Plant Gene Silencing: Methods and Protocols

300 Pages·2015·9.043 MB·English

by  Kirankumar S. Mysore, Muthappa Senthil-Kumar (eds.)

Methods in
Molecular Biology 1287
Kirankumar S. Mysore
Muthappa Senthil-Kumar Editors
Plant Gene
Silencing
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
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Plant Gene Silencing
Methods and Protocols
Edited by
Kirankumar S. Mysore
Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
Muthappa Senthil-Kumar
National Institute of Plant Genome Research, New Delhi, India
Editors
Kirankumar S. Mysore Muthappa Senthil-Kumar
Plant Biology Division, The Samuel Roberts National Institute of Plant Genome Research
Noble Foundation Aruna Asaf Ali Marg, New Delhi, India
Ardmore, OK , USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-2452-3 ISBN 978-1-4939-2453-0 (eBook)
DOI 10.1007/978-1-4939-2453-0
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Prefa ce
Gene silencing is being popularly used as a functional genomics tool to determine plant gene
function. In addition, gene silencing is also used as one of the plant genetic engineering
strategies to produce better crop varieties. It is anticipated that the use of gene silencing
technology in commercial plant varieties will increase in the future. This volume will provide
a comprehensive overview of various gene silencing methodologies and its applications.
Gene silencing can be either transcriptional gene silencing (TGS) or posttranscriptional
gene silencing (PTGS). PTGS is more popularly used for gene function analyses. PTGS is
commonly achieved by either RNA interference (RNAi) or virus-induced gene silencing
(VIGS). RNAi in plants can be achieved by expressing hairpin RNA (hpRNA) that fold
back to create a double-stranded RNA (dsRNA). These hpRNAs are potent inducers of
PTGS and give rise to 21–23 nucleotides small interfering RNAs (siRNAs) derived from
the dsRNA by RNase III-like enzymes called Dicers. Then the siRNAs assemble into
endoribonuclease-containing complexes known as RNA-induced silencing complex (RISC).
The siRNA strands subsequently guide the RISCs to complementary mRNA molecules,
where they cleave and destroy the cognate mRNA thus causing PTGS. VIGS involves deliv-
ery of a fragment of plant gene (intended to be silenced) into plant cells via a recombinant
virus. The plant defense mechanism silences both the targeted endogenous plant gene and
the virus through PTGS. The plant RNA will be converted into dsRNA by RNA-dependent
RNA polymerase. The dsRNA will then be degraded in a similar mechanism as that of
RNAi. In addition to RNAi and VIGS, PTGS can also be induced by direct delivery of
dsRNA into plants.
In addition to siRNA microRNA (miRNA) can also cause PTGS. miRNA-mediated
PTGS is a natural targeted gene silencing phenomenon inherent in plants for gene regula-
tion during plant development and stress responses. Some miRNAs trigger the production
of secondary siRNAs from their targets. miRNA-induced gene silencing (MIGS) is an
emerging fi eld to silence more than one gene that may not have overall sequence similarity.
This volume will cover historical overview of gene silencing mechanisms in plants, vec-
tors and strategies available for plant gene silencing, practical applications of gene silencing,
and bioinformatics tools and other resources for plant gene silencing. In addition to these
review articles, this volume will include methodology for VIGS in various different plant
species, understanding plant stress responses using VIGS, miRNA identifi cation, DNA
interference, host-induced gene silencing, use of artifi cial miRNAs for gene silencing, high
throughput RNAi, and others.
Ardmore, OK, USA K irankumar S . Mysore
New Delhi, India Muthappa S enthil-Kumar
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
PART I REVIEW CHAPTERS
1 Advances in Plant Gene Silencing Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Prachi Pandey , Muthappa Senthil-Kumar , and Kirankumar S . Mysore
2 S trategies for Altering Plant Traits Using Virus-Induced Gene
Silencing Technologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 5
Christophe Lacomme
3 B ioinformatics Tools for Achieving Better Gene Silencing in Plants. . . . . . . . . 4 3
Firoz Ahmed , X inbin D ai , and Patrick X uechun Z hao
4 P rofiling of Small RNAs Involved in Plant–Pathogen Interactions. . . . . . . . . . 6 1
Dongdong Niu , Z haoyun W ang , S hune Wang , L ulu Qiao ,
and Hongwei Z hao
5 R NAi-Mediated Resistance to Viruses in Genetically Engineered Plants. . . . . . 8 1
Abdulrazak B . Ibrahim and Francisco J . L . A ragão
PART II METHODS CHAPTER
6 Simplifying Transgene Locus Structure Through Cre-lox Recombination . . . . 9 5
Vibha S rivastava and David W . Ow
7 T ransgene-Induced Gene Silencing in Plants. . . . . . . . . . . . . . . . . . . . . . . . . . 1 05
Yun J in and H ui-Shan Guo
8 G ene Silencing by DNA Interference in Fern Gametophytes. . . . . . . . . . . . . . 1 19
Masamitsu W ada and H idenori T suboi
9 I nduction of Stable Epigenetic Gene Silencing in Plants
Using a Virus Vector. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Akira K anazawa and Megumi Kasai
10 A Method for Validating MicroRNAs in Plants by miR-RACE. . . . . . . . . . . . . 1 39
Jinggui F ang and X in S un
11 M R VIGS: MicroRNA-Based Virus-Induced Gene Silencing in Plants. . . . . . . 1 47
Weiwei C hen , Q i Z hang , J unhua K ong , Feng H u , B in L i , C haoqun Wu ,
Cheng Q in , P engcheng Z hang , Nongnong S hi , and Yiguo Hong
12 A High-Throughput RNA Interference (RNAi)-Based Approach
Using Hairy Roots for the Study of Plant–Rhizobia Interactions. . . . . . . . . . . 159
Senjuti S inharoy , Catalina I. P islariu , and M ichael K. Udvardi
13 A Functional Genomics Method for Assaying Gene Function
in Phytopathogenic Fungi Through Host-Induced Gene Silencing
Mediated by Agroinfiltration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Vinay Panwar , B rent M cCallum , and Guus B akkeren
vii
viii Contents
14 An Effective and Convenient Method for the Delivery
of Apple Latent Spherical Virus (ALSV)-Based Vectors into Plant Cells
by Agroinoculation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Tatsuya K on and Nubuyuki Yoshikawa
15 V irus-Induced Gene Silencing (VIGS) for Functional Genomics
in Rice Using Rice tungro bacilliform virus (RTBV) as a Vector. . . . . . . . . . . . 201
Ravi K ant , Shweta S harma , and Indranil D asgupta
16 Virus-Induced Gene Silencing of Fiber-Related Genes in Cotton. . . . . . . . . . . 2 19
John R . T uttle , C andace H . H aigler , and D ominique (Niki) Robertson
17 Establishment of an Efficient Virus-Induced Gene Silencing (VIGS)
Assay in Arabidopsis by Agrobacterium-Mediated Rubbing Infection. . . . . . . . 235
Ana Marcia E . d e A. Manhães , M arcos V . V. de Oliveira , and Libo Shan
18 V irus-Induced Gene Silencing as a Scalable Tool
to Study Drought Tolerance in Plants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Gavin M. G eorge , M ichael E. R uckle , and James R. L loyd
19 VIGS for Dissecting Mechanisms Involved in the Symbiotic Interaction
of Microbes with Plants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Mette Grønlund
20 Construction of a Cotton VIGS Library for Functional Genomics Study. . . . . 2 67
Maoying L i , Fangjun L i , and Ping H e
21 S ynthetic Gene Complementation to Determine Off-Target Silencing. . . . . . . 2 81
Dhirendra Kumar
22 Construction of Mismatched Inverted Repeat (IR) Silencing Vectors
for Maximizing IR Stability and Effective Gene Silencing in Plants . . . . . . . . . 295
M. E. Chrissie R ey , Johan Harmse , Sarah H . Taylor , P atrick Arbuthnot ,
and Marc S . W einberg
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 05
Contributors
FIROZ AHMED • Center for Genomics and Systems Biology , N ew York University , N ew York ,
NY , U SA ; Plant Biology Division, T he Samuel Roberts Noble Foundation , A rdmore ,
OK, U SA
FRANCISCO J. L . ARAGÃO • Embrapa Recursos Genéticos e Biotecnologia , Brasília , D F , B razil ;
Departamento de Biologia Celular, Universidade de Brasília , B rasília , DF, Brazil
PATRICK A RBUTHNOT • School of Molecular and Cell Biology , University of the Witwatersrand ,
Johannesburg, South Africa
GUUS BAKKEREN • Agriculture and Agri-Food Canada, Pacifi c Agri-Food Research Centre ,
Summerland, BC, C anada
WEIWEI C HEN • Research Centre for Plant RNA Signaling, College of Life
and Environmental Sciences, H angzhou Normal University , H angzhou, C hina
XINBIN DAI • Plant Biology Division, T he Samuel Roberts Noble Foundation , A rdmore ,
OK, USA
INDRANIL D ASGUPTA • Department of Plant Molecular Biology , U niversity of Delhi South
Campus , N ew Delhi, India
JINGGUI F ANG • College of Horticulture , Nanjing Agricultural University , N anjing,
Jiangsu, P R China
GAVIN M. G EORGE • Department of Biology, ETH Zurich, Zurich, Switzerland
METTE GRØNLUND • Department of Chemical and Biochemical Engineering, Technical
University of Denmark , Roskilde , D enmark ; Department of Plant and Environmental
Sciences, U niversity of Copenhagen , F rederiksberg, D enmark
HUI-SHAN GUO • State Key Laboratory of Plant Genomics, Institute of Microbiology,
Chinese Academy of Sciences , B eijing, China ; N ational Center for Plant Gene Research,
Institute of Microbiology, Chinese Academy of Sciences , B eijing, C hina
CANDACE H . HAIGLER • Department of Crop Science, N orth Carolina State University ,
Raleigh , N C, U SA ; D epartment of Plant and Microbial Biology, North Carolina
University , R aleigh, NC, USA
JOHAN H ARMSE • School of Molecular and Cell Biology , U niversity of the Witwatersrand ,
Johannesburg, S outh Africa
PING HE • Department of Biochemistry and Biophysics, Institute for Plant Genomics
and Biotechnology, Texas A&M University , C ollege Station, T X , U SA
YIGUO HONG • Research Centre for Plant RNA Signaling, College of Life
and Environmental Sciences, Hangzhou Normal University , H angzhou, C hina ;
School of Life Sciences, University of Warwick , Coventry , U K
FENG HU • Research Centre for Plant RNA Signaling, College of Life and Environmental
Sciences, Hangzhou Normal University , Hangzhou, C hina
ABDULRAZAK B. IBRAHIM • Embrapa Recursos Genéticos e Biotecnologia , B rasília, DF,
Brazil ; D epartamento de Biologia Celular, Universidade de Brasília , B rasília , D F,
Brazil ; D epartment of Biochemistry , A hmadu Bello University , Z aria , N igeria
YUN JIN • State Key Laboratory of Plant Genomics, Institute of Microbiology, C hinese
Academy of Sciences , Beijing, C hina ; N ational Center for Plant Gene Research,
Institute of Microbiology, Chinese Academy of Sciences , B eijing, C hina
AKIRA KANAZAWA • Research Faculty of Agriculture , H okkaido University , S apporo, J apan
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