Rice Protocols

With the completion of a finished rice genome sequence, increasing efforts have focused on functional characterization of rice genes, elucidation of the underlying mechanisms involved in major agronomic traits (e.g., high yield, grain quality, abiotic stress tolerance, and disease resistance), and the subsequent translation of genomic knowledge into agricultural productivity via molecular breeding and improved cultural practice. To meet increasing interest in this field, Rice Protocols has been compiled to provide a series of core techniques and approaches commonly used in studying rice molecular biology and functional genomics. These approaches include genetic and molecular techniques such as artificial hybridization, fluorescence in situ hybridization, generation and characterization of chemical and T-DNA insertional mutants, quantitative trait loci (QTLs) analysis and map-based cloning, site-specific transgene integration, and artificial microRNA-mediated gene silencing, along with a variety of “omics” techniques.  Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and easy to use, Rice Protocols will prove useful for both beginners and experienced researchers whether they are molecular biologists who want to study rice plants or rice researchers who are interested in learning molecular techniques.

1. Rice Artificial Hybridization for Genetic Analysis

            Xueyan Sha

2. Fluorescence In Situ Hybridization Techniques for Cytogenetic and Genomic Analyses

            Jason G. Walling, Wenli Zhang, and Jiming Jiang

3. Generation of Rice Mutants by Chemical Mutagenesis

            Thomas H. Tai

4. TILLING and Ecotilling for Rice

            Jennifer L. Cooper, Steven Henikoff, Luca Comai, and Bradley J. Till

5. Functional Characterization of Rice Genes Using a Gene-Indexed T-DNA Insertional Mutant Population

            Ki-Hong Jung and Gynheung An

6. QTL Analysis and Map-Based Cloning of Salt Tolerance Gene in Rice

            Ji-Ping Gao and Hong-Xuan Lin

7. Site-Specific Gene Integration in Rice

            Vibha Srivastava

8. Transcriptome Profiling Analysis Using Rice Oligonucleotide Microarrays

            Ki-Hong Jung and Pamela C. Ronald

9. Cloning of Small RNAs for the Discovery of Novel MicroRNAs in Rice

            Guru Jagadeeswaran and Ramanjulu Sunkar

10. Global Identification of Small RNA Targets in Rice by Sequencing Sliced Ends of Messenger RNAs

            Yong-Fang Li and Ramanjulu Sunkar

11. Artificial MicroRNAs for Specific Gene Silencing in Rice

            Norman Warthmann, Stephan Ossowski, Rebecca Schwab, and Detlef Weigel

12. Rice Proteomic Analysis: Sample Preparation to Protein Identification

            Ganesh Kumar Agrawal, Nam-Soo Jwa, Young-Ho Jung, Sun Tae Kim, Dea-Wook Kim, Kyoungwon Cho, Junko Shibato, and Randeep Rakwal

13. Quantification of Jasmonic and Salicylic Acids in Rice Seedling Leaves

            Kyoungwon Cho, Oksoo Han, Shigeru Tamogami, Junko Shibato, Akihiro Kubo, Ganesh Kumar Agrawal, and Randeep Rakwal

14. Analysis of Insect-Induced Volatiles from Rice

            Nan Zhao, Xiaofeng Zhuang, Gitika Shrivastava, and Feng Chen

15. Phenotypic and Physiological Evaluation for Drought and Salinity Stress Responses in Rice

            Utlwang Batlang, Niranjan Baisakh, Madana M.R. Ambavaram, and Andy Pereira

16. Phenotypic, Physiological, and Molecular Evaluation of Rice Chilling Stress Response at the Vegetative Stage

            Benildo G. de los Reyes, Song Joong Yun, Venura Herath, Fuyu Xu, Myoung Ryoul Park, Jeong Il Lee, and Ki Young Kim

17. Analysis of Rice Root Hair Morphology Using Cryo-Scanning Electron Microscopy

            Zhiming Yu, Hanmin Chen, Yanli Tong, and Ping Wu

18. Inoculation and Virulence Assay for Bacterial Blight and Bacterial Leaf Streak of Rice

            Bing Yang and Adam Bogdanove

19. Inoculation and Scoring Methods for Rice Sheath Blight Disease

            Yulin Jia, Guangjie Liu, Dong-Soo Park, and Yinong Yang

20. Molecular Approaches to Improve Rice Abiotic Stress Tolerance

            Junya Mizoi and Kazuko Yamaguchi-Shinozaki

21. Molecular Strategies to Improve Rice Disease Resistance

            Emily E. Helliwell and Yinong Yang

22. Molecular Strategies to Engineer Transgenic Rice Seed Compartments for Large-Scale Production of Plant-Made Pharmaceuticals

            Trevor Greenham and Illimar Altosaar

Appendix: Genomic and Bioinformatic Resources for Rice Research

            Wenhua Liu, Kabin Xie, and Yinong Yang

            Vibha Srivastava