Contents	5
	Abbreviations	14
	1 The fundamentals of plant pathology	19
	1.1 The concept of plant disease	19
	1.2 The causal agents	20
	1.2.1 Fungi	20
	1.2.2 The Oomycota	21
	1.2.3 Protozoa	21
	1.2.4 Bacteria	21
	1.2.5 Phytoplasmas and Spiroplasmas	23
	1.2.6 Viruses	25
	1.2.7 Other agents of plant disease	26
	1.3 The significance of plant diseases	26
	1.3.1 Historically important diseases	26
	1.3.2 Emerging diseases	30
	1.4 The control of plant diseases	31
	1.5 Molecular biology in plant pathology	32
	1.5.1 A historical perspective	32
	1.5.2 The use of model organisms	32
	1.5.3 Transformation techniques	33
	1.5.4 Forward genetics	35
	1.5.5 Reverse genetics	42
	1.5.6 Dissection of signalling pathways	43
	1.5.7 Gene expression profiling	43
	1.5.8 Proteomics	47
	1.5.9 Metabolite profiling	48
	1.5.10 Bioinformatics	48
	References and further reading	48
	2 Fungal and oomycete diseases—establishing infection	50
	2.1 Dispersal of spores	50
	2.2 Finding a suitable host	50
	2.3 Spore attachment to the plant	52
	2.4 The germination process	52
	2.5 Penetration methods	53
	2.6 Germ-tube elongation	56
	2.7 Induction of appressorial development	57
	2.7.1 Physical factors	57
	2.7.2 Chemical factors	60
	2.8 Appressorial development	61
	2.8.1 Morphology	61
	2.8.2 Hydrophobins	63
	2.8.3 Melanisation	63
	2.8.4 Turgor pressure	65
	2.9 Cell-wall degrading enzymes (CWDEs)	66
	References and further reading	68
	3 Fungal and oomycete diseases—development of disease	69
	3.1 The basic concepts—necrotrophy versus biotrophy	69
	3.2 Host barriers	70
	3.3 Overcoming host barriers	70
	3.3.1 Quiescence	70
	3.3.2 Detoxification of phytoanticipins	71
	3.3.3 Detoxification of phytoalexins	71
	3.3.4 ATP-binding cassette (ABC) transporters	72
	3.3.5 Suppression of active oxygen species	73
	3.3.6 Avoidance of recognition	74
	3.4 Establishing infection	75
	3.5 Cell-wall-degrading enzymes	75
	3.6 The role of toxins	76
	3.6.1 Host-selective toxins	77
	3.6.2 Host non-selective toxins	80
	3.6.3 Mycotoxins	81
	3.7 Biotrophy	84
	3.7.1 Haustorial structure	84
	3.7.2 Haustorial function	85
	3.8 Prevention of leaf senescence	87
	3.8.1 The role of cytokinins	87
	3.8.2 The role of polyamines	88
	References and further reading	89
	4 Fungal and oomycete genetics	91
	4.1 The concept of race structure	91
	4.2 Avirulence genes	92
	4.2.1 General concepts	92
	4.2.2 Cloning of avirulence genes	92
	4.2.3 Avr protein structure and function	94
	4.2.4 The significance of avirulence genes in species specificity	95
	4.3 Fungicide resistance	95
	4.4 Mechanisms for generating genetic variation in fungi	97
	4.5 Mating-type genes	98
	4.6 Chromosome instability	99
	4.7 Alien genes/horizontal gene transfer	101
	4.8 Role of transposable elements	105
	4.9 Role of heterokaryosis	105
	4.10 Role of mitochondrial DNA	106
	4.11 Role of mycoviruses	106
	References and further reading	107
	5 Bacterial diseases—establishing infection	110
	5.1 Bacterial-bacterial communication—quorum sensing	110
	5.2 Plant penetration	112
	5.2.1 Foliar bacteria	112
	5.2.2 Soil-borne bacteria	113
	5.3 Attachment	114
	5.4 Stimulation of gene expression in response to host factors	116
	5.5 The role of cell-wall-degrading enzymes (CWDEs)	117
	5.6 The role of toxins	119
	5.7 The role of hormones	123
	5.8 The role of extracellular polysaccharides (EPSs)	128
	References and further reading	130
	6 Bacterial diseases—determinants of host specificity	131
	6.1 The cloning of avirulence genes	131
	6.2 The products of avirulence genes	131
	6.3 Type III secretion mechanisms	132
	6.4 Type III secretion in plant pathogens	134
	6.5 Hrp-pili	134
	6.6 Regulation of hrp genes	135
	6.7 Secreted proteins	139
	6.8 Secretion signals	140
	6.9 Pathogenicity islands	141
	6.10 The role of plasmids	141
	References and further reading	142
	7 Plant viruses—structure and replication	143
	7.1 The structure of plant viruses	143
	7.2 Virus infection of plants	144
	7.3 Translation and replication of positive-strand RNA viruses	144
	7.3.1 The production of sub-genomic RNAs and virus replication	145
	7.3.2 Segmented genomes	149
	7.3.3 Polyprotein processing	149
	7.3.4 Readthrough and frameshifting	150
	7.4 Negative-strand RNA viruses	152
	7.5 Double-strand RNA viruses	153
	7.6 Single-strand DNA viruses	153
	7.7 Double-strand DNA viruses	155
	7.8 Viroids	157
	7.9 Other sub-viral entities	157
	7.10 Viral assembly	159
	7.10.1 Assembly of rod-shaped viruses	159
	7.10.2 Assembly of isometric particles	160
	7.10.3 Assembly of membrane-bound particles	160
	References and further reading	161
	8 Plant viruses—movement and interactions with plants	163
	8.1 Transmission of viruses	163
	8.2 Transmission by insect vectors	164
	8.3 Transmission by nematodes	166
	8.4 Transmission by zoosporic ‘fungi’	166
	8.5 Seed and pollen transmission	167
	8.6 Short-distance movement of viruses in plants	167
	8.7 Long-distance movement in plants	170
	8.8 Viral affects on plants	171
	8.8.1 Alterations in host gene expression	171
	8.8.2 Alterations in host cell metabolism	172
	8.8.3 Suppression of defence responses	173
	8.9 Gene-for-gene interactions with plant viruses	176
	8.10 Genomic variation in plant viruses	176
	References and further reading	177
	9 Resistance mechanisms in plants	178
	9.1 Classical concepts of resistance	178
	9.2 Preformed defences	180
	9.2.1 Structural barriers	180
	9.2.2 Root border cells	180
	9.2.3 Phytoanticipins	181
	9.3 Induced defences	181
	9.3.1 Local signals	182
	9.3.2 Programmed cell death (PCD)	182
	9.3.3 Induced structural barriers	182
	9.3.4 Phytoalexins	183
	9.3.5 Pathogenesis-related proteins	187
	9.3.6 Other defence-related proteins	189
	9.3.7 Post-transcriptional gene silencing (PTGS)	189
	9.4 Systemic resistance mechanisms	190
	9.5 ‘Communal’ resistance	191
	References and further reading	192
	10 Resistance genes	193
	10.2 Features of cloned resistance genes	195
	10.3 R gene specificity	198
	10.3.1 Leucine-rich repeats (LRRs)	198
	10.3.2 Cellular location of recognition	200
	10.3.3 Does the R gene interact directly with the pathogen elicitor?	201
	10.4 The TIR domain	202
	10.5 The NBS (NB) domain	203
	10.6 Other R gene domains	203
	10.6.1 Protein kinases	203
	10.6.2 Coiled coil (leucine zipper) domains	203
	10.7 Genetic organisation of resistance genes	204
	10.8 Mechanisms for generating new R gene specificities	205
	10.9 Coevolution of resistance genes	207
	10.10 Recessive resistance genes	208
	10.11 Quantitative resistance	209
	References and further reading	209
	11 Signalling in plant disease resistance mechanisms	211
	11.1 Genetic analyses	211
	11.2 MAP kinases (MAPK)	213
	11.3 Ion fluxes and calcium homeostasis	216
	11.4 The oxidative burst	218
	11.5 Nitric oxide (NO)	221
	11.6 (p)ppGpp signalling	223
	11.7 Low-molecular-weight signalling molecules	224
	11.8 RNA as a signal	227
	11.9 Co-ordination of cell death responses	227
	11.10 Interplay of downstream signalling pathways	229
	11.10.1 The EDS1 and NDR1 pathways	229
	11.10.2 The role of NPR1	230
	11.10.3 Pathways that are independent of NPR1	232
	References and further reading	233
	12 Molecular diagnostics	235
	12.1 Classical approaches	235
	12.2 The use of antibodies	236
	12.2.1 Polyclonal antibodies (Pabs)	237
	12.2.2 Monoclonal antibodies (Mabs)	237
	12.2.3 Recombinant DNA techniques	238
	12.3 Serological tests	240
	12.3.1 ELISA (enzyme-linked immunosorbent assay)	240
	12.3.2 Lateral flow techniques	240
	12.3.3 Other uses of antibodies	242
	12.4 Nucleic acid-based techniques	243
	12.4.1 Identification of pathogen-specific markers	243
	12.4.2 Hybridisation techniques	244
	12.4.3 PCR-based techniques	244
	12.4.4 Gene-array-based techniques	246
	12.4.5 Quantitative PCR	246
	12.5 Phylogenetic analysis	247
	References and further reading	248
	13 Application of molecular biology to conventional disease control strategies	249
	13.1 Breeding for resistance	249
	13.1.1 The basis of resistance breeding programmes	249
	13.1.2 The conventional breeding strategy	250
	13.2 The use of tissue culture in plant breeding	251
	13.3 Marker-assisted breeding	252
	13.4 The identification of novel resistance gene specificities	253
	13.5 The use of chemicals for disease control	255
	13.6 The use of molecular biology in agrochemical production	256
	13.7 Engineering chemicals that elicit defence responses in plants	257
	References and further reading	258
	14 Transgenic approaches for crop protection	259
	14.1 Pathogen-derived resistance	259
	14.1.1 Coat-protein-mediated resistance	259
	14.1.2 Replicase-mediated resistance	260
	14.1.3 Movement protein-mediated resistance	261
	14.1.4 RNA-mediated resistance	261
	14.1.5 Pathogen-derived resistance against bacterial and fungal diseases	262
	14.2 Plantibodies	262
	14.3 Over-expressing defence genes	263
	14.4 Expressing defence genes under the control of inducible promoters	265
	14.5 The use of cloned resistance genes	266
	14.6 Engineering broad-spectrum resistance	267
	14.7 Resistance based on antagonistic microbes	270
	14.8 Expression of vaccines in plants	273
	14.9 Concluding remarks	274
	References and further reading	274
	Index	276