Rice Functional Genomics: Challenges, Progress and Prospects

Edited by Upadhyaya, Narayana M. 
Springer  2007  

Hardcover  500 pp  ISBN 9780387489032      £146.00
Rice has been chosen as the model cereal for functional genomics by the international scientific community not only because it is a major global food crop but also because of its small genome, the ease with which it can be transformed, its well understood genetics with detailed genome physical maps and dense molecular markers, and the existence of great similarities in gene sequence, gene structure, gene order and gene function among all the cereals and grasses. Genes identified in rice as being important agronomically are also important in other cereals, and any understanding of rice genes is directly applicable to other cereals.

The book covers the whole spectrum of rice functional genomics. The contributed chapters reflect the collective wisdom of more than 70 leading scientists working in this emerging and fascinating area of science. In addition to overviews of the current status of genome sequencing and annotation, various chapters describe the tools and resources being developed worldwide such as expressed sequence tags (ESTs), full-length cDNAs, gene expression profiles (transcriptome, proteome and metabolome), chemical- and radiation-induced mutants, TILLING resources, insertional knockout mutants (T-DNA, transposon and retrotransposon) and activation tags. Exploitation of naturally occurring alleles, Oryza map alignments, gene targeting by homologous recombination and gene silencing by RNAi as well as the application of functional genomics tools for crop improvement and the power of comparative genomics are covered in separate chapters. Various bioinformatics tools and resources pertinent to rice functional genomics are also described and discussed. It is hoped that scientists involved in all aspects of rice research will find this book useful as it spans the divide between molecular biology and plant improvement.

Of interest to researchers, institutes, and professors in Plant Science, Genetic Engineering, and Food Sciences


1 Introduction Narayana M. Upadhyaya and Elizabeth S. Dennis
2 Rice Genome Sequence: The Foundation for Understanding Takashi Matsumoto, Rod A. Wing, Bin Han and Takuji Sasaki
3 Rice Genome Annotation: Beginnings of Functional Genomics, Takeshi Itoh
4 Genome-Wide RNA Expression Profiling in Rice , Shoshi Kikuchi, Guo-Liang Wang, and Lei Li
5 Rice Proteomics: A Step Toward Functional Analysis, Setsuko Komatsu
6 Metabolomics: Enabling Systems-Level Phenotyping in Rice Functional Genomics , Lee Tarpley and Ute Roessner
7 Use of Naturally Occurring Alleles for Crop Improvement , Anjali S. Iyer-Pascuzzi, Megan T. Sweeney, Neelamraju Sarla, and Susan R. McCouch
8 Chemical- and Irradiation-Induced Mutants and TILLING, Ramesh S. Bhat, Narayana M. Upadhyaya, Abed Chaudhury, Chitra Raghavan, Fulin Qiu, Hehe Wang, Jianli Wu, Kenneth McNally, Hei Leung, Brad Till, Steven Henikoff and Luca Comai
9 T-DNA Insertion Mutants as a Resource for Rice Functional Genomics, Emmanuel Guiderdoni, Gynheung An, Su-May Yu, Yue-ie Hsing and Changyin Wu
10 Transposon Insertional Mutants: A Resource for Rice, Qian-Hao Zhu, Moo Young Eun, Chang-deok Han, Chellian Santhosh Kumar, Andy Pereira, Srinivasan Ramachandran, Venkatesan Sundaresan, Andrew L. Eamens, Narayana M. Upadhyaya and Ray Wu
11 Gene Targeting by Homologous Recombination for Rice, Shigeru Iida, Yasuyo Johzuka-Hisatomi, and Rie Terada
12 RNA Silencing and Its Application in Functional Genomics, Shaun J. Curtin, Ming-Bo Wang, John M. Watson, Paul Roffey, Chris L. Blanchard, and Peter M. Waterhouse
13 Activation Tagging Systems in Rice, Alexander A.T. Johnson, Su-May Yu, and Mark Tester
14 Informatics Resources for Rice Functional Genomics , Baltazar A. Antonio, C. Robin Buell, Yukiko Yamazaki, Immanuel Yap, Christophe Perin, and Richard Bruskiewich
15 The Oryza Map Alignment Project (OMAP): A New Resource Oryza, Rod A. Wing, Hye-Ran Kim, Jose Luis Goicoechea, Yeisoo Yu, Dave Kudrna, Andrea Zuccolo, Jetty Siva S. Ammiraju, Meizhong Luo, Will Nelson, Jianxin Ma, Phillip SanMiguel, Bonnie Hurwitz, Doreen Ware, Darshan Brar, David Mackill, Cari Soderlund, Lincoln Stein and Scott Jackson
16 Application of Functional Genomics Tools for Crop , Motoyuki Ashikari, Makoto Matsuoka and Masahiro Yano
17 From Rice to Other Cereals: Comparative , Richard Cooke, Benoit Piégu, Olivier Panaud, Romain Guyot, Jérome Salse, Catherine Feuillet and Michel Delseny
Sequence Annotation

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