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QTL Analysis in Plant Breeding 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 Jurˇícˇek, and Timothy C. Hall 28 Plant RNAi
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