Plant Pathology: Techniques and Protocols

365 Pages·2015·11.731 MB·English

by  Christophe Lacomme

Methods in
Molecular Biology 1302
Christophe Lacomme Editor
Plant
Pathology
Techniques and Protocols
Second Edition
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
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Plant Pathology
Techniques and Protocols
Second Edition
Edited by
Christophe Lacomme
Virology & Zoology, SASA, Edinburgh, UK
Editor
Christophe L acomme
Virology & Zoology
SASA, E dinburgh , U K
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-2619-0 ISBN 978-1-4939-2620-6 (eBook)
DOI 10.1007/978-1-4939-2620-6
Library of Congress Control Number: 2015938158
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Prefa ce
Pathogens pose a threat to plants in natural communities (i.e., forests, grasslands), horticul-
tural commodities, or cultivated crops. Risks of pathogen spread have increased with
increased human mobility and the globalization of trade. In addition, factors such as envi-
ronmental changes (local or global climate fl uctuations) and changes to pesticide legislation
impact on whether pathogens and their vectors establish in different habitats and the selec-
tive pressures that will give rise to new pathotypes and pesticide- or antibiotic-resistant
variants. Damages caused worldwide by either emerging, re-emerging or endemic patho-
gens are signifi cantly important. The International Plant Protection Convention, Regional
and National Plant Protection Organizations, have developed phytosanitary measures to
prevent the spread of regulated pathogens (particularly quarantine pathogens) between
countries in order to protect agricultural and natural plant systems.
Safeguarding plant biosecurity relies heavily on the early detection and diagnosis of the
pathogen. Other than diagnoses based on morphological characteristics, diagnostic meth-
ods can be separated into three main categories: bioassay, serological and molecular meth-
ods, and sometimes a combination of these methods will be used. Since the late 1970s, the
serological method of ELISA, using polyclonal and especially monoclonal antibodies, has
been the method of choice for most diagnostic laboratories, due to its cost effectiveness and
capacity to provide reliable detection and diagnosis for a large number of samples. However,
over the past decade an increasing number of DNA/RNA-based assays, particularly PCR-
based assays, are routinely used in diagnostic laboratories because of their increased sensi-
tivity and specifi city, the relative ease with which tests can be developed, their adaption to
detect multiple targets, their requirement for minimal quantities of target, and their capac-
ity to be automated for high-throughput testing. Moreover sequencing has contributed
considerably to the increased knowledge of plant and microbial genomes and is now widely
used either as stand-alone methods or in addition to other methods for diagnosis. Techniques
such as end-point (conventional) PCR, real-time PCR, and diagnostic microarrays are ver-
satile and can be used as either a generic or species-specifi c detection/diagnostic method.
One of their drawbacks, however, is their reliance on prior knowledge of the genome of the
target pathogen or pathogens. The rapid evolution of bioinformatics and computing tech-
nology to analyze very high numbers of complex datasets will make next-generation, high-
throughput parallel sequencing platforms (also known as deep sequencing) accessible as a
detection and diagnostic method. The application of these metagenomic approaches to
diseased material offers the possibility to identify pathogens that have yet to be fully char-
acterized or described. Importantly, recent advances in plant pathogen diagnoses have
delivered fi eld deployable portable diagnostic systems that do not require thermal cycling
equipment. This allows rapid on-site identifi cation of pathogenic agents, thereby passing
the need for laboratory-based analysis. The development of any diagnostic assay requires
thorough validation to ensure for example sensitivity, specifi city, repeatability, and repro-
ducibility and that the assay is fi t for purpose.
This second edition of P lant Pathology Techniques and Protocols covers diagnostic
methods that are currently used in laboratories for a broad range of plant species and
matrixes. These include serological and molecular methods that have one or more of the
v
vi Preface
following characteristics: suitability for high-throughput testing, detection of a group of
pathogens or of sometimes uncharacterized pathogens, detection and identification
of specifi c pathogens, and high sensitivity. Qualitative and quantitative tests are described,
as well as recently developed cutting-edge diagnostic methods. These chapters target an
audience of plant pathologists and molecular biologists who will fi nd information on how
to perform the tests in their laboratories. Also provided is background information on
many pathogens, which are endemic, nonendemic, or emerging and with different lifecy-
cles that cause diseases of signifi cant importance in a wide variety of hosts. Finally I would
like to thank all authors that have contributed to this second edition of Plant Pathology
Techniques and Protocols.
Edinburgh, UK C hristophe Lacomme
Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 Detection of the Bacterial Potato Pathogens Pectobacterium
and Dickeya spp. Using Conventional and Real-Time PCR . . . . . . . . . . . . . . . 1
Sonia N. Humphris , G reig C ahill , John G . E lphinstone , R achel Kelly ,
Neil M. P arkinson , L eighton P ritchard , I an K. Toth ,
and Gerry S. S addler
2 D etection and Identification of Phoma Pathogens of Potato . . . . . . . . . . . . . . 1 7
Denise A’Hara
3 D iagnosis of Ramularia collo-cygni and Rhynchosporium spp. in Barley . . . . . . 2 9
Neil H avis , J ames F ountaine , Kalina G orniak , L inda Paterson ,
and Jeanette Taylor
4 A Real-Time Multiplex PCR Assay Used in the Identification
of Closely Related Fungal Pathogens at the Species Level . . . . . . . . . . . . . . . . 3 7
Dominie G. Wright
5 D iagnostics of Tree Diseases Caused by Phytophthora austrocedri Species. . . . . 59
Vincent M ulholland , Matthew E lliot , and S arah G reen
6 Real-Time LAMP for Chalara fraxinea Diagnosis. . . . . . . . . . . . . . . . . . . . . . 75
Jenny T omlinson and Neil B oonham
7 L oop-Mediated Isothermal Amplification Procedure (LAMP)
for Detection of the Potato Zebra Chip Pathogen
“Candidatus Liberibacter solanacearum” . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Aravind R avindran , Julien L évy , E lizabeth Pierson ,
and Dennis C. G ross
8 L oop-Mediated Isothermal Amplification (LAMP) for Detection
of Phytoplasmas in the Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 9
Matt Dickinson
9 D iagnosis of Phytoplasmas by Real-Time PCR Using Locked
Nucleic Acid (LNA) Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Sabrina Palmano , V incent M ulholland , D avid K enyon ,
Gerry S addler , and Colin Jeffries
10 Q -Bank Phytoplasma: A DNA Barcoding Tool for Phytoplasma
Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 23
Nicoletta C ontaldo , S amanta Paltrinieri , O lga M akarova ,
Assunta Bertaccini , and Mogens N icolaisen
11 High-Throughput Diagnosis of Potato Cyst Nematodes in Soil Samples . . . . . 1 37
Alex R eid , F iona Evans , V incent M ulholland , Y vonne Cole , and Jon P ickup
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viii Contents
12 Detection of Nepovirus Vector and Nonvector Xiphinema
Species in Grapevine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 49
C. V an Ghelder , A . Reid , D. K enyon , and D. E smenjaud
13 Molecular and Serological Methods for the Diagnosis of Viruses
in Potato Tubers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Christophe Lacomme , Ross H olmes , and Fiona Evans
14 Immunocapture-Multiplex RT-PCR for the Simultaneous Detection
and Identification of Plant Viruses and Their Strains: Study Case,
Potato Virus Y (PVY) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 77
Mohamad C hikh-Ali and A lexander V . K arasev
15 SNaPshot and CE-SSCP: Two Simple and Cost-Effective Methods
to Reveal Genetic Variability Within a Virus Species. . . . . . . . . . . . . . . . . . . . . 187
Agnès Delaunay , Sylvie D allot , Denis Filloux , V irginie Dupuy ,
Philippe R oumagnac , and Emmanuel J acquot
16 D etection and Characterization of Viral Species/Subspecies
Using Isothermal Recombinase Polymerase Amplification (RPA) Assays . . . . . 207
Laurent G lais and Emmanuel Jacquot
17 Virus Testing by PCR and RT-PCR Amplification in Berry Fruit. . . . . . . . . . . 2 27
Stuart M acFarlane , W endy M cGavin , and Ioannis Tzanetakis
18 Metagenomics Approaches Based on Virion-Associated Nucleic
Acids (VANA): An Innovative Tool for Assessing Without A Priori
Viral Diversity of Plants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Denis F illoux , S ylvie D allot , A gnès D elaunay , S erge G alzi ,
Emmanuel Jacquot , and Philippe Roumagnac
19 D etection of Potato spindle tuber viroid and Other Related Viroids
by a DIG Labelled RNA Probe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Wendy A . Monger and Colin J effries
20 M icroarray Platform for the Detection of a Range of Plant Viruses
and Viroids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
Ian Adams , C atherine Harrison , J enny Tomlinson , and Neil B oonham
21 Multiplex Detection of Plant Pathogens Through the Luminex
Magplex Bead System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
René A. A . van der Vlugt , Henry v an Raaij , M arjanne de Weerdt ,
and J an H. W. B ergervoet
22 N ext-Generation Sequencing of Elite Berry Germplasm and Data Analysis
Using a Bioinformatics Pipeline for Virus Detection and Discovery. . . . . . . . . 301
Thien Ho , R obert R . M artin , and Ioannis E. T zanetakis
23 Metagenomic Next-Generation Sequencing of Viruses
Infecting Grapevines. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
Johan T. Burger and Hans J . M aree
24 D roplet Digital PCR for Absolute Quantification of Pathogens. . . . . . . . . . . . 3 31
Ion Gutiérrez-Aguirre , Nejc R ački , T anja Dreo , and Maja Ravnikar
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 49
Contributors
IAN ADAMS • Food and Environment Research Agency , Y ork , U K
DENISE A’HARA • Science and Advice for Scottish Agriculture , E dinburgh, U K
JAN H. W. B ERGERVOET • Wageningen UR , Wageningen, T he Netherlands
ASSUNTA B ERTACCINI • DipSA, Plant Pathology, Alma Mater Studiorum – University
of Bologna , B ologna, Italy
NEIL B OONHAM • Food and Environment Research Agency , Y ork , U K
JOHAN T. BURGER • Department of Genetics, Stellenbosch University , S tellenbosch, South Africa
GREIG C AHILL • Science and Advice for Scottish Agriculture , E dinburgh, U K
MOHAMAD C HIKH-ALI • Department of Plant Soil and Entomological Sciences, University
of Idaho , M oscow , I D, USA
YVONNE COLE • Science and Advice for Scottish Agriculture , Edinburgh, U K
NICOLETTA CONTALDO • DipSA, Plant Pathology, Alma Mater Studiorum – University of
Bologna , B ologna , I taly
SYLVIE D ALLOT • INRA-Cirad-Montpellier SupAgro, UMR 385 BGPI, Cirad TA A-54K ,
Montpellier cedex, France
AGNÈS DELAUNAY • INRA-Cirad-Montpellier SupAgro, UMR 385 BGPI, Cirad TA A-54K ,
Montpellier cedex, France
MATT D ICKINSON • School of Biosciences, University of Nottingham , L oughborough, U K
TANJA DREO • Department of Biotechnology and Systems Biology , N ational Institute
of Biology , L jubljana, Slovenia
VIRGINIE DUPUY • INRA-Cirad, UMR 15 CMAEE, Cirad TA A-15G,
Montpellier cedex, France
MATTHEW E LLIOT • Centre for Ecosystems, Society and Biosecurity , F orest Research ,
Edinburgh, U K
JOHN G . E LPHINSTONE • Food and Environment Research Agency , York, UK
DANIEL ESMENJAUD • INRA-UMR1355 Institut Sophia Agrobiotech , Nice , F rance ;
UMR Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis , Nice , F rance ;
CNRS-UMR7254 Institut Sophia Agrobiotech , N ice , F rance
FIONA EVANS • Science and Advice for Scottish Agriculture , E dinburgh, U K
DENIS FILLOUX • Cirad-INRA-Montpellier SupAgro, UMR 385 BGPI, Cirad TA A-54K,
Montpellier Cedex , F rance
JAMES F OUNTAINE • Biological Sciences, Jealott’s Hill International Research Centre,
Bracknell, UK
SERGE G ALZI • CIRAD-UMR BGPI , Montpellier, France
CYRIL V AN GHELDER • INRA-UMR1355 Institut Sophia Agrobiotech , Nice, France ;
UMR Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis , Nice, France ;
CNRS-UMR7254 Institut Sophia Agrobiotech , N ice , F rance
LAURENT G LAIS • INRA-UMR1349 IGEPP , L e Rheu, F rance ; F édération Nationale des
Producteurs de Plants de Pomme de Terre (FN3PT) , P aris , F rance
KALINA GORNIAK • Crop and Soils Systems , E dinburgh, U K
SARAH GREEN • Centre for Ecosystems, Society and Biosecurity, F orest Research , Edinburgh, U K
DENNIS C . G ROSS • Department of Plant Pathology and Microbiology, T exas A&M
University , C ollege Station, TX, USA
ix