Molecular Techniques in Crop Improvement: 2nd Edition

759 Pages·2009·9.35 MB·English

by  Maria J. Asins

Molecular Techniques in Crop Improvement
S. Mohan Jain D.S. Brar
●
Editors
Molecular Techniques
in Crop Improvement
2nd Edition
Editors
S. Mohan Jain D.S. Brar
Department of Applied Biology International Rice Research
University of Helsinki Institute (IRRI)
Finland Social Sciences Division
[email protected] Metro Manila
Philippines
[email protected]
ISBN 978-90-481-2966-9 e-ISBN 978-90-481-2967-6
DOI 10.1007/978-90-481-2967-6
Springer Dordrecht Heidelberg London New York
Library of Congress Control Number: 2009929346
© Springer Science+Business Media B.V. 2010
No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by
any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written
permission from the Publisher, with the exception of any material supplied specifically for the purpose
of being entered and executed on a computer system, for exclusive use by the purchaser of the work.
Printed on acid-free paper
Springer is part of Springer Science+Business Media (www.springer.com)
Preface
Most of the plant breeding programs aim to increase yield, disease and insect
resistance, abiotic stress tolerance and to improve quality characteristics. The value
of new plant breeding products and varieties in increasing food production has been
demonstrated time and again. To meet growing need of ever increasing human
population, we need to enhance food production for sustaining food supply.
Furthermore, several biotic and abiotic stresses continue to threaten crop productiv-
ity. Moreover with urbanization, land for cultivation is shrinking and several envi-
ronment concerns involving excessive use of fertilizers and agro-chemicals, soil
and water pollution including water scarcity are key issues in increasing crop pro-
ductivity and food sustainability. Plant breeders therefore, has the major challenge
how to increase crop productivity with limited land, limited water, limited chemi-
cals and limited labour particularly in the context of global climate changes. In the
genomics era, advances in molecular biology have opened new opportunities to
accelerate plant breeding processes and in overcoming some of the above con-
straints limiting crop productivity. Molecular markers have become important tools
in the hands of plant breeders in marker assisted breeding and for enhancing the
selection efficiency for various agronomic traits in precision ‘plant’ breeding. The
isolation, cloning and moving of genes from diverse biological sources into plant
genomes holds promise to broaden the gene pool of crops and develop new plant
varieties for specific traits that determine yield, quality, and resistance to biotic and
abiotic stresses. New genomics tools will be of great value to support conventional
breeding for sustainable food production especially under the climate change and
meet demand of ever growing human population.
The first edition of this book, “Molecular techniques in crop improvement”
published in 2002 covered various topics related to molecular markers and their
application in plant breeding. Since then, major advances have been made in
molecular tagging of genes/QTLs governing complex agronomic traits, identifica-
tion of candidate genes and in applying marker assisted breeding for tolerance to
biotic and abiotic stresses and quality traits. Recent advances in transgenic tech-
nologies, genome sequencing and functional genomics offer tremendous opportuni-
ties to support plant breeding programs. Therefore, we are encouraged to cover
recent advances and come out with the second edition of this book. In this edition
we have included 31 chapters, which are divided into four parts. Part I is on Plant
vi Preface
Breeding in the genomic era and has four chapters. Part II deals with Molecular
Markers and their application and contains six chapters. Eleven chapters dealing
with different aspects of Genomics are covered in Part III. The remaining ten chap-
ters dealing with Transgenic Technologies are dealt in Part IV. Some of the major
topics covered in this book are on: QTL analysis, comparative genomics, functional
genomics, bioinformatics, gene-based marker systems, automation of DNA marker
analysis, molecular markers for abiotic and biotic stresses as well as for germ
plasm conservation, gene pyramiding, gene stacking, gene silencing, TILLING,
CISGENESIS, microarray, metablomics, proteomics, transcriptomics, microRNAs,
marker-free transformation, Plant RNAi, and floriculture genetic engineering. All
manuscripts were peer reviewed and revised accordingly. We are thankful to all
reviewers for sparing precious time to review manuscripts, and that certainly helped
to improve their quality.
This edition will certainly benefit plant breeders, biotechnologists, and molecu-
lar biologists, and an excellent source to provide advanced knowledge of molecular
biology to post graduate students involved in biotechnology and plant breeding
research.
We take this opportunity to express our gratitude to Springer publisher for giving
us this opportunity to bring out the second edition of this book.
S. Mohan Jain
D.S. Brar
Contents
Part I Plant Breeding in the Genomics Era
1 QTL Analysis in Plant Breeding ........................................................... 3
Maria J. Asins, Guillermo P. Bernet, Irene Villalta,
and Emilio A. Carbonell
2 Comparative Genomics in Crop Plants ............................................... 23
Mehboob-ur-Rahman and Andrew H. Paterson
3 Functional Genomics For Crop Improvement .................................... 63
Seedhabadee Ganeshan, Pallavi Sharma, and Ravindra N. Chibbar
4 Bioinformatics Tools for Crop Research and Breeding ...................... 97
Jayashree B and Dave Hoisington
Part II Molecular Markers and Their Application
5 Gene-Based Marker Systems in Plants: High Throughput
Approaches for Marker Discovery and Genotyping ........................... 119
Rajeev K Varshney
6 Automation of DNA Marker Analysis for Molecular
Breeding in Crops .................................................................................. 143
Christophe Dayteg and Stine Tuvesson
7 Pyramiding Genes for Enhancing Tolerance
to Abiotic and Biotic Stresses ................................................................ 163
Raveendran Muthurajan and Ponnuswami Balasubramanian
8 Application of Molecular Markers for Breeding
Disease Resistant Varieties in Crop Plants .......................................... 185
Ana M. Torres
viii Contents
9 Molecular Markers Based Approaches for Drought Tolerance......... 207
Deepmala Sehgal and Rattan Yadav
10 Molecular Markers for Characterizing and Conserving
Crop Plant Germplasm ......................................................................... 231
G. Barcaccia
Part III Genomics
11 Rice Genomics ........................................................................................ 257
Narayana M. Upadhyaya and Elizabeth S. Dennis
12 Genomics for Wheat Improvement ...................................................... 281
Michael G. Francki
13 TILLING for Mutations in Model Plants and Crops ......................... 307
Zerihun Tadele, Chikelu MBA, and Bradley J. Till
14 Microarray Analysis for Studying the Abiotic Stress
Responses in Plants ................................................................................ 333
Motoaki Seki, Masanori Okamoto, Akihiro Matsui, Jong-Myong Kim,
Yukio Kurihara, Junko Ishida, Taeko Morosawa, Makiko Kawashima,
Taiko Kim To, and Kazuo Shinozaki
15 Roles of MicroRNAs in Plant Abiotic Stress ....................................... 357
Ricky Lewis, Venugopal Mendu, David Mcnear, and Guiliang Tang
16 Molecular Tools for Enhancing Salinity Tolerance in Plants ............. 373
Jesus Cuartero, Maria C. Bolarin, Vicente Moreno, and Benito Pineda
17 DNA Microarray as Part of a Genomic-Assisted
Breeding Approach ................................................................................ 407
Eva Vincze and Steve Bowra
18 Unravelling Gene Function Through Mutagenesis ............................. 437
Andrea Hricová, Pedro Robles, and Víctor Quesada
19 Techniques in Plant Proteomics ............................................................ 469
Ludovít Škultéty, Maxym Danchenko, Anna Pret’ová,
and Martin Hajduch
20 Metabolomics: Novel Tool for Studying
Complex Biological Systems .................................................................. 493
Federica Maltese and Robert Verpoorte
Contents ix
21 Transcriptomic Analysis of Multiple Enviornmental
Stresses in Plants .................................................................................... 511
Niranjani Jambunathan, Michael Puckette,
and Ramamurthy Mahalingam
Part IV Transgenic Technologies
22 Marker-Free Targeted Transformation ............................................... 527
Hiroyasu Ebinuma and Kazuya Nanto
23 Promoter Trapping in Plants Using T-DNA Mutagenesis .................. 545
R. Srinivasan and Dipnarayan Saha
24 Plant Genome Engineering Using Zinc Finger Nucleases .................. 579
Sandeep Kumar and William F. Thompson
25 Cisgenesis ................................................................................................ 591
Evert Jacobsen and Henk J. Schouten
26 Gene Stacking ......................................................................................... 613
E. Douglas and C. Halpin
27 Gene Silencing ........................................................................................ 631
Sunee Kertbundit, Miloslav Juˇrícˇek, and Timothy C. Hall
28 Plant RNAi and Crop Improvement .................................................... 653
Masayuki Isshiki and Hiroaki Kodama
29 Metabolomics in Fruit Development .................................................... 675
Kati Hanhineva and Asaph Aharoni
30 Genetic Engineering in Floriculture ..................................................... 695
Yoshikazu Tanaka and Ryutaro Aida
31 Transgenesis and Genomics in Forage Crops ...................................... 719
Toshihiko Yamada, Ken-ichi Tamura, Xun Wang,
and Yukiko Aoyagi
Author Index................................................................................................... 745
Part I
Plant Breeding in the Genomics Era