Plant-Pathogen Interactions : Methods and Protocols

Preface ..............................................................................................................v Contributors ..................................................................................................... ix 1 The Use of Protoplasts to Study Innate Immune Responses .................. 1 Ping He, Libo Shan, and Jen Sheen 2 Marker-Exchange Mutagenesis and Complementation Strategies for the Gram-Negative Bacteria Xanthomonas oryzae pv. oryzae ...................................................... 11 Sang-Won Lee and Pamela C. Ronald 3 Whole-Genome Analysis to Identify Type III-Secreted Effectors .........19 Boris A. Vinatzer and Jean T. Greenberg 4 In planta Expression of Oomycete and Fungal Genes .........................35 Thirumala-Devi Kanneganti, Edgar Huitema, and Sophien Kamoun 5 Use of Nipponbare BAC Clones for Physical Mapping of an R Gene Locus in Rice.............................................................45 Jong-Seong Jeon and Pamela C. Ronald 6 Agrobacterium-Mediated Transformation to Create an Insertion Library in Magnaporthe grisea ........................................................ 57 Sara L. Tucker and Marc J. Orbach 7 Identification of Components in Disease-Resistance Signaling in Arabidopsis by Map-Based Cloning ............................................69 Yuelin Zhang, Jane Glazebrook, and Xin Li 8 Yeast Two-Hybrid Approaches to Dissecting the Plant Defense Response ............................................................79 Mawsheng Chern, Todd Richter, and Pamela C. Ronald 9 Use of Rolling-Circle Amplification for Large-Scale Yeast Two-Hybrid Analyses ......................................................................85 Xiaodong Ding, Yan Zhang, and Wen-Yuan Song 10 Preparative Denaturing Isoelectric Focusing for Enhancing Sensitivity of Proteomic Studies ......................................................99 Antonio Serna-Sanz, Greg Rairdan, and Scott C. Peck 11 Use of Massively Parallel Signature Sequencing to Study Genes Expressed During the Plant Defense Response .............................105 Blake C. Meyers, Christian D. Haudenschild, and Kalyan Vemaraju viii Contents 12 Use of Microarray Analysis to Dissect the Plant Defense Response .........................................................................121 Jane Glazebrook 13 Use of Robust-Long Serial Analysis of Gene Expression to Identify Novel Fungal and Plant Genes Involved in Host–Pathogen Interactions ......................................................131 Malali Gowda, R. C. Venu, Yulin Jia, Eric Stahlberg, Vishal Pampanwar, Carol Soderlund, and Guo-Liang Wang 14 Analysis of Gene Function in Rice Through Virus-Induced Gene Silencing ..............................................................................145 Xin Shun Ding, C. Srinivasa Rao, and Richard S. Nelson 15 Use of RNA Interference to Dissect Defense-Signaling Pathways in Rice ...........................................................................161 Chuansheng Mei, Xiangjun Zhou, and Yinong Yang 16 Virus-Induced Gene Silencing in Plant Roots ...................................173 Isgouhi Kaloshian 17 Methods for Engineering Resistance to Plant Viruses ........................183 Mysore R. Sudarshana, Gourgopal Roy, and Bryce W. Falk 18 Development of Genetically Engineered Resistant Papaya for papaya ringspot virus in a Timely Manner: A Comprehensive and Successful Approach................................. 197 Savarni Tripathi, Jon Suzuki, and Dennis Gonsalves Index ............................................................................................................