Plant-Pathogen Interactions: Methods and Protocols, Second Edition expands upon the first edition with current, detailed protocols for the study of plant pathogen genome sequences. It contains new chapters on techniques to help identify and characterize effectors and to study their impacts on host immunity and their roles in pathogen biology. Additional chapters focus on protocols to identify avirulence and resistance genes, investigate the roles of effector targets and other defence-associated proteins in plant immunity. 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 cutting-edge, Plant-Pathogen Interactions: Methods and Protocols, Second Edition seeks to aid scientists in the further study of plant immunity.

Presents current up-to-date methodologies

Part 1:  Bioinformatics 1.             Galaxy as a Platform for Identifying Candidate Pathogen EffectorsPeter J. A. Cock and Leighton Pritchard2.             Bioinformatic analysis of expression data to identify effector candidatesAdam J. Reid and  John T. Jones 3.             Two-dimensional data binning for the analysis of genome architecture in filamentous plant pathogens and other eukaryotesDiane G.O. Saunders, Joe Win, Sophien Kamoun, and  Sylvain Raffaele4.             On The Statistics Of Identifying Candidate Pathogen EffectorsLeighton Pritchard amd David Broadhurst Part 2:  Cell Biology 5.      High-throughput imaging of plant immune responsesMartina Beck, Ji Zhou, Christine Faulkner, and Silke Robatzek6.      In vivo protein-protein interaction studies with BiFC: conditions, cautions and caveatsPetra Boevink, Hazel McLellan, Tatyana Bukharova, Stefan Engelhardt, and  Paul R.J. Birch7.      Particle bombardment-mediated transient expression to identify localization signals in plant disease resistance proteins and target sites for the proteolytic activity of pathogen effectorsDaigo Takemoto and David Jones8.      Purification of fungal haustoria from infected plant tissue by flow cytometryDiana P. Garnica and John P. Rathjen Part 3:  From assays of pathogen virulence to effector function 9.      Functional Characterisation of Nematode Effectors in PlantsAxel A. Elling and John T. Jones10.  Silencing of aphid genes by feeding on stable transgenic Arabidopsis thalianaAlexander D. Coleman, Marco Pitino, and Saskia A. Hogenhout 11.  Leaf-disc assay based on transient over-expression in Nicotiana benthamiana to allow functional screening of candidate effectors from aphidsPatricia A. Rodriguez, Saskia A. Hogenhout, and Jorunn I.B. Bos12.  A growth quantification assay for Hyaloperonospora arabidopsidis isolates in Arabidopsis thalianaDaniel F.A. Tomé, Jens Steinbrenner, and Jim L. Beynon13.  Simple quantification of in planta fungal biomassMichael Ayliffe, Sambasivam K Periyannan, Angela Feechan, Ian Dry, Ulrike Schumann, Evans Lagudah, and Anthony Pryor14. Virus-induced Gene Silencing and Agrobacterium Tumefaciens-Mediated Transient Expression in Nicotiana TabacumZhao Zhang and Bart P.H.J. Thomma15.  DIGE-ABPP by click chemistry: Pairwise comparison of serine hydrolase activities from the apoplast of infected plantsTram Ngoc Hong and Renier A.L. van der Hoorn16. A Simple and Fast Protocol for Protein Complex Immunoprecipitation (Co-IP) of Effector-Host Protein ComplexesJens Steinbrenner, Matthew Eldridge, Daniel F.A. Tomé, and Jim L. Beynon17.  An Arabidopsis and Tomato Mesophyll Protoplast System for fast Identification of early MAMP-triggered Immunity-Suppressing EffectorsMalou Fraiture, Xiangzi Zheng, and  Frédéric Brunner18.  Production of RXLR effector proteins for structural analysis by X-ray crystallographyRichard K. Hughes and Mark J. Banfield Part 4:  Methods to identify Resistance genes and avirulence genes 19.  The Dös and Don¿ts of effectoromicsJuan Du and Vivianne G.A.A. Vleeshouwers20.  Protoplast cell death assay to study Magnaporthe oryzae AVR gene function in riceHiroyuki Kanzaki, Kentaro Yoshida, Hiromasa Saitoh, Muluneh Tamiru, and Ryohei Terauchi21.  A Bacterial Type III Secretion Based Delivery System for Functional Assays of Fungal Effectors in CerealsNarayana M. Upadhyaya, Jeffery G. Ellis, and Peter N. Dodds22.  Capture arrays to annotate resistance genes in plant genomes and to accelerate plant resistance gene discoveryFlorian Jupe, Xinwei Chen, Walter Verweij, Kamil Witek, Jonathan D.G. Jones,  and Ingo Hein