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Molecular Plant Pathology
M.Dickinson
School of Biosciences, University of Nottingham, Nottingham, UK
LONDON AND NEW YORK
© BIOS Scientific Publishers, 2003
First published 2003
This edition published in the Taylor & Francis e-Library, 2005.
“To purchase your own copy of this or any of Taylor & Francis or Routledge’s collection of thousands of eBooks please go to www.eBookstore.tandf.co.uk.”
All rights reserved. No part of this book may be reprinted or reproduced or utilised in any form or by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying and recording, or in any information storage or retrieval system, without permission in writing from the publishers.
A CIP catalogue record for this book is available from the British Library.
ISBN 0-203-50330-9 Master e-book ISBN
ISBN 0-203-59724-9 (Adobe eReader Format) ISBN 1 85996 044 8 (Print Edition)
BIOS Scientific Publishers
Taylor & Francis Group
11 New Fetter Lane, London EC4P 4EE and 29 West 35th Street, New York, NY 10001–2299, USA Tel: (+1) 212 216 7800, Fax: (+1) 212 564 7854
BIOS Scientific Publishers is a member of the Taylor & Francis Group.
Production Editor: Andrew Watts
3.3.5
5.3
5.4
5.5
5.6
5.7
7.3
7.4
7.5
7.6
7.7
7.8
8.9
9.3.1
9.3.2
9.3.3
14.2
14.5
14.6
14.7
14.8
14.9
Abbreviations
Aadenine
ABAabscisic acid
ABCATP-binding cassette
ACC1-aminocyclopropane-1-carboxylate
ACMV African cassava mosaic virus
ADCarginine decarboxylase
AFLPamplified fragment length polymorphism
AOSactive oxygen species
avr avirulence genes
BBTV Banana bunchy top virus
BCTV Beet curly top virus
BIBACbinary bacterial artificial chromosome
BMV Brome mosaic virus
BSMG Barley stripe mosaic virus
BSV Banana streak virus
BTHbenzathiodioazole
CaMV Cauliflower mosaic virus
CAPScleaved amplified polymorphic sequence
CCcoiled coil
CHSchalcone synthases
CCMV Cowpea chlorotic mottle virus
CCRcentral conserved region
CDPKcalcium-dependent protein kinase
CPMV Cowpea mosaic virus
CRPcatabolite activator protein
CWAcell-wall apposition
CWDEcell-wall-degrading enzyme
DAGdiacylglycerol
DASdouble-antibody sandwich
DHNdihydroxynaphthalene
DHPLCdenaturing high-performance liquid chromatography
DIdefective interfering
DMIdemethylase inhibitor
dsdouble-stranded
ELISAenzyme-linked immunosorbent assay
EMSethylmethane sulphonate
EPSexopolysaccharide/ extracellular polysaccharide
EREBPethylene response element-binding protein
ESTexpressed sequence tag
FITCfluorescein isothiocyanate
FRETfluorescence resonance energy transfer
Gguanine
G+Cguanine plus cytosine
GEARgenetically engineered acquired resistance
GIPglutamine amidotransferase/ indoleglycerolphosphate synthase/ phosphoribosyl-anthranilate
GPCRG-protein coupled receptor
GUSglucuronidase
HABShigh-affinity binding site
HChelper component
HRhypersensitive response
hrchypersensitivity response, pathogenicity and conserved genes
HRGPhydroxyproline-rich glycoprotein
hrphypersensitivity response and pathogenicity genes
IAAindole-3-acetic acid
IAMindoleacetamide
IGSintragenic spacers
IpyAindolepyruvic acid
ISRinduced systemic resistance
ITRinverted terminal repeat
ITSinternal transcribed spacers
LINElong interspersed nuclear element
LPSlipopolysaccharide
LRRleucine-rich repeat
LTRlong terminal repeat
LZleucine zippers
MALDI TOFmatrix-assisted laser desorption/ionisation-time of flight
MAPKmitogen-activated protein kinase
MBCmethyl-benzimidazole-carbamate
MeJAmethyl jasmonate
MFSmajor facilitator superfamily
MHCmajor histocompatibility complex
MPmovement protein
NBSnucleotide-binding site
NOnitric oxide
NOSnitric oxide synthase
OCTornithine carbamoyltrans-ferase
ODCornithine decarboxylase
ORFopen reading frame
PAphosphatidic acid
PAIpathogenicity island
PALphenylalanine ammonia lyase
PAMPpathogen-associated molecular pattern
PAPpokeweed antiviral protein
PCDprogrammed cell death
PGpolygalacturonase
PGIPpolygalacturonase inhibitor protein
PKprotein kinase
PKCprotein kinase C
PLpectate lyase
PMEpectin methylesterase
PPV Plum pox virus
PRpathogenesis-related
PRPproline-rich protein
PSbMV Pea seed-borne mosaic virus
PTAplate-trapped antigen
PTGSpost-transcriptional gene silencing
PVX Potato virus X
PWL pathogenicity on weeping lovegrass
QTLquantitative trait loci
RAPDrandomly amplified polymorphic DNA
RBRretinoblastoma-related
RdRpRNA-dependent RNA polymerase
REMIrestriction enzyme-mediated insertion
RFLPrestriction fragment length polymorphism
RGAresistance gene analogue
RIPribosome-inactivating protein
RITCrhodamine isothiocyanate
RNAiRNA interference
ROIreactive oxygen intermediates
ROSreactive oxygen species
SAGEserial analysis of gene expression
SAMsphinganine-analogue mycotoxin
SARsystemic acquired resistance
SASsystemic acquired silencing
SCSV Subterranean clover stunt virus
SINEshort interspersed nuclear element
siRNPsmall interfering ribonucleo-protein
SNPsingle nucleotide polymorphism
SODsuperoxide dismutase
sssingle-stranded
SSHsuppression subtractive hybridisation
SSLPsimple sequence length polymorphism
SSRsimple sequence di, tri and tetranucleotide repeats
TACtransformation-competent artificial chromosome
TAStriple-antibody sandwich
Tβltabtoxine-β-lactan
T-cmsTexas cytoplasmic male sterility factor
Titumour inducing
TMV Tobacco mosaic virus
TSWV Tomato spotted wilt virus
TVCV Tobacco vein-clearing virus
TYMV Turnip yellow mosaic virus
UTRuntranslated
VIGSvirus-induced gene sequencing
YACyeast artificial chromosome
ZYMV Zucchini yellow mosaic virus
The fundamentals of plant pathology
1.1
The concept of plant disease
So much of our existence and our society depends on the ability of plants to harness light and produce oxygen and organic matter. Domestication of plants for agriculture resulted in many of the great civilisations of the past, Asian civilisations based on rice, Middle Eastern on wheat and barley, and American on maize. Over the past few thousand years, more than half of the suitable land on Earth and virtually all of the most fertile land, has been converted for agricultural use. Agriculture today is a global business, and a necessity for the production of food, drinks and other vital commodities such as building materials, fibres, clothing, drugs and medicines. New products from, and uses for, plants are constantly being sought and developed, and plants are crucial for maintaining the environment, both globally in maintaining our atmosphere, and locally in the form of recreational facilities. Today, plants dominate our lives and economy, just as they have in all civilisations.
Mankind is not alone in the need to live off plants. Indeed, since plants first colonised land around 460 million years ago, they have probably been the main nutrient source for microbes such as fungi. Most of these microbes are saprophytic, living off nutrients released from dead and decaying plants, but many have also found ways to tap into living plants for their own growth and development. Some of these are considered beneficial for agriculture, such as the nitrogen-fixing Rhizobia, or the mutualistic mycorrhizal fungi that often enhance nutrient uptake. However, it is when the interactions between plants and microbes infringe on our food supply and environment that we consider the organisms to be pathogens and the result to be disease. So just as the field of medicine has developed to understand and combat diseases on humans, plant pathology has filled this role in agriculture, horticulture and forestry.
1.2
The causal agents
1.2.1
Fungi
Of the more than 74000 known species of fungi that have been described, the majority are saprophytes, living off dead and decaying organic matter. A few cause human, animal, fish and insect diseases. However, there are more than 10000 that can parasitise living plants to cause varying degrees of damage. Some have developed a biotrophic lifestyle, in which they obtain nutrients from living host tissue, and reduce plant vigour and yield through the diversion of nutrients for their own growth and development (see Section 3.1). Other fungi exhibit a necrotrophic lifestyle in which they utilise toxins or cell-wall-degrading enzymes to kill plant cells and then metabolise the nutrients that are released. Physical damage to plants is a prerequisite for these fungi. There are also many fungi that use a combination of strategies, the hemi-biotrophs. These will initially adopt a biotrophic infection and subsequently cause more significant damage and cell death to plants as the infection progresses and sporulation commences.
All plant species are susceptible to fungal infections, and there are many fungi for which their only hosts are living plants (obligate pathogens). Other fungi can colonise plants but are also able to survive as saprophytes on dead tissue. In some cases these fungi must colonise plants for part of their life cycle, for example apple scab Venturia inaequalis and maize smut Ustilago maydis, but others may be able to survive and reproduce exclusively as saprophytes and merely use living plants as an alternative source of nutrients.
The spread of fungi from plant to plant is generally through transmission of spores. These may be carried long distances by wind and air currents, such as occurs for the rusts and powdery mildews, or they may be deposited in the soil and remain viable but inactive until triggered to germinate, often through detection of the presence of potential host plants in the vicinity. The life cycles of fungi and the different spore-producing stages that they go through are often complex and vary greatly between species. Such information is beyond the scope of this book, and readers are encouraged to refer to other texts, in particular ‘The Biology of Fungi’ by Ingold and Hudson (1993) and ‘Plant Pathology’ by Agrios (1997), for more detailed information on the life cycles of these and other plant pathogens. Table 1.1 lists some of the major species of fungi in their phyla. Whilst there are a few examples of plant pathogens in the Chytridiomycota and Zygomycota, the majority belong to the filamentous class of the Ascomycota (the filamentous ascomycetes) or to the Basidiomycota. The nomenclature of fungi can be further complicated by the presence of both imperfect (asexual) and perfect (sexual) stages to the life cycles, and fungi for which no perfect stage has yet been identified can be classified in the Deuteromycotina. Some ascomycete fungi are commonly referred to by the name of their anamorph (imperfect stage),
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