Rice Functional Genomics

Challenges, Progress and Prospects

Editors: Upadhyaya, Narayana M. (Ed.)

  • Details rice functional genomics
  • Takes a multi-pronged genome-wide approach using structural similarities, expression profiles, and mutant phenotypes
  • Includes the current status of genome sequencing and annotation
  • Covers various tools and resources being developed worldwide in the form of expressed sequence tags (ESTs), full-length cDNA, gene expression profiles and gene tagging (knockouts and activation tags)
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About this book

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.

Rice Functional Genomics - Challenges, Progress and Prospects 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.

About the Editor:

Narayana M. Upadhyaya is currently a Principal Research Scientist at CSIRO Plant Industry, Canberra, Australia and leads the group working on Rice Functional Genomics. Previously, he pioneered research into the sequencing of the Rice Ragged Stunt Oryzavirus (RRSV) genome and produced RRSV genome-based synthetic resistance gene constructs while working on a Rockefeller Foundation-funded Rice Biotechnology project (1990-1997) which involved international collaboration. He has been the principal investigator in the bilateral science and technology collaborative research with China (1997-2000). He was instrumental in developing and setting up the rice transformation facility at CSIRO Plant Industry not only for RRSV research but also for other research projects where rice has been used as a model system. He has developed the T-DNA double right border (DRB) vector technology for generating selectable marker-free (SMF) transgenic plants. Since then he has developed a research project on "Rice Functional Genomics" (funded by Australia’s RIRDC and the NSW Centre for Agricultural Genomics) aimed at determining the function of rice genes using an insertional mutagenesis approach. The tools and resources being developed in the group are internationally competitive and as a result CSIRO Plant Industry has become an active member of the International Rice Functional Genomics Consortium. Dr. Upadhyaya has 50 refereed papers, 11 invited presentations and over 50 conference presentations to his credit.

About the authors

Narayana M. Upadhyaya is currently a Principal Research Scientist at CSIRO Plant Industry, Canberra, Australia and leads the group working on Rice Functional Genomics. Previously, he pioneered research into the sequencing of the Rice Ragged Stunt Oryzavirus (RRSV) genome and produced RRSV genome-based synthetic resistance gene constructs while working on a Rockefeller Foundation-funded Rice Biotechnology project (1990-1997) which involved international collaboration. He has been the principal investigator in the bilateral science and technology collaborative research with China (1997-2000). He was instrumental in developing and setting up the rice transformation facility at CSIRO Plant Industry not only for RRSV research but also for other research projects where rice has been used as a model system. He has developed the T-DNA double right border (DRB) vector technology for generating selectable marker-free (SMF) transgenic plants. Since then he has developed a research project on "Rice Functional Genomics" (funded by Australia’s RIRDC and the NSW Centre for Agricultural Genomics) aimed at determining the function of rice genes using an insertional mutagenesis approach. The tools and resources being developed in the group are internationally competitive and as a result CSIRO Plant Industry has become an active member of the International Rice Functional Genomics Consortium. Dr. Upadhyaya has 50 refereed papers, 11 invited presentations and over 50 conference presentations to his credit.

Reviews

From the reviews:

"This book represents an excellent set of (reviewed) reviews that explains what is happening in the world of rice genomic research now. … This is a useful book for genetic resources workers because understanding the way in which the genome works is generating huge numbers of mutants required for forward (from phenotype to genome sequence) and reverse genetics (genome sequence to phenotype)." (D. Vaughan, Genetic Resources and Crop Evolution, Vol. 54, 2007)


Table of contents (5 chapters)

  • Rice Genome Sequence: The Foundation for Understanding the Genetic Systems

    Takashi Matsumoto, Rod A. Wing, Bin Han, et al.

    Pages 5-20

  • T-DNA Insertion Mutants as a Resource for Rice Functional Genomics

    Emmanuel Guiderdoni, Gynheung An, Su-May Yu, Yue-ie Hsing, Changyin Wu

    Pages 181-221

  • Transposon Insertional Mutants: A Resource for Rice Functional Genomics

    Qian-Hao Zhu, Moo Young Eun, Chang-deok Han, et al.

    Pages 223-271

  • Gene Targeting by Homologous Recombination for Rice Functional Genomics

    Shigeru Iida, Yasuyo Johzuka-Hisatomi, Rie Terada

    Pages 273-289

  • The Oryza Map Alignment Project (OMAP): A New Resource for Comparative Genome Studies within Oryza

    Rod A. Wing, HyeRan 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, Scott Jackson

    Pages 395-409

Buy this book

eBook $229.00
price for USA (gross)
  • ISBN 978-0-387-48914-8
  • Digitally watermarked, DRM-free
  • Included format: PDF
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Hardcover $299.00
price for USA
  • ISBN 978-0-387-48903-2
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
Softcover $299.00
price for USA
  • ISBN 978-1-4419-2375-2
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
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Bibliographic Information

Bibliographic Information
Book Title
Rice Functional Genomics
Book Subtitle
Challenges, Progress and Prospects
Editors
  • Narayana M. Upadhyaya
Copyright
2007
Publisher
Springer-Verlag New York
Copyright Holder
Springer-Verlag New York
eBook ISBN
978-0-387-48914-8
DOI
10.1007/0-387-48914-2
Hardcover ISBN
978-0-387-48903-2
Softcover ISBN
978-1-4419-2375-2
Edition Number
1
Number of Pages
XXXIV, 500
Number of Illustrations and Tables
59 b/w illustrations
Topics