtacgggatgccgtggtgcgacgtcctggctgctgccggcggcggcggcggcttcggtgagttttacggagtggacgagtgggatgaccagctgcaggtcgcctccgtggatgagtgggaggtggcatccaaggataactcggatgcttccacggagggcaaggcggcggcggcggagcgggcggagccggtggccgccgggaggaggaaacggaggcggacgaaggtcgtcaagaacaaggaggagatcgagtgccagcggatgacccacattgccgtcgagcgcaaccgccgccgccagatgaacgagtacctcgccgtgctccgctccctcatgccggcgtcctactcgcagagggtacaacactaactacgcatgcttcaattaatcgcttttacgcatactgttatgattcgttaatcatcattaaatcgaatccattttctgctcagggtgatcaagcatcgatcgtcggaggagcaatcaactacgtgaaggagctggagcagctactgcagtcgctggaagtccaaaagagcctcaagaaccgcagcggcgccatggacgccgccggcgattcccctttcgccggcttcttcagcttcccacagtactccacgtcgcctcgcactggctgcagcgccgccgccagcgccgggagctccggcagtgcgagcagcgtcgtcatggacgacacggcgggctccgcggagagcggccggcagtcggcggccatcgccgacatcgaggtgaccatggtggaagggcacgcgagcctcaaggtgctcgcgcggcggcgaccgaagcagctgctgaagctggtcgtcgggctgcagcagctgcgcatcccgccgctgcatctcaacgtgaccaccgtcgacgccatggtcctctactccttcagcctcaaggtaaaaaccaatcgacaatttgcacctattttactaccacgactgcatgcttagttagtttaggctagcagcacagacaaattaagcgattggaacgtcgcgggtgagcgaagattcgctcccatttttctacaacgccgatgataatgtcatcgctttcgtttggatgttaggtggaggatgattccaagctgggctctgtggaagacattgccaccgctgtgcatcagatcctgggcagcattcagcagcaggaggccgtcctctccatcagctgacgccgcgatcgatggagacgacaaccgagacggccgccatgtgaagcctctgcctcgtccgtcctggaaatggaaccatggcgcctcgatcgatagcttgttagcttgtaatgtgtgaatgtgattgtaccctagccaacagagtgctgcatgcatgcagtatctccggcgaccttaatgagaaatctataccaacattttgagctcttgtaaacgt</dnaseqindica>|
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| − | Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055752.1 RefSeq:Os03g0188400]|
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| − | }}
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| | [[Category:Genes]] | | [[Category:Genes]] |
| | [[Category:Japonica mRNA]] | | [[Category:Japonica mRNA]] |
