Acknowledgments	6
	Contents	7
	Contributors	9
	Roles of Plant Hormones in Plant Resistance and Susceptibility to Pathogens	17
	1 Introduction	17
	2 Flg22 Triggers Auxin-Signaling Repression by Inducing a Specific miRNA	18
	3 Does Auxin Play a Role in Bacterial Pathogenenity?	21
	4 Flg22 Triggers Growth Inhibition of Arabidopsis Seedlings	22
	5 Role of DELLA Proteins in Plant Disease Resistance and Susceptibility	23
	6 Are DELLA Proteins Integrators of Plant Defense Pathways?	24
	References	25
	Canine Genetics Facilitates Understanding of Human Biology	27
	1 Introduction to Dogs and Breeds	27
	2 Mapping Disease Genes in Dogs	28
	3 Canine Breed Relationships	31
	4 Advances in Canine Genomics	32
	5 Mapping Genes for Morphology in the Dog	35
	6 Summary and Future Aims	36
	References	37
	Xanthomonas oryzae pv. oryzae AvrXA21 Activity Is Dependent on a Type One Secretion System, Is Regulated by a Two- Component Regulatory System that Responds to Cell Population Density, and Is Conserved in Other Xanthomonas spp.	41
	1 Detection of Pathogens by Plants and Animal Hosts	42
	2 The PRR XA21 Represents a Large Class of Kinases Predicted to Be Involved in Innate Immunity	44
	3 AVRXA21 Activity Requires a Type One Secretion System	44
	4 The AVRXA21 Pathogen-Associated Molecule Is Conserved in Xanthomonas campestris pv. campestris	47
	5 Cell Density Dependent Expression of Rax Genes	48
	6 Perspective	50
	References	53
	Unraveling the Genetic Mysteries of the Cat: New Discoveries in Feline- Inherited Diseases and Traits	57
	1 Cat Phenotypes	57
	2 Cat Diseases	60
	3 Feline Genetic Resources	63
	4 Reproductive Technologies	64
	5 Future of Cat Genetics	65
	References	66
	APPENDIX: Table references	70
	Variation in Chicken Gene Structure and Expression Associated with Food-Safety Pathogen Resistance: Integrated Approaches to Salmonella Resistance	73
	1 Rationale and Strategies for Uncovering Genetic Resistance to Food- Safety Pathogens in Poultry	73
	2 Genetic Control of Salmonella Resistance in Poultry	77
	3 Conclusions	79
	References	80
	Functional Genomics and Bioinformatics of the Phytophthora sojae Soybean Interaction	83
	1 Introduction	83
	2 Sequencing of Oomycete Genomes	85
	3 Effector Genes in Oomycete Genomes	86
	4 Counter-Play of Plant and Pathogen Genes During Phytophthora Infection of Soybean	89
	References	92
	Canine SINEs and Their Effects on Phenotypes of the Domestic Dog	95
	1 Short Interspersed Elements	95
	2 Merle Patterning	96
	3 A-Tails Are Important	100
	4 Summary	101
	References	101
	Ovine Disease Resistance: Integrating Comparative and Functional Genomics Approaches in a Genome Information- Poor Species	104
	1 Introduction	105
	2 Tools Used to Obtain Candidate Genes 2.1 Resource Flocks for QTL Analysis and Mapping	107
	2.2 Integrated Maps, Comparative Mapping and Meta-analysis	107
	2.3 Association Studies, SNP Chips and LD Mapping	109
	2.4 Microarrays, SELDI-TOF MS and Other High Density Genomic or Proteomic Functional Tools	113
	2.5 Positional Functional Integration	114
	3 An Example: Mapping Genes for Ruminant Fasciolosis	115
	3.1 Resistance to Fasciola	116
	3.2 The Resource Flock for Mapping Fasciolosis Resistance	116
	3.3 Linkage and QTL Analysis for Fasciolosis	117
	3.4 Mapping Fasciolosis QTL in Cattle and Buffalo	120
	3.5 Immunological Characterisation for Functional Positional Integration	120
	3.6 High Density Proteomic and Genomic Functional Screening	122
	3.7 Future Studies and Potential Applications	122
	References	124
	Integrating Genomics to Understand the Marek’s Disease Virus – Chicken Host – Pathogen Interaction	129
	1 Introduction	129
	2 Marek’s Disease	130
	2.1 MD as a Model	131
	2.2 Genetic Resistance	131
	3 Integrating Genomics, Version 1.0 (Before the Genome Sequence)	132
	3.1 Genome-Wide QTL Scans	133
	3.2 Gene Profiling	134
	3.3 VirusÒHost ProteinÒProtein Interaction Screens	134
	4 Integrating Genomics, Version 2.0 (After the Genome Sequence)	136
	4.1 Genome-Wide QTL Scans	136
	4.2 Gene Profiling	137
	4.3 VirusÒHost ProteinÒProtein Interaction Screens	137
	5 Some Final Thoughts	138
	References	138
	Combining Genomic Tools to Dissect Multifactorial Virulence in Pseudomonas aeruginosa	141
	1 Introduction	141
	2 Background 2.1 Pseudomonas aeruginosa is an Opportunistic Human Pathogen	142
	2.2 The Model Host System for Studying Pathogenesis	143
	3 Genomic Sequence of P. aeruginosa, Strain PA14 3.1 Comparative Alignments with Strain PAO1	145
	3.2 Annotation of the PA14 Genome	148
	4 Relationship Between Genomic Content and Virulence 4.1 Conservation of PA14- Specific Genes and Their Potential Role in Virulence	151
	4.2 Identification of PA14-specific Virulence Genes and Their Conservation in Other Strains	153
	5 Future Directions: Testing Additional Model Hosts	156
	5.1 Wax Moth Injection Model	156
	5.2 Wax Moth Feeding Model	159
	6 Discussion	160
	References	162
	Genetic Dissection of the Interaction Between the Plant Pathogen Xanthomonas campestris pv. vesicatoria and Its Host Plants	165
	1 Introduction	165
	2 Results and Discussion 2.1 The T3SS of Xcv	167
	2.2 Control of T3S by Xcv	168
	2.3 The AvrBs3 Effector Protein	168
	2.4 Plant Target Proteins of AvrBs3	169
	2.5 Plant Target Genes of AvrBs3	170
	References	172
	Structure and Function of RXLR Effectors of Plant Pathogenic Oomycetes	175
	1 Introduction	175
	2 The RXLR Sequence Defines a Conserved Domain of Oomycete Avr Proteins	176
	3 The Phytophthora RXLR Domain Mediates Host Targeting in Plasmodium	178
	4 The RXLR Domain Is Not Required for Effector Activities	179
	5 The C-Terminal Region of RXLR Effectors Is Typically More Polymorphic than the Signal Peptide and RXLR Domains	179
	6 Can RXLR Effectors Enter Host Plants in the Absence of the Pathogen?	180
	7 A Model for RXLR Effector Delivery into the Host	181
	8 Virulence Functions of RXLR Effectors	182
	9 Outlook: Too Many Effectors, Too Little Time	183
	References	183
	The Biotrophic Phase of Ustilago maydis: Novel Determinants for Compatibility	186
	1 Introduction	186
	2 Ustilago maydis Does Not Use Aggressive Infection Strategies	189
	3 Ustilago maydis Regulates its Interaction with the Host via a Set of Novel Secreted Protein Effectors	190
	4 Discussion and Outlook	192
	References	193
	Virulence Evolution in Malaria	195
	1 A Hypothesis for Pathogen Virulence	195
	2 Malaria	197
	2.1 Mouse Malaria	198
	2.2 Human Malaria	198
	2.3 Consequences of Malaria Vaccination	201
	3 Vaccine-Driven Virulence Evolution in Other Diseases	205
	4 Conclusions	206
	References	207
	The Ins and Outs of Host Recognition of Magnaporthe oryzae	210
	1 Sequence Analysis of the AVR1-CO39 Locus	213
	2 Distribution of AVR1-CO39-Like Sequences in Grass-Infecting Isolates of M. orzyae	216
	3 Structure of AVR1-CO39 in Non-rice-Infecting Isolates of M. orzyae	217
	4 Structure of AVR1-CO39 Locus in Rice Isolates of M. oryzae	218
	5 Genetic and Physical Mapping of the Pi-CO39 (t) Locus	218
	6 Comparative DNA Sequence Analysis of Resistant and Susceptible Cultivars at the Pi- CO39 ( t) Locus	219
	+	221
	References	222
	Index	228