3. OUTLINE
Introduction
Serological based detection methods
Nucleic acid based detection methods
Optical sensors based detection methods
Digital imaging based detection methods
Biosensors based detection methods
3
Case studies
Conclusion
Future Prospects
4. Importance
Effective crop management and regulatory programmes
Determination of cause, epidemiology and distribution of
diseases
Providing suitable plant protection measures
Resolving the components of complex diseases
Seed certification and quarantine
Studying taxonomic and evolutionary relationship of plant
pathogens
Detection and identification of new pathogens
Assessment of disease incidence and yield loss in field
4
5. Implications
Risk of movement of pathogens and their vectors from one
country to another
Preventing outbreaks and potentially devastating crop diseases
Identifying variability of the organism
To detect pathogens before symptom development
To screen large number of samples accurately, reliably, quickly
with greater sensitivity
To find the ways that provide additional information
Improvements
5
6. Current diagnostic methods for plant disease detection
Use of recombinant antibodies
Serological tests
• R-ELISA
• Lateral flow devices
Micro-arrays (Bio-chips)
Nucleic acid based tests
• Real-time PCR
• Nested and Multiplex PCR
Digital Consulting System or imaging
FISH
Flow Cytometry
Thermography
Hyperspectral techniques
Gas Chromatography
6
8. Polyclonal antibodies (Pabs)
Demerits:
Cross-reactions to contaminants
Lack of sustainable source of Abs
Lack of specificity
Monoclonal antibodies (Mabs)
Superior to Pabs as can provide constant supply of specific antibodies
Expensive to produce and maintain
Recombinant antibodies
Phage expressing complete Ab variable domain
Commercial available libraries can be screened with plant pathogen to
identify clones
Clones formed are used as a source of Abs for a diagnostic system e.g.
Potato leaf roll virus, Tomato spotted wilt virus, Alternaria alternata,
Ralstonia solanacearum, Phytophthora infestans, Cucumber mosaic virus
(Zienglar and Torrance, 2002)
Advantages
No need to immunize any animal
Monovalency
Rapid, sensitive and low cost
Potential to be used for a wide range of plant pathogens
8
11. Pros and cons of using ELISA
Advantages
Simple, Specific, accurate and quick
Little expertise required
Detection of pathogens with variable or latent symptoms
Disadvantages
Not effective for viroids
High initial cost
11
13. Limitations
Ideal for viruses and
bacteria (symptomatic
material)
Limited use for fungi
(difficulty to achieve
species specificity)
Life stage specific
13
15. Polymerase Chain Reaction (PCR)
Most important technique in molecular biology
Amplifies specific DNA sequence exponentially,
by chain reaction
15
16. Classical PCR has not been
adopted by most plant disease
regulatory and diagnostic labs
Why ?
Give results of PCR test in real
time
As a diagnostic technology, it
is remarkably:
• Rapid
• Sensitive
• Specific
Real time or quantitative PCR
16
17. Detection and quantification of
a fluorescent transmitter
during the process of
amplification
Increase in the fluorescent
signal is directly proportional
to the quantity of amplicon
produced during the reaction
Hybridization of fluorescently
labeled oligonucletide probe
sequences
Specific region within the
target amplicon
Amplification using traditional
forward and reverse PCR
primers
• Probe hydrolysis
(Taqman probe)
17
21. PCR can be used in combination
with pathogen isolation on agar
media
Using a combine viable
enrichment (growth media) with
an enzymatic amplification (PCR)
Target bacterium can be enriched
in liquid or solid media and
detected extremely low levels in
seeds and other propagative
materials
• Increased sensitivity
• Elimination of PCR inhibition
• Detection of viable cell only
BIO-PCR
21
Extracting a sample
Plating a sample onto agar media
Incubating for 15-72 h
Washing plates and
centrifugation
1 or 10 µL for direct PCR
22. Nested PCR
A second round of PCR is performed with
amplified DNA as template and primers internal to
first round primers
Multiplex PCR
Allows the simultaneous and senstivity detection
of different DNA or RNA targets in a single
reaction
Multiplex nested PCR
combines both multiplex and nested PCR
22
25. Nested PCR in plant pathology
Pythium ultimum, Plasmodiophora brassicae, Verticillium dahliae
Clavibacter michiganensis subsp. sepedonicus, Xanthomonas axonopodis pv.
manihotis ,Erwinia amylovora, Pseudomonas savastanoi pv. Savastanoi, X.
fastidiosa
Cucumber mosaic virus, Cherry leaf roll virus, Strawberry latent ring spot
virus, Arabis mosaic virus
(Pabla et al., 2000; Edson et al., 2002 ;Ojeda & Verdier, 2005)
Limitations
False positive reaction due to contamination
Cost of test is high
Additional cost of reverse transcriptase for cDNA in case of
plant viruses
25
26. Micro-arrays (Bio-chip)
Array:orderly arrangement
of samples
Medium for matching
known and unknown NA
samples
Generated by depositing a
few nanolitres of DNA on
a solid support
Developed for high
throughout measurement
expression patterns of
thousands of genes
Principle: Base pairing of
complementary sequences
by hybridization
26
28. Loop mediated isothermal amplification
Loop-mediated
Refers to the loop structures formed when the LAMP
primers amplify their target DNA sequences
Isothermal
The reaction takes place at single temperature (63-
67oC
Amplification
The highest efficient polymerase enzyme used amplifies
the very small amount of target in the sample, generating
millions of the copies of the sequence
LAMP
28
LAMP is used in rapid diagnosis of viral and bacterial plant pathogens
31. PCR based techniques
Genomic assay Targeted taxa References
PCR Agrobacterium tumefaciens
Candidatus Liberobacter, E.
carotovora
Tospo &Citrus Tristeza virus
Tilletia indica
Cubero et al 2002, Ahlawat et
al., 2004, Dorasse et al ., 2003
Okuda et al., 2000,
Ramachandran et al., 2002
Frederick et al., 2000
Co-PCR R. solanacearum Caruso et al., 2003
Multiplex nested
PCR
Pseudomonas savastanoi pv.
savastanoi Begomo virus
Bertolini et al., 2003
Potter et al, 2003
Multiplex PCR Xiphinema index
Globodera rostochiensis, G.
pallida
Cucumovirus, Nepovirus
Necrovirus, Olea virus
Wang et al., 2002
Mulholand et al., 2001
Bertolini et al., 2001
Nested PCR X. axonopodis pv. citri, P.
savastanoi pv. savastanoi
Hartung et al. (1996)
(Bertolini et al., 2003)
31
33. Applied for bacterial detection in combination with microscopy and
hybridization of DNA probes and target gene from plant samples
Due to the presence of pathogen specific rRNA sequences in plants
Advantage of high sensitivity (103 CFU/mL)
Could also be used to detect fungi and viruses and other
endosymbiotic bacteria that infect the plant
33
This technique could also be used to detect unculturable or yet-to-be
cultured organisms to investigate complex microbiome
34. Indian Scenario
DAS- ELISA
DAC-ELISA
DIBA
PNC- ELISA
R-PAGE
Lily carla virus, Carnation
mottle virus, Bean yellow
mosaic, Groundnut bud
necrosis virus, CMV,
Banana streak virus, Water
melon mosaic virus, Stripe
teniuvirus in Fodder,
Viroids, TSV
Bhaik et al 2004, Singh et
al 2004, Roy et al 2005,
Raja & Jain, 2006,Bhat et
al 2004, Bhadramurthy et
al 2005, Biswas &Verma
2005, Narayana 2004,
Suryanarayana et al 2004
TEM (leaf dip
serology) ISEM
Watermelon mosaic virus,
Indian citrus ringspot virus
Biswas &Verma 2005
Hoa & Ahlawat 2004
RT-PCR Groundnut bud necrosis
virus, Indian citrus ringspot
virus, Banana streak virus,
Citrus yellow mosaic virus
in P. citri,
Raja & Jain 2006, Hoa &
Ahlawat 2004, Raman et
al 2004, Saxena et al 2005
Singh et al 2004
PCR (ITS) R. solanacearum ,
C.gloesporioides & falcatum
U.scitaminea
Kumar & Anandaraj
2006, Pandey & Pandey
2006, Naik & Gaikwad
2005
PCR (16s rRNA) Grassy shoot of sugarcane Srivastava et al 2004
Nested PCR GSD and yellow leaf
syndrome of sugarcane
Rao et al 2004
PCR-RFLP RTV,X. axonopodis pv.
malvacearum, CLCuV
Niazi et al 2005,
Chakraborthy et al 2004,
Microsatelite
markers
Fusarium spp. Prasad et al 2004
34
36. FCM (Flow cytometry)
Flow cytometry (FCM) is a laser-
based optical technique widely
used for cell counting and sorting,
biomarker detection and protein
engineering
The technique uses an incident
laser beam and measures the
scattering and fluorescence of the
laser beam reflected from the
sample
FCM is used for rapid
identification of cells while cells
pass through an electronic detection
apparatus in a liquid stream
(Chitarra et al., 2003) 36
37. Thermography
Allows imaging the differences in surface temperature of plant leaves
and canopies
Emitted infrared radiation can be captured by thermographic cameras
and color difference can be analyzed
Also a promising tool to monitor the heterogenity in the infection of
soilborne pathogens
The practical applicability of thermography for disease monitoring is
limited due to its high sensitivity to the change of environmental
conditions during measurement
(Chaerle, et al., 2007)
37
38. Fluorescence imaging
The chlorophyll fluorescence is measured on the leaves as a function
of the incident light and the change in fluorescence parameters can be
used to analyze pathogen infections, based on changes in the
photosynthetic apparatus and photosynthetic electron transport
reactions
Temporal and spatial variations of chlorophyll fluorescence were
analyzed for precise detection of leaf rust and powdery mildew
infections in wheat leaves at 470 nm
(Kuchenberg, et al., 2009)
38
The practical application of this technique in a field setting is limited
39. Hyperspectral techniques
Used to obtain useful information
about the plant health over a wide
range of spectrum between 350 and
2500 nm
Highly robust and it provides a
rapid analysis of the imaging data
Magnaporthe grisea infection of
rice, Phytophthora infestans
infection of tomato and Venturia
inaequalis infection of apple trees
have been identified and reported
using hyperspectral imaging
techniques
(Kobayashi, et al., 2007)
39
40. 40
How does hyperspectral imaging work
• Hyperspectral imaging deals with the
imaging of narrow spectral bands over
a continuous spectral range, and
produces the spectra of all pixels in the
scene
• Hyperspectral sensors collect
information as a set of “images”
• These images are then combined and
formed into three-dimensional
hyperspectral data cube for processing
and analysis
41. Gas chromatography
A completely different non-
optical indirect method for plant
disease detection involves the
profiling of the volatile chemical
signature of the infected plants
An infection by Phytophthora
cactorum, the fungus that causes
crown rot diseases in strawberries,
results in the release of p-
ethylguaiacol and p-ethylphenol
as characteristic VOCs from the
infected portion of the strawberry
plant/fruit (Fang et al., 2014)
41
42. The volatile signature of plants could be analyzed using gas-
chromatography (GC) technique to analyze the presence of the
specific VOC that is indicative of a particular disease
It also allows the detection of diseases at different stages based on
the quantitative information collected from the VOC sample
42
43. VOCs emitted from whole, intact tomato plants or
detached leaves, and biotic stress causing agents
responsible for increase in VOC emissions
43
45. Digital imaging system
Distant analysis can be used
in first line diagnostic
Can save a lot of time
Better and faster
communication between
inspectors and specialists
Sharing of knowledge
Developing central database
Always final identification
by diagnostic specialist
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46. Imaging techniques Use
Magnetic resonance
microscopy (MRM)
Pine wilt disease (Utsuzawa et al.,
2005 )
Atomic force
microscopy (AFM)
Tobacco mosaic viruses
X-Ray
Spectroscopy
Mass spectrometry
based proteomics
Rhizoctonia solani, Fusarium
graminearum, and Ustilago maydis,
Uromyces appendiculatus (Padliya
and Copper, 2006)
46
47. Ideal diagnostic strategy
High detectability
Specificity
Sensitivity
Accuracy supported with simplicity
Amenable to automation
Low cost
Issues related to diagnostics
Cost
Specificity
Sensitivity
47
49. 49
How does biosensors work?
Analyte of
interest
Biorecepter Transducer Signal
Detection of plant diseases using portable sensors
Antibody
Enzymes
Phages
Oligonucleotides
Optical
Electrochemi
cal
Mechanical
Cantilever
Luminescence
Fluorescence
UV-VS
Magnetic
Resonance
50. Biosensor platforms based on nanomaterials
Affinity biosensors
Antibody-based biosensors
DNA/RNA-based affinity biosensor
Enzymatic electrochemical biosensors
Bacteriophage-based biosensors
50
Types of biosensors
(Singh et al., 2010)
51. Comparison of affinity biosensors, enzymatic biosensors,
nanomaterials modified sensors and ELISA
51
56. Multispectral imaging system (MSIS) developed for sunlight-induced fluorescence
imaging of outdoor plants
56
*EMCCD: Electron multiplying charge coupled device
Non-destructive method for detection and
classification of CMD infection based on
far:far-red chlorophyll fluorescence image ratio
Study was carried out in 14 varieties of
potted cassava plant with a MSIS consisting of
an EMCCD camera
Sunlight induced chl fluorescence (SICF)
images of plants were recorded using the MSIS
at different wavelength
The red: far red ratio was computed and
correlated with the laser induced chlorophyll
fluorescence (LICF) detetermined by point
monitoring, chl content and net photosynthetic
rate
57. Image recorded from a typical irrigated cassava plant : (a) a colour photo, (b)
monochrome image recorded at 687 nm, (c) monochrome image recorded at 760 nm,
and (d) ratio image (F687:F760) produced from (b) and (C), with colour ramp as
indicated by the legend
57
58. Scatter plot diagram of (a) net photosynthesis rate (Pn) and (b) total leaf
chl for different varieties of cassava plants
58
59. Scatter plot diagram of the red:far red fluorescence intensity ratio (a) F687:F760 ratio
from SICF imaging measurement and (b) F685:F735 ratio from point monitoring of
LICF. The cut-off lines for discrimination are drawn at the mean ratio value of the
adjoining groups
59
63. Conclusions
Validation of diagnostic test
Integration of methods
Sanitary and phyto-sanitary standards
Seed certification programs and epidemiological studies
intended to monitor the distribution and spread of pathogens
Modified PCR is adaptable to any experimental objectives
Molecular techniques can reduce the time required for assay
and increase the sensitivity of assay, allowing detection of
pathogen before symptom expression
Biosensor have new analytical tools this form allows for a
rapid response, is ideal for the plant disease detection
63
64. 64
Fabrication of test strips on ELISA will be an innovative strategy
Affinity sensors , although extensively studied, still remain in the
laboratory in many cases
Thermography being non-specific and susceptible to ambient
environment, therefore are less suitable for on-field crop disease
detection
It is also promising that the enzymatic and affinity sensors can be
fabricated for multiple pathogen detection rather for single pathogens
Future Prospects