Legume Genomics: Methods and Protocols

323 Pages·2013·5.1 MB·English

by  Steven B. Cannon (auth.), Ray J. Rose (eds.)

Methods in
Molecular Biology 1069
Ray J. Rose Editor
Legume
Genomics
Methods and Protocols
M M B ™
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

Legume Genomics
Methods and Protocols
Edited by
Ray J. Rose
Environmental and Life Sciences, CILR, The University of Newcastle, Callaghan, NSW, Australia
Editor
Ray J. Rose
Environmental and Life Sciences,
CILR, The University of Newcastle
Callaghan, NSW, Australia
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-62703-612-2 ISBN 978-1-62703-613-9 (eBook)
DOI 10.1007/978-1-62703-613-9
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Pref ace
Legumes, with their nitrogen-fi xing capacity, are the third largest family of fl owering plants
and are critical for agricultural and ecological sustainability. They are important for food,
feed, human nutrition, bioenergy, and industrial purposes.
Genomics can now be readily applied to legumes with the increasing sequence informa-
tion and analysis tools available. Model legumes such as Medicago and Lotus, as well as
soybean and pea, have provided much of this information, which is now being applied to
the legume family more broadly. This book provides a consideration of a range of methods
and protocols, including available resources, used to discover new genes and to understand
genes and their interactions.
The book is targeted to plant molecular biologists, molecular breeders, plant physiolo-
gists and biochemists, developmental biologists, and those interested in plant–microbe
interactions. The chapters are suitable for those already in the fi eld, those plant scientists
entering the fi eld, and graduate students. Legume genomics offers a potentially productive
fi eld for new investigators.
The fi rst chapter provides an overview of legume genomes followed by chapters on
techniques used in genome characterization and analysis. Chapters then follow on tran-
scriptome analysis and miRNA identifi cation and analysis. Also considered are a range of
resources available for forward and reverse genetics in Medicago, Lotus, and pea. These
approaches have an increasing role in identifying gene function. Molecular markers devel-
oped through genomics are also considered. A number of chapters deal with a range of
transformation strategies used to investigate gene function using transformed roots, stable
plant transformation, and transient expression, and there is a guide to investigating subcel-
lular localization using fl uorescent fusion proteins. There are chapters on proteomics, phos-
phoproteomics, and metabolomics where, increasingly, mass spectrometry developments
provide new approaches for investigating the products of genes—the proteins and the
metabolism they regulate and support.
Callaghan, NSW , Australia Ray J. Rose
v

Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 The Model Legume Genomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Steven B. Cannon
2 Fluorescent In Situ Hybridization (FISH) on Pachytene Chromosomes
as a Tool for Genome Characterization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
René Geurts and Hans de Jong
3 Targeted Mutagenesis for Functional Analysis of Gene
Duplication in Legumes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Shaun J. Curtin, Justin E. Anderson, Colby G. Starker, Nicholas J. Baltes,
Dhananjay Mani, Daniel F. Voytas, and Robert M. Stupar
4 RNA-Seq for Transcriptome Analysis in Non-model Plants. . . . . . . . . . . . . . 43
Rohini Garg and Mukesh Jain
5 Functional Analysis of Legume Genome Arrays. . . . . . . . . . . . . . . . . . . . . . . . 59
Nicolas Goffard and Georg Weiller
6 Genome-Wide Identification of MicroRNAs in Medicago truncatula
by High-Throughput Sequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Tian-Zuo Wang and Wen-Hao Zhang
7 Determining Abundance of MicroRNAs and Other Small
RNAs in Legumes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Cecilia Contreras-Cubas, Alejandra A. Covarrubias, and José Luis Reyes
8 Forward Genetics Screening of Medicago truncatula Tnt1
Insertion Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Juan Carlos Serrani Yarce, Hee-Kyung Lee, Million Tadege,
Pascal Ratet, and Kirankumar S. Mysore
9 Reverse Genetics in Medicago truncatula Using a TILLING
Mutant Collection.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Maria Carelli, Ornella Calderini, Francesco Panara, Andrea Porceddu,
Ilaria Losini, Pietro Piffanelli, Sergio Arcioni, and Carla Scotti
10 High-Throughput and Targeted Genotyping
of Lotus japonicus LORE1 Insertion Mutants. . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Dorian Fabian Urbański, Anna Małolepszy, Jens Stougaard,
and Stig Uggerhøj Andersen
11 Isolation and Forward Genetic Analysis of Developmental
Genes in Pea. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
James L. Weller, Valérie F.G. Hecht, and Frances C. Sussmilch
vii
viii Contents
12 Gene Silencing in Medicago truncatula Roots Using RNAi . . . . . . . . . . . . . . . 163
Daniela S. Floss, Alexa M. Schmitz, Colby G. Starker,
J. Stephen Gantt, and Maria J. Harrison
13 Molecular Markers for Genetics and Plant Breeding: The MFLP
Marker System and Its Application in Narrow-Leafed
Lupin (Lupinus angustifolius) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Islam Shahidul, Huaan Yang, and Guijun Yan
14 Stable Transformation of Medicago truncatula cv. Jemalong for Gene
Analysis Using Agrobacterium tumefaciens . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Youhong Song, Kim E. Nolan, and Ray J. Rose
15 Transient Gene Expression in Medicago truncatula
Leaves via Agroinfiltration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
Kelsey Picard, Robyn Lee, Roger Hellens, and Richard Macknight
16 Subcellular Localization of Transiently Expressed Fluorescent
Fusion Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
David A. Collings
17 Proteomics and the Analysis of Nodulation. . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Nijat Imin
18 Phosphoproteomic Analysis of Peptides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Mark A. Baker
19 Plant Metabolomics: From Experimental Design
to Knowledge Extraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
Amit Rai, Shivshankar Umashankar, and Sanjay Swarup
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
Contributors
STIG UGGERHØJ ANDERSEN • Department of Molecular Biology and Genetics, Centre
for Carbohydrate Recognition and Signalling, Aarhus University , Aarhus , Denmark
JUSTIN E. ANDERSON • Department of Agronomy and Plant Genetics , University of
Minnesota , St. Paul, MN , USA
SERGIO ARCIONI • Consiglio Nazionale delle Ricerche (CNR) - Istituto di Genetica Vegetale ,
Perugia, Italy
MARK A. BAKER • Biological Sciences, Priority Research Centre in Reproductive Science ,
School of Environmental and Life Sciences, University of Newcastle , Callaghan,
NSW , Australia
NICHOLAS J. BALTES • Department of Genetics, Cell Biology, and Development, University
of Minnesota , Minneapolis, MN , USA ; Center for Genome Engineering, University of
Minnesota , Minneapolis, MN , USA
ORNELLA CALDERINI • Consiglio Nazionale delle Ricerche (CNR) - Istituto di Genetica
Vegetale , Perugia, Italy
STEVEN B. CANNON • Agricultural Research Service , United States Department of
Agriculture , Ames , IA , USA
MARIA CARELLI • Consiglio per la Ricerca e la sperimentazione in Agricoltura (C.R.A.) -
Centro di ricerca per le Produzioni Foraggere e Lattiero-casearie , Lodi , Italy
DAVID A. COLLINGS • Biomolecular Interaction Centre , School of Biological Sciences,
The University of Canterbury , Christchurch, New Zealand
CECILIA CONTRERAS-CUBAS • Departamento de Biología Molecular de Plantas, Instituto de
Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca, Mexico
ALEJANDRA A. COVARRUBIAS • Departamento de Biología Molecular de Plantas, Instituto de
Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca, Mexico
SHAUN J. CURTIN • Department of Agronomy and Plant Genetics , University of Minnesota ,
St. Paul, MN , USA
DANIELA S. FLOSS • Boyce Thompson Institute for Plant Research , Ithaca , NY , USA
J. STEPHEN GANTT • Department of Plant Biology , University of Minnesota , St. Paul,
MN , USA
ROHINI GARG • National Institute of Plant Genome Research , New Delhi, India
RENÉ GEURTS • Laboratory of Molecular Biology , Wageningen University , Wageningen,
The Netherlands
NICOLAS GOFFARD • Plant Science Division, Research School of Biology, College of Medicine,
Biology and Environment, The Australian National University , Canberra, ACT ,
Australia ; Computational Biology & Bioinformatics, IP&Science, Thomson Reuters ,
London, UK
MARIA J. HARRISON • Boyce Thompson Institute for Plant Research , Ithaca , NY , USA
VALÉRIE F. G. HECHT • School of Plant Science, University of Tasmania , Hobart ,
TAS , Australia
ix