Genomics of Disease (eBook)

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