Table Of ContentPlant Reverse Genetics
Methods and Protocols
Edited by
Andy Pereira
Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
Editor
Andy Pereira, Ph.D.
Virginia Bioinformatics Institute
Virginia Tech
Blacksburg, VA
USA
[email protected]
ISSN 1064-3745 e-ISSN 1940-6029
ISBN 978-1-60761-681-8 e-ISBN 978-1-60761-682-5
DOI 10.1007/978-1-60761-682-5
Springer New York Dordrecht Heidelberg London
Library of Congress Control Number: 2010935805
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Preface
Plant biology is at the crossroads, integrating the data from genomics into knowledge and
understanding of important biological processes. With the generation of genome sequence
data from model and other plants, databases are filled with sequence information of genes
with no known biological function. While bioinformatics tools can help analyze genome
sequences and predict gene structures, experimental approaches to discover gene func-
tions need to be widely implemented. This book deals with plant functional genomics
using reverse genetics methods, namely, from gene sequence to plant gene functions. The
methods developed and described by leading researchers in the field are high-throughput
and genome-wide in the models Arabidopsis and rice as well as other plants to provide
comparative functional genomics information.
This book describes methods for the analysis of high-throughput genome sequence
data, the identification of noncoding RNA from sequence information, the comprehen-
sive analysis of gene expression by microarrays, and Metabolomic analysis, all of which are
supported by scripts to aid their computational use. A series of mutational approaches to
ascribe gene function are described using insertion sequences such as T-DNA and trans-
posons as well as methods for the silencing and overexpression of genes. The cataloging
of developmental mutant phenotypes as well as analysis of functions using specific phe-
nome screens described can be adapted to any lab conditions. The integration of the
diverse comparative functional genomics information in a database, such as Gramene,
provides the capabilities for an understanding of how plant genes work together in a sys-
tems biology view.
Blacksburg, VA Andy Pereira
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Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Analysis of High-Throughput Sequencing Data .......................... 1
Shrinivasrao P. Mane, Thero Modise, and Bruno W. Sobral
2 Identification of Plant microRNAs Using Expressed
Sequence Tag Analysis ............................................. 13
Taylor P. Frazier and Baohong Zhang
3 Microarray Data Analysis ........................................... 27
Saroj K. Mohapatra and Arjun Krishnan
4 Setting Up Reverse Transcription Quantitative-PCR Experiments............. 45
Madana M.R. Ambavaram and Andy Pereira
5 Virus-Induced Gene Silencing in Nicotiana benthamiana
and Other Plant Species ............................................ 55
Andrew Hayward, Meenu Padmanabhan, and S.P. Dinesh-Kumar
6 Agroinoculation and Agroinfiltration: Simple Tools
for Complex Gene Function Analyses .................................. 65
Zarir Vaghchhipawala, Clemencia M. Rojas, Muthappa Senthil-Kumar,
and Kirankumar S. Mysore
7 Full-Length cDNA Overexpressor Gene Hunting System
(FOX Hunting System) ............................................ 77
Mieko Higuchi, Youichi Kondou, Takanari Ichikawa,
and Minami Matsui
8 Activation Tagging with En/Spm-I/dSpm Transposons in Arabidopsis.......... 91
Nayelli Marsch-Martínez and Andy Pereira
9 Activation Tagging and Insertional Mutagenesis in Barley................... 107
Michael A. Ayliffe and Anthony J. Pryor
10 Methods for Rice Phenomics Studies .................................. 129
Chyr-Guan Chern, Ming-Jen Fan, Sheng-Chung Huang, Su-May Yu,
Fu-Jin Wei,Cheng-Chieh Wu, Arunee Trisiriroj, Ming-Hsing Lai,
Shu Chen, and Yue-Ie C. Hsing
11 Development of an Efficient Inverse PCR Method
for Isolating Gene Tags from T-DNA Insertional Mutants in Rice............. 139
Sung-Ryul Kim, Jong-Seong Jeon, and Gynheung An
12 Transposon Insertional Mutagenesis in Rice ............................. 147
Narayana M. Upadhyaya, Qian-Hao Zhu, and Ramesh S. Bhat
13 Reverse Genetics in Medicago truncatula
Using Tnt1 Insertion Mutants ....................................... 179
Xiaofei Cheng, Jiangqi Wen, Million Tadege, Pascal Ratet,
and Kirankumar S. Mysore
vii
viii Contents
14 Screening Arabidopsis Genotypes for Drought Stress Resistance .............. 191
Amal Harb and Andy Pereira
15 Protein Tagging for Chromatin Immunoprecipitation
from Arabidopsis.................................................. 199
Stefan de Folter
16 Yeast One-Hybrid Screens for Detection
of Transcription Factor DNA Interactions............................... 211
Pieter B.F. Ouwerkerk and Annemarie H. Meijer
17 Plant Metabolomics by GC-MS and Differential Analysis ................... 229
Joel L. Shuman, Diego F. Cortes, Jenny M. Armenta,
Revonda M. Pokrzywa, Pedro Mendes, and Vladimir Shulaev
18 Gramene Database: A Hub for Comparative Plant Genomics ................ 247
Pankaj Jaiswal
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Contributors
Madana M. R. aMbavaRaM • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
GynheunG an • Department of Plant Molecular Systems Biotechnology and Crop
Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
Jenny M. aRMenta • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
Michael a. ayliffe • CSIRO Plant Industry, Canberra, ACT, Australia
RaMesh s. bhat • University of Agricultural Sciences, Dharwad, Karnataka, India
shu chen • Taiwan Agricultural Research Institute, Wufeng, Taichung, Taiwan
Xiaofei chenG • Plant Biology Division, The Samuel Roberts Noble Foundation,
Ardmore, OK, USA
chyR-Guan cheRn • Taiwan Agricultural Research Institute,
Wufeng, Taichung, Taiwan
dieGo f. coRtes • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
s. P. dinesh-KuMaR • UC Davis Genome Center, 1319 Genome and Biomedical
Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616, USA
MinG-Jen fan • Department of Biotechnology, Asia University, Wufeng, Taichung,
Taiwan
stefan de folteR • Laboratorio Nacional de Genómica para la Biodiversidad
(Langebio), Centro de Investigación y de Estudios Avanzados del Instituto
Politécnico Nacional (CINVESTAV-IPN), Irapuato, Mexico
tayloR P. fRazieR • Department of Biology, East Carolina University,
Greenville, NC, USA
aMal haRb • Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
andRew haywaRd • Department of Molecular, Cellular, and Developmental Biology,
Yale University, New Haven, CT, USA
MieKo hiGuchi • RIKEN Plant Science Center, Yokohama Kanagawa, Japan
yue-ie c. hsinG • Institute of Plant and Microbial Biology, Academia Sinica,
Taipei, Taiwan
shenG-chunG huanG • Taiwan Agricultural Research Institute, Wufeng, Taichung,
Taiwan
taKanaRi ichiKawa • RIKEN Plant Science Center, YokohamaKanagawa, Japan;
Gene Research Center, Tsukuba University, Tsukuba, Japan
PanKaJ Jaiswal • Department of Botany and Plant Pathology,
Oregon State University, Corvallis, OR, USA
JonG-seonG Jeon • Graduate School of Biotechnology & Plant Metabolism Research
Center, Kyung Hee University, Yongin, Korea
ix
x Contributors
sunG-Ryul KiM • National Research Laboratory of Plant Functional Genomics,
Division of Molecular and Life Sciences, POSTECH Biotech Center,
Pohang University of Science and Technology, Pohang, Korea
youichi Kondou • RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
aRJun KRishnan • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
MinG-hsinG lai • Taiwan Agricultural Research Institute, Wufeng, Taichung,
Taiwan
shRinivasRao P. Mane • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
nayelli MaRsch-MaRtínez • Laboratorio Nacional de Genómica para la
Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del
Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, México
MinaMi Matsui • RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
anneMaRie h. MeiJeR • Clusius Laboratory, Institute of Biology (IBL),
Leiden University, Leiden, The Netherlands
PedRo Mendes • Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA,
USA; School of Computer Science, University of Manchester, Manchester, UK;
Department of Cancer Biology, Wake Forest University School of Medicine,
Winston-Salem, NC, USA
theRo Modise • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
saRoJ K. MohaPatRa • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
KiRanKuMaR s. MysoRe • Plant Biology Division, The Samuel Roberts
Noble Foundation, Ardmore, OK, USA
PieteR b. f. ouweRKeRK • Sylvius Laboratory, Institute of Biology (IBL), Leiden Uni-
versity, Leiden, The Netherlands
Meenu PadManabhan • Department of Molecular, Cellular,
and Developmental Biology, Yale University, New Haven, CT, USA
andy PeReiRa • Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
Revonda M. PoKRzywa • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
anthony J. PRyoR • CSIRO Plant Industry, Canberra, ACT, Australia
Pascal Ratet • Institut des Sciences du Vegetal, CNRS, Gif sur Yvette Cedex, France
cleMencia M. RoJas • Plant Biology Division, The Samuel Roberts Noble
Foundation, Ardmore, OK, USA
MuthaPPa senthil-KuMaR • Plant Biology Division, The Samuel Roberts Noble
Foundation, Ardmore, OK, USA
vladiMiR shulaev • Department of Horticulture, Virginia Bioinformatics Institute,
Virginia Tech, BlacksburgVA, USA; Department of Cancer Biology, Wake Forest
University School of Medicine, Winston-Salem, NC, USA
Joel l. shuMan • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
bRuno w. sobRal • Virginia Bioinformatics Institute, Virginia Tech,
Blacksburg, VA, USA
Contributors xi
Million tadeGe • Plant Biology Division, The Samuel Roberts Noble Foundation,
Ardmore, OK, USA
aRunee tRisiRiRoJ • Institute of Plant and Microbial Biology, Academia Sinica,
Taipei, Taiwan
naRayana M. uPadhyaya • CSIRO Plant Industry, Canberra, ACT, Australia
zaRiR vaGhchhiPawala • Plant Biology Division, The Samuel Roberts Noble
Foundation, Ardmore, OK, USA
fu-Jin wei • Institute of Plant and Microbial Biology, Academia Sinica,
Taipei, Taiwan
JianGqi wen • Plant Biology Division, The Samuel Roberts Noble Foundation,
Ardmore, OK, USA
chenG-chieh wu • Institute of Plant and Microbial Biology, Academia Sinica,
Taipei, Taiwan
su-May yu • Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
baohonG zhanG • Department of Biology, East Carolina University,
Greenville, NC, USA
qian-hao zhu • CSIRO Plant Industry, Canberra, ACT, Australia
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