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Identification of Rhizome-Specific Genes by Genome-wide Differential Expression Analysis in Oryza longistaminata
Ting Zhang, Institute of Crop Sciences, Chinese Acadamy of Agricultural Science, Beijing, China (zhangting19861101@163.com,fuby@caas.net.cn,lizhk@caas.net.cn)
Experiment design (15 hybridizations)
tissue type name
•shoot tip •rhizome tip •rhizome internodes •shoot internodes •young leaf

This experiment has been imported by PLEXdb from NCBI GEO (GSE24228) Series_summary: The Oryza longistaminata is a perennial wild rice species ...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Identification of Rhizome-Specific Genes by Genome-wide Differential Expression Analysis in Oryza longistaminata
Accession No: OS57
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
tissue type name
•shoot tip   •rhizome tip   •rhizome internodes   •shoot internodes   •young leaf
Quality Control: biological replicates
Treatment summary:
 tissue type name  # replicates
 shoot tip  3
 rhizome tip  3
 rhizome internodes  3
 shoot internodes  3
 young leaf  3
Total hybridizations: 15
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE24228)

Series_summary:
The Oryza longistaminata is a perennial wild rice species with AA genome, which characterized by the presence of rhizomatous stem. The rhizomatousness trait in rice was previously identified quantitatively controlled by many genes, but the molecular mechanism related to the rhizome initiation and elongation is still unknown. In this study, the specific gene expression patterns across five tissues in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform, the rhizome-specific expressed genes and its corresponding regulatory were further analyzed. The different gene sets were determined exclusively expressed in five tissues; strikingly 58 genes with functions related to transcription regulation and cell proliferation were identified as prevalent sets in rhizome tip, of them, several genes were functionally involved in tiller initiation and elongation. And a set of genes were differentially regulated in the rhizome tip relative to shoot tip, the predominant repressed genes are involved in photosynthesis, while genes related to phytohormone and the gene families with redundancy function were obviously differentially regulated. Several cis-regulatory elements, including CGACG, GCCCORE, GAGAC and a Myb Core, were highly enriched in rhizome tip or internode, and two cis-elements such as RY repeat and TAAAG, which implicated in the ABA signaling pathway, were found overrepresented in the rhizome tip in comparison with shoot tip. A few rhizome-specific expressed genes were co-localized on the rhizome-related QTLs regions, indicating these genes may be good functional candidates for the rhizome related gene cloning.
The whole genome profiling of oryza longistaminata indicated that a very complex gene regulatory network underlies rhizome development and growth, and there might be an overlapping regulatory mechanism in the establishment of rhizome and tiller. Phytohormone such as IAA and GA are involved in the signaling pathway in determining rhizome. Several cis-elements enriched in rhizome and the identified rhizome-specific genes co-localized on the rhizome-related QTL intervals provide a base for further dissection of the molecular mechanism of rhizomatousness

Series_overall_design:
In this study, the specific gene expression patterns across five tissues including rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform.
Publication: 'Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata.', Hu F, Wang D, Zhao X, Zhang T, Sun H, Zhu L, Zhang F, Li L, Li Q, Tao D, Fu B, Li Z.
BMC Plant Biol 2011 Jan 24;11(1):18.
pubmed: 21261937
Created: 2011-04-01 13:09:00
Last Update: 2011-04-01 13:48:17
Released: 2011-04-27
GEO Accession GSE24228
Submitter: PLEXdb Curator
Name: Ting Zhang
Institution: Institute of Crop Sciences, Chinese Acadamy of Agricultural Science, Beijing, China
Head of Laboratory: Binying Fu and Zhikang L
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