Genome-wide analysis of root hair-preferential genes in rice

Rice
Sunok MoonKi-Hong Jung

Abstract

Root hairs are valuable in taking up nutrients and water from the rhizosphere and serving as sites of interactions with soil microorganisms. By increasing the external surface area of the roots or interacting with rhizobacteria, root hairs directly and indirectly promote plant growth and yield. Transcriptome data can be used to understand root-hair development in rice. We performed Agilent 44 K microarray experiments with enriched root-hair samples and identified 409 root hair-preferential genes in rice. The expression patterns of six genes were confirmed using a GUS reporter system and quantitative RT-PCR analysis. Gene Ontology (GO) analysis demonstrated that 13 GO terms, including oxygen transport and cell wall generation, were highly over-represented in those genes. Although comparative analysis between rice and Arabidopsis revealed a large proportion of orthologous pairs, their spatial expression patterns were not conserved. To investigate the molecular network associated with root hair-preferential genes in rice, we analyzed the PPI network as well as coexpression data. Subsequently, we developed a refined network consisting of 24 interactions between 10 genes and 18 of their interactors. Identification of root hair-prefe...Continue Reading

References

Jul 1, 1990·Molecular & General Genetics : MGG·A K WilsonM Estelle
Dec 1, 1984·Applied and Environmental Microbiology·F B DazzoS H Pankratz
Jul 23, 1996·Proceedings of the National Academy of Sciences of the United States of America·F R LauterW B Frommer
Aug 26, 1998·Proceedings of the National Academy of Sciences of the United States of America·A W SowaR D Hill
Feb 26, 1999·The Plant Journal : for Cell and Molecular Biology·R J PittsM Estelle
Feb 9, 2000·Trends in Plant Science·S Gilroy, D L Jones
Jul 8, 2000·The Plant Journal : for Cell and Molecular Biology·J S JeonG An
Dec 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·P W HuntE S Dennis
Jan 30, 2003·Journal of Experimental Botany·Guilhem DesbrossesLiam Dolan
Jan 20, 2004·Plant Physiology·Margarete Müller, Wolfgang Schmidt
Oct 20, 2005·Journal of Bioscience and Bioengineering·Takaki MaekawaYoshikatsu Murooka
Feb 5, 2009·The Plant Cell·Ji-Yul JungDaniel P Schachtman
Nov 7, 2009·Nucleic Acids Research·Gabriel OstlundErik L L Sonnhammer
Dec 15, 2010·Bioinformatics·Michael E SmootTrey Ideker
Feb 12, 2011·The Plant Journal : for Cell and Molecular Biology·Yu ZhiMingWu Ping
Jan 19, 2012·PLoS Genetics·Angela BruexJohn Schiefelbein
Jan 1, 2002·The Arabidopsis Book·Claire Grierson, John Schiefelbein
Jul 31, 2012·Molecular & Cellular Proteomics : MCP·Tran Hong Nha NguyenGary Stacey
Sep 22, 2012·Proteomics·Laurent BrechenmacherGary Stacey
Nov 7, 2012·Plant Physiology·Miroslaw KwasniewskiIwona Szarejko
Jun 27, 2013·Genome Biology·Ping LanWolfgang Schmidt
Jan 1, 2012·Rice·Chai-Ling HoMatt Geisler
Feb 14, 2014·Plant Signaling & Behavior·Marek MarzecIwona Szarejko
May 20, 2014·Journal of Experimental Botany·Chuang WangHuixia Shou
May 9, 2015·Nucleic Acids Research·Timothy L BaileyWilliam S Noble

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Citations

Jan 23, 2020·Plants·Yo-Han YooKi-Hong Jung
Nov 13, 2020·Frontiers in Plant Science·Chidi Afamefule, Christine A Raines
May 21, 2021·Biochemical Society Transactions·Manuela Désirée BienertGerd Patrick Bienert

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Datasets Mentioned

BETA
GSM943445
GSM943446

Methods Mentioned

BETA
reverse transcription-PCR
PCR
transgenic
affinity purification
RNA-Seq

Software Mentioned

MEME
Inparanoid
MapMan
CytoScape
rice interactions viewer
Tomtom
affy
Feature Extraction
R

Related Concepts