The document discusses strategies used by IITA to address virus threats to food crops in sub-Saharan Africa. It focuses on cassava, describing efforts to characterize cassava mosaic viruses, understand their diversity and epidemiology. This includes tracking the spread of the recombinant EACMV-UG virus across countries. Research is also presented on developing diagnostic tools and investigating host resistance and alternative virus hosts. The approach involves interdisciplinary collaboration between virology, plant breeding, biotechnology and other fields.

1. Winning the race against virus threats to
food crops in sub-Saharan Africa:
What we do and how we do it!
A review from August 2007
P Lava Kumar
Contract Review Seminar, 12 April 2010 www.iita.org

2. Outline
1. Introduction: The challenges
2. What we do and how we do it!
• Clonal crops
• Seed crops
• Germplasm health and quarantine
• Diagnostics
• Capacity building
3. Future plan
Stay fit and competitive
4. Conclusions
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3. 1. The challenges
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4. Food security and poverty reduction
through agriculture development
• 10% increase in agriculture productivity in Africa is associated
with 7.2% decrease in poverty (IFPRI 2004).
N = 327.2 million t
76% IITA crops 6%
35 7% 140
Production, tonnes (x 1 000,000)
1 1 8% 37%
30 2 120
cassava
Area, ha (x 1 000,000)
25 11% 100
musa
20 80
15 2 3
yam
15%
16%
3 60
maize
10
4 5 4 40
4 6 7 6
7
5 20
0 0
Maize Sorghum Cassava Rice Wheat Musa Yams
www.iita.org

5. Virus diseases
•Cause yield and quality loses
•Losses are often insidious.
Frequently less conspicuous and
go unnoticed or untreated.
Direct and indirect losses:
•Reduction in growth
•Reduction in vigor
•Reduction in quality & market value
•Reduction in transboundary trade
•Costs of maintaining health
• MSV: $180 million to $480 million at
5% annual incidence
• CMD: 42% yield reduction in
EACMV-UG affected region
• CBSD: $100 million in 2003
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6. Drivers of virus spread/evolution
Agriculture intensification
• Raising population demand on food production
• Rapid expansion in area
• New crops & varieties, continuous cultivation (absence of breaks)
Effects of Global Warming Effects of climate variability / change
• Distribution of pests and diseases
• Changes in geographical
distribution of hosts and pathogens
• Altering crop yields and losses due
to changes in efficacy of
management strategies
Source: Nature Vol 438, No. 7066
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7. Viruses are built to win?
• Intracellular pathogens, completely dependent on hosts.
• Difficult to eliminate them, without eliminating the host
• Do viruses are there to protect hosts from invasive plants?
• For instance virus resistance in wild relatives / landraces and susceptibility
of introduced species supports this thought.
(new encounter diseases of introduced crops)
CMD in cassava
MSV in maize
CSSV in cocoa
Rosette of groundnut
• New paradigm - Viruses are evolutionary drivers
• There is little choice for host and virus – either they
Source:Wiki
adjust or both will perish Virus
• Why is it important here?
•Viruses have mechanisms to negate preventive tactics
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8. • Diverse crops
• Diverse viruses
• Diverse vectors
• Diverse modes of virus spread &
• Diverse agro-ecologies
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9. Diversity in viruses
Types worked at IITA
www.iita.org

10. Diverse vectors and modes of dissemination
Whiteflies Aphids
Beetles Thrips
Leafhoppers Mealybugs
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11. Ecological diversity:
Clonal and seed crops
Viruses of clonal crops –STATIC Viruses of seed crops - DYNAMIC
• Infected clones retain viruses • Only seed-transmitted viruses are
indefinitely (What goes in stays retained and passed to next
forever!). generation.
• Increase in incidence incrementally • Incidence depends on the vectors
Reduction depends on the and virus sources (seed-borne /
replacement of infected stocks. volunteer plants / alternative hosts).
Conditions favoring insects favor
high incidence
• In general viruses have narrow host
range. • In general, broad host range
• Predictable annual situation. • Unpredictable annual situation.
Different viruses – crops demands different tactics
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12. 2. What we do?
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13. What we do?
Strategic Objectives
1. Understand the foe
2. Develop tools to monitor them
3. Establish technologies to prevent viruses (win over the virus)
4. Disseminate the technologies
Characterize viruses Develop serological and nucleic acid-
(Biological and biochemical) based diagnostic tools
Fundamental and applied
Study virus-vector interactions and virology research for Ensure germplasm health safety and
disease epidemiology mitigating the impact of virus quarantine monitoring
diseases
Develop disease control options, Knowledge and technology transfer
including resistant varieties to stakeholders
www.iita.org

14. What we do?
Ways to win the race
Plant Health Monitoring Breeding Programs
Virus-free stocks
All All
Exclusion Prevention
(Cassava & banana)
Quarantine & Inspection Cultivation of resistant
varieties
Breeding programs
(From countries)
Planting virus free material Conventionally bread /
IPM / IDM
transgenics
Reduce spread
Methods to reduce Reduce impact
All
Vector control
impact of virus Cultivation of
Physical barriers
tolerant varieties
Seed testing infections
Avoidance by cultural
methods Reduce sources of inoculum
Field isolation Eliminate crop refuge,
Plant spacing / alternative alternate sources
dates
Not effective in SSA www.iita.org

15. 3. How do we do it?
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16. Inter-disciplinary approach
Core business Inter-disciplinary business
Virus Disease Transgenic Plant Breeding
resistance Resistant
Viral genes Varieties
Virus isolation Host R genes
Germplasm screening for
resistance
Biochemical, molecular &
Wild and Cultivated DISEASE
Virus characterization species
MANAGEMENT
Biological Properties
Virus isolates Diagnostic tools Disease Epidemiology Monitoring
Quarantine
Bioassays Vector biology
Serological & Virus survival and spread
Nucleic-acid assays Environmental factors
Virology – Breeding – Biotechnology – Germplasm – Quarantine – Extension
www.iita.org

17. Crop specific activities
Cassava
Cassava mosaic begomoviruses & brown streak Maize
•Epidemiology Maize streak virus
•Virus diversity and diagnostics • Host resistance
•Host resistance and seed systems
•Whitefly control Cowpea & soybean
Bean pod mottle virus
Yam Blackeye cowpea mosaic virus
Yam potyvirus & badnavirus complex Cowpea mottle virus
•Epidemiology Cowpea mild mottle virus
•Virus diversity and diagnostics Cowpea yellow mosaic virus
•Host plant resistance Cowpea aphid-borne mosaic virus
•Seed systems Cucumber mosaic virus
Southern bean mosaic virus
Banana Cowpea chlorotic mottle
Banana bunchy top Soybean mosaic virus
•Epidemiology Tobacco ringspot virus
•Investigations on management options Tobacco streak virus
Soybean begomoviruses
Cocoa • Host resistance
Cocoa swollen shoot virus • Diversity and distribution
•Distribution and diversity
•Seed systems
www.iita.org

18. Generic activities
Plant health monitoring & quarantine
•Virus indexing
•Establishment of virus-free clonal and seed germplasm
•Facilitation of germplasm distribution
Diagnostics
•PCR and ELISA-based approaches
•Viruses, fungi, bacteria and others
•Mycotoxins
Capacity building
•Graduate and post-graduates (MSc & PhD)
•Training courses & workshops for groups
•Methods manual
•Public database
•Supply of tools and materials
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19. How we do it!
Case Studies
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20. Cassava virology
1. CMD and CBSD diversity
2. Alternative hosts of CMD
3. Improve diagnostics
4. Virus-host interactions and host resistance
5. Whitefly vector: dynamics, host interaction and control
OJ Alabi and RA Naidu (WSU, USA) SA Akinbade & Ope
R Hanna, J Legg, G Melaku, E Kanju, P Ntawuruhunga & P Kulakow
•USAID-linkage grant, GLCI, IFAD, USAID
•IITA Opportunity Grant, Travel Grant & Strategic Grant
www.iita.org

21. Cassava mosaic disease
Caused by a complex of 7 species either alone or in mixed infection
•African cassava mosaic virus (ACMV)
•East African cassava mosaic virus (EACMV)
•South African cassava mosaic virus (SACMV)
•EACMV-Cameroon, EACMV-Malawi, EACMV-Kenya, EACMV-Zanzibar
EACMV-Uganda (Recombinant virus)
www.iita.org

22. CMG Distribution
• Surveys were conducted in 7 countries
• Samples analyzed by differential PCR &
sequencing
80
70
60 ACMV
% incidence
50 Both
40 None
30 EACMV
20 UgV
10
0
9
9
09
8
ia
08
08
89
-0
-0
-0
er
ie
08
e
la
a
a
07
ig
on
or
n
n
go
on
N
ha
ha
n
Iv
Le
An
ni
o
d'
G
G
er
Be
ra
e
am
er
ot
C
Si
C
•Only ACMV was detected in samples in Mali and Niger.
•EACMV-UG was detected in Angola and Cameroon.
www.iita.org

23. Tracking the spread of EACMV-UG
2009
2008
2009
•As of 2005, Spread in 2.6 million sq. km causing an
estimated loss of 47% in affected countries.
•Spread into Cameroon in West-Central Africa
•Spread into Angola in Southern Africa
•Also reported from Burkina Faso and Togo in 2009
Kumar et al, 2008; Akinbade et al., 2010
www.iita.org

24. CMG Distribution
Conclusions
•ACMV is predominate, followed by mixed infection of ACMV and EACMV.
•Other viruses found are EACMV and EACMCV, but not SCMV or other EACMV’s
•EACMV-UG was detected only in Angola and Cameroon
•DNA-A segments of ACMV, EACMCV and EACMV-UG sequenced were
96-98% identical to previously reported sequences
g i|1 4 8 8 9 7 7 4 7 || E a s t Afric a
• Evidence of EACMCV (recombinant
g i|2 2 1 3 6 0 4 3 4 |E a s t Afr ic a
g i|8 9 3 3 0 6 1 7 |e E a s t Afr ic a n
species) in Ghana even in 1989, ten 99
g i|8 9 3 3 0 6 7 1 |e E a s t Afric a n
g i|7 2 2 9 2 8 8 | E a s t Afric a n c
years before its discovery. g i|7 2 2 9 2 8 2 | E a s t Afric a n c
g i|1 4 8 8 9 7 7 4 0 || E a s t Afric a
g i|8 9 3 3 0 5 5 5 |E a s t Afr ic a n
• Isolates have same age as the first ever 100
51 g i|8 9 3 3 0 5 8 3 |E a s t Afr ic a n
g i|8 9 3 3 0 9 4 2 |E a s t Afr ic a n
sequences of ACMV published in 1980s. g i|8 9 3 3 0 7 4 8 | E a s t Afric a n
g i|8 9 3 3 0 9 6 3 |E a s t Afr ic a n
74
g i|8 9 3 3 0 9 6 3 E a s t Afr ic a n
g i|3 8 9 2 5 6 9 |E a s t Afr ic a n
• First ever recombinant ACMV 70 g i|7 0 0 8 1 1 3 |S o u th Afric a n
AC M V F N4 3 5 2 7 7
found in in Angola 100 G h a n a 1 9 8 9 AC M V
IC M V AY 7 3 0 0 3 5 .2
100 S L C M V |NC 0 0 3 8 6 1
E AC M C V -T z 1 AY 7 9 5 9 8 3
100
E AC M C V -NG E U6 8 5 3 2 3
100
E AC M C V -Iv o ry AF 2 5 9 8 9 6
G h a n a -1 9 8 9 - E AC M C V
Kumar et al., 2008; Akinbade et al., 2010 www.iita.org

25. Recombinant ACMV
•Two types of ACMV detected: Wild type and Recombinant ACMV
• Entire AV1 and AV2 (ca 1000 bp) in DNA-A segment in recombinant
ACMV has high similarities with EACMV.
• Named as ACMV-ANG. Further studies required to assess its affect on
pathogenicity.
A16.3RecACMV Recombinant ACMV-ANG
A16.3UGMld Potential parent of ACMV
ACMVX17095
ACMVAJ427910
ACMVICAF259894
ACMVSvrAF126802
ACMVMldAF126800
ACMVTZAY795982
EACMZVAJ717562
EACMKVKEAJ71758
0
SACMVNC003803
EACMCVAF112354
EACMCVNG
EACMCVIC
EACMMVAJ006460
EACMVKEAJ717542
EACMVTZ
EACMVUG2Mld Potential parent of
AV1 and AV2
EACMVUG2Svr
EACMVNC004674 www.iita.org

26. Alternative hosts to CMGV
ACMV+EACMV
Senna occidentalis
Leucana leucocephala
Manihot glaziovii
Combretum confertum
Glycine max (soybean)
ACMV only
Ricinus communis Centrosema Sida
Abelmoschus esculentus (Okra)*
Centrosema pubescens
Sida cordifolia*
• ACMV and EACMCV has high
homologies
• Indicates active migration
between cassava and other hosts Leucana Okra
• Risk of novel recombination's
*New record in 2009 Alabi et al., 2008
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27. Cassava brown streak virus
Potyviridae: Ipomovirus
?
Prior to 2005
Post 2005
?
• First recognized in 1920s.
• Affecting 1.6 million people in Eastern Africa
• Kenya, Uganda, Tanzania, Malawi and Mozambique
• Suspected in DRC, Burundi and Rwanda
www.iita.org

28. FJ687181 CBSV (GRL00508) pCP
FJ687175 CBSV (GRE05008) pCP
FJ687169 CBSV (GRE03908) pCP
AY008440 CBSV (type C) CP
GQ329864 CBSV-Tz (full sequence) 200...
FJ687179 CBSV (GRL00108) pCP
FJ687178 CBSV (GRE07108) pCP
FN434437 CBSV-Tan 70 (full sequence) ...
Ug Ke CBSV Diversity
FJ687182 CBSV (GRL00808) pCP
FJ687184 CBSV (GRL01008) pCP
FJ687164 CBSV (GRAO7208) pCP
Tz
FJ687197 CBSV (GRS00608) pCP
FJ687170 CBSV (GRE04408) pCP
FJ687176 CBSV (GRE05108) pCP
FJ687166 CBSV (GRE03108) pPC
FJ687173. CBSV (GRE04708) pCP
FJ687172 (GRE04608) pCP
FJ687168 CBSV (GRE03708) pCP
• About 50 partial coat protein (3’end)
sequences generated at IITA.
FJ687167 CBSV (GRE03608) pCP
FN434436 CBSV-Mo 83 (full sequence) 2...
M
FJ687191 CBSV (GRL02708) pCP
FJ687186 CBSV (GRL01408) pCP
FJ687202 CBSV (GRS05708) partial CP
61
82
FJ687201 CBSV (GRS05608) Partial CP
FJ687185 CBSV (GRL01308) pCP
FJ687183 CBSV (GRL00908) pCP
• High diversity, two groups, but no
FN423417 CBSV-CP (Nampula-Mozambique ...
FJ687196 CBSV (GRS00208) pCP
FJ687192 CBSV (GRL02908) pCP
evidence of geographic separation.
FJ687188 CBSV (GRL01808) pCP
FJ687165 CBSV (GRA07308) pCP
81 FJ687194 CBSV (GRL03308) pCP
61 FJ687180 CBSV (GRL00408) pCP
AY007597 CBSV CP
FJ687205 CBSV (GRS07008) partial CP
FJ687199 CBSV (GRS03208) pCP
FJ687203CBSV (GRS5908) partial CP
FJ687200 CBSV (GRS05208) partial CP
FJ687204 CBSV (GRS06308) partial CP
FJ687198 CBSV (GRS01708) pCP
FJ687189 CBSV (GRL02308) pCP 100 FN433933 CBSVM 43 2007 (M
a alawi:Salima)
AY008442 CBSV (type A) CP
FJ821795 CBSV (KBH1) CP 79 FN433932 CBSV-M 42 2007 (M
a alawi:Chit...
UG, Ken, Mal
64 FJ821794 CBSV (KBH2) CP
92-95%
AF311053 CBSV
61
69 AF311052 CBSV FN434109 CBSV-Ug 23 (full sequence) 2...
86-87%
67 FJ687195 CBSV (GRL03408) pCP
FJ687193 CBSV (GRL03108) pCP 70
66 FN423418 CBSV-CP (Naliendele-2-Tanzan... FN433930 CBSVKenya 125 1999 (Kenya:K...
FN423416 CBSV-CP (Naliendele-1 Tanzan...
100
70-71%
AY008441 CBSV (type B) CP
FN433930 CBSV Kenya 125 1999 (Kenya:K...
FN433931 CBSV-Ke 54 1997 (Kenya:Kilifi)
95 Sh1.1 U 100
89 Sh1.4 U
CBSV-TZ-Short-1
FJ185044. CBSV-Uganda (2006)
92 CBSV-TZ-Short-2
61 EU916832 CBSV (BSA4) CP N 012698 CBSVisolate M full geno...
C LB3
EU916830 CBSV (IGA8) CP
FN434437 CBSV-Tan 70 (full sequence) ...
79-80%
EU916827 CBSV (NTG10) CP
Tz, Moz
EU916829 CBSV (LWR2) CP
EU916828 CBSV (HMA9) CP
96%
FN434109 CBSV-Ug 23 (full sequence) 2...
100
FN434436 CBSV-M 83 (full sequence) 2...
o
DQ837304 CBSV (WKS) pCP
99 DQ837303 CBSV (NAM) pCP
DQ837302 CBSV (MKN) p 100 GQ329864 CBSV-Tz (full sequence) 200...
54 Ten11.2 U
72
EU916831 CBSV (BSA2) CP
EU916825 CBSV (MLB3) CP
NC 006941 CVYV
84 NC 012698
EU916826 CBSV (MLB9) CP
84 FN433932 CBSV-Ma 42 2007 (Malawi:Chit...
FN433933 CBSV Ma 43 2007 (Malawi:Salima)
NJ Tree of full-length CBSV genomes
FN433931 CBSV-Ke 54 1997 (Kenya:Kilifi)
0.1
Sequences from Genebank
CBSV-TZ-Long-1
Lg1.1 U
87 Lg1.3 U
CBSV-TZ-Long-2
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29. Improved diagnostics
CBSV and CMBVs are complex and often necessitates multiple tests.
Cassava brown streak virus
•Sequence information points to divergent types (2 species and several strains?)
Cassava mosaic begomoviruses (CMBVs) in SSA
• African cassava mosaic
• East African cassava mosaic
• East African cassava mosaic Cameroon virus
• East African cassava mosaic Zanzibar virus
• East African cassava mosaic Malawi virus
• East African cassava mosaic Kenya virus
• East African cassava mosaic virus-Uganda
• South African cassava mosaic virus
• Indian cassava mosaic
www.iita.org

30. Simultaneous detection of
ACMV and EACMV complex
Primer Sequence (5’ to 3’) Length (nts) Size (bp)
CMBRep/F CRTCAATGACGTTGTACCA 19
ACMVRep/R CAGCGGMAGTAAGTCMG 17 368 for ACMV
EACMVRep/R GGTTTGCAGAGAACTACATC 20 650 for EACMV
• Detects all CMBs reported in SSA, with
exception of EACMZV, SACMV, ICMV, SLCMV
Alabi et al., 2008
www.iita.org

31. Multiplex PCR for simultaneous
ACMV
EACMCV detection of CMBV and CBSV
CBSV-S1/S2 + CMB CBSV-L1/L2 + CMB
Sap DNA&RNA
ACMV & Sap DNA & RNA
M1 2 3 4 5 6 7 1 2 34 5 6 7 M1 2 3 4 5 6 7 1 2 34 5 6 7 M
EACMCV
EACMV
ACMV
CBSV
Lanes 1 to 4: CBSV infected samples
Lane 5: Healthy cassava
Lane 6: CMD afffected cassava
Primer name Sequence (5’ to 3’) Lane 7: CBSD affected cassava
Lane M: Molecular weight marker (100 kb ladder)
CBSVcp-L1 CAGAATAGTGTTGCTGCAGGTAA
CBSVcp-L2 CTACATTATTATCATCTCC
CBSVcp-S1 GCAGGTAAGGCGTTTGTG
CBSVcp-S2 TCTACCAACATTCGCTG
Kumar et al., 2009
www.iita.org

32. Ongoing / future priorities
CBSD
• Improvement in diagnostics – NASH and RT-PCR (GLCI)
• Alternative hosts for CBSV (GLCI)
• Impact of CBSV strains on host resistance (GLCI & USAID)
• Understand the causation of root necrosis (GLCI)
• CBSV evolution and within field and location diversity (USAID)
• ELISA-based assays to CBSV (USAID / GLCI)
• Protocol for the production of CBSV-free tissue culture material (GLCI)
CMD and CBSD
• Whitefly management programs as away to reduce disease incidence (IITA
Strategic grant)
Generic
• Monitoring programs to prevent the spread of CBSD and EACMV-UG spread
CMGV and CBSV diversity and its impact on host resistance
• Development of dual resistant cassava varieties
www.iita.org

33. Maize virology
1. Host plant resistance to Maize streak virus
2. Mechanisms of resistance
3. High-throughput phenotyping for MSV
• MSV is restricted to only Africa
• The most damaging disease of maize in SSA
• Annual losses, $120 – 480 million
• Breeding for MSV resistance is integral in our programs
A Menkir and S Hearne
M Salaudeen, O Taiwo, A Razaq
•DTMA and Core funds
www.iita.org

34. Screening for MSV resistance
6-7 DAS
Material selection
1 0
7
60
54 Days after 10
3
48 sowing
42
36
30
14
9-10 DAS
Inoculation with leaf hoppers
30 to 50 DAS
Symptom scoring
at weekly intervals
13-14 DAS
First symptoms
(most genotypes have 3-4
days incubation period)
www.iita.org

35. High-throughput phenotyping for MSV
Disease evaluation
0 = No infection or escape
1 = Most resistant (less than 10% streaks)
2 = Resistant (10-25% streaks)
3 = Moderately resistant (25-50% streaks)
4 = Susceptible (50-75% streaks)
5 = Highly susceptible (>75% streaks)
Virus quantification in plants by ELISA
Rep # 1 Rep # 2 Rep # 3 Rep # 4
Control line
Test line
S5 S4 S3 S2 S1
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36. Good recovery Susceptible
Good recovery
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37. Performance of maize genotypes
Group A
High recovery
5.0
MsvS10
Severity score
4.0
MsvS09
3.0
MsvS18
2.0
MsvS08
1.0
Msv S26
0.0
MsvS07
1 2 3 4 5 6
MsvS12
MsvS04 Weeks
Group B
MsvS11
MsvS20
5.0
MsvS03
4.0
MsvS17
3.0
score
Msv S30
2.0
MsvS19
1.0
MsvS02
No recover Group C
0.0 MsvS22
1 2 3 4 5 6 MsvS06 Msv S27
Weeks MsvS01 6.0 MsvS16
MsvS14 5.0 MsvS15
Moderate recovery
Severity
MsvS24 4.0
Msv S28
3.0
MsvS13
2.0
MsvS21
1.0
MsvS23
0.0
1 2 3 4 5 6 Msv S25
Msv S29
Weeks
Pool 6 control
www.iita.org

38. Virus concentration vs Severity score
0.80
0.60
Leaf 1
ODv values
0.40 leaf 2
Leaf 3
0.20
After 6 weeks
0.00
MX10 MX5 MX3 MX4
6.0
5.0 Week 1
4.0 Week 2
score
Week 3
3.0
week 4
2.0
week 5
1.0 week 6
0.0
MX10 MX5 MX3 MX4
Group A B Genotype
C D
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39. Recovery mechanism offers
protection to MSV
6.0
5.0
4.0 Group A
Group B
3.0
Group C
2.0 Pool 6 control
1.0
0.0
1 2 3 4 5 6
• No evidence of resistance to leafhopper feeding.
• Incubation period is 3-4 days in genotypes evaluated so far
• Most genotypes showed recover type resistance (reduction in chlorotic
streaks as well as virus concentration)
• No indication of symptom remission.
• No immunity
www.iita.org

40. MSV resistance in S1 testcrosses
• Field experiment for incidence, severity and agronomic performance
• 6 S1 crosses were highly resistant to MSV and good agronomic performance.
• Resistance is superior to what has been found in MSV transgenics
(Shepherd et al., 2007)
80.0 3.5
67.6
Disease incidence (%)
70.0 3.0 3
58.3
Disease severity
2.8
60.0 2.5
2.5
50.0 45.0 45.2 2.1
2.0 2.02 Incidence
40.0
1.5 Severity
30.0
20.0 1
10.0 0.5
0.0 0
1WPI WPI3WPI WPI5WPI6WPI WPI8WPI WPI
2 4 7 9
Time (week)
Salaudeen et al., 2010
www.iita.org

41. On-going and future plans
• Further characterization of promising lines and release to farmers
• Augment resistance to MSV in other backgrounds
• Identification of association markers for MSV (DTMA)
• Mechanisms of resistance
• Host-MSV interactions
www.iita.org

42. Yam virology
• Diversity and distribution of viruses infecting yams
in West Africa
• Characterization of YBSD
• Development of diagnostic tools
• Symptomology and synergistic interactions
• Host resistance
• Evaluation of mapping population
• Virus-free seed systems
R Asiedu and A Sartie
O Patricia, R Ronke, M Toually and S Asala,
•IFAD and Core funds
www.iita.org

43. Virus reported to infect
Dioscorea yams in West Africa
Virus Distribution Disease importance
Yam mosaic virus Worldwide High
(YMV; Potyvirus)
Yam mild mosaic virus Worldwide High*
(YMMV; Potyvirus)
Cucumber mosaic virus Worldwide High*
(CMV; Cucumovirus)
Dioscorea bacilliform viruses (many Worldwide High*
strains and species) (DBV; Badnavirus)
Dioscorea sansibarensis bacilliform Benin Not known***
virus (DsBV; Badnavirus)
Yam internal brown spot virus Cote d’Ivory, Benin(?), High**
(IBSV; Badnavirus*) The Caribbean
Dioscorea ring mottle virus Togo Not known***
(DaRMV; Potyvirus)
Dioscorea mottle virus Nigeria Not known***
(DMoV; Comovirus?)
*Often detected in mixed infection; known to have synergistic effect on symptom expression
**Virus-like disease of unknown etiology
***Limited information on virus characters
www.iita.org

44. Yam virus diagnostics
• Diagnostic tools established for all major yam
viruses.
-Poly and monoclonal antibodies for Yam
mosaic virus, Yam mild mosaic virus, Yam
badna viruses available.
-Specific and generic primers for PCR/RT-PCR
based diagnostics.
-Methods for virus detection in tubers
established.
www.iita.org
©Lava - 09

45. Yam virus diagnostics &
symptomatology
• Uneven distribution of viruses in tubers
• Variation in symptom expression in plants
germinated from the same tuber.
• Evidence of synergistic interaction
between YMV and YMMV.
www.iita.org
©Lava - 09

46. Evaluation of mapping population
Virus indexing Following evaluation
Sl. Accession
No. name Genotype details* Tuber Plant
1 TDr 93-2 Resistant to YMV Y ng -
2 TDr 1621 Resistant to YMV Y ng -
3 TDr 1640 Resistant to YMV Y Y Susceptible
4 TDr 89/ 02665 Resistant to YMV Y - -
5 TDr 97/ 00777 Highly susceptible to YMV Y Y, B Susceptible
6 TDr 93-32 Highly susceptible to YMV Y Y Moderately Tolerant (Promising)
7 TDr 95/ 18531 Susceptible to YMV Y Y, B Susceptible
8 TDr 747 Susceptible to YMV Y Y, B Susceptible
9 TDr3661 Susceptible to YMV - Y, B Moderately Tolerant (Promising)
10 TDr 2261 Susceptible to YMV Y Y, B Susceptible
11 TDr 95-127 No information Y Y, B Susceptible
12 TDr 95/ 01932 No information Y ng -
13 TDr 99/ 02789 No information Y Y, B Moderate
14 TDr 98/ 01317 No information Y Y, B Moderately Tolerant (Promising)
15 TDa85/ 00250 Resistant to anthracnose Y,B Y, B Moderately Tolerant (Promising)
16 TDa87/ 01091 Resistant to anthracnose Y Y, B Moderately Tolerant (Promising)
17 TDa95/ 00328 Susceptible to anthracnose Y, B Y, B Tolerant (Recommended
18 TDa95- 310 Susceptible to anthracnose Y, B Y, B Tolerant Recommended
19 TDa92- 2 Susceptible to anthracnose Y, B Y, B Susceptible
20 TDa98/ 01166 No information Y Y, B Tolerant (Recommended)
www.iita.org

47. Evaluation of mapping population
www.iita.org

48. Yam brown spot disease (YBSD)
(Potential CBSD of yam?)
• A virus-like disease of unknown etiology
recognized in Cote d’Ivory in early 1980s,
and in Benin in 2008.
• Symptoms are similar to the internal
brown spot disease (IBSD) first reported
from the Caribbean in mid 1970s.
• Loss in tuber quality.
• This can emerge as a serious threat.
B
www.iita.org
©Lava - 09

49. Studies on IBSD etiology
1
2
3
1
4
3
2 5
1 2 3 4 5
www.iita.org
©Lava - 09

50. Studies on IBSD etiology
• Wide spread in Cote d’Ivoire
• Known for about 40 to 60 years
5
3
4
1
2
• Bètè-bètè is highly susceptible
Distribution and severity of necrotic symptoms in tuber
Tubers sections (mean)*
4
No. No. Percent 1 2 (apico- 3 (median-
observed symp* symp* (Top) median) (middle) base) 5 (base)
178 105 60 3.0 3.0 2.8 2.5 2.1
www.iita.org

51. Phenotyping yams for
virus resistance
•D. rotundata accessions were
evaluated in 2008-09 season.
•987 accessions in total (3488
plants)
Score:
1 = highly resistant (no visible symptoms)
2 = resistant (mild mottling/mosaic on few leaves)
3 = moderately resistant (mild mottling/mosaic on most leaves)
4 = susceptible (severe mottling / mosaic on most leaves)
5 = highly susceptible (severe mosaic/mottling, stunting and distortion) www.iita.org

52. Phenotyping yams for
virus resistance
Susceptible 5%
(Score 4)
Resistant 7%
Highly susceptible 5% (Score 2)
(Score 5) •There is no immunity or very
high resistance in these
germplasm.
N = 987
Moderately resistant 83%
(Score 3)
Score:
1 = highly resistant (no visible symptoms)
2 = resistant (mild mottling/mosaic on few leaves)
3 = moderately resistant (mild mottling/mosaic on most leaves)
4 = susceptible (severe mottling / mosaic on most leaves)
5 = highly susceptible (severe mosaic/mottling, stunting and distortion) www.iita.org

53. Next steps
• Determine the diversity of viruses in West Africa and improve diagnostic
tools
• Understand the etiology of YBSD
• Symptomology and yield losses
• Evaluation of mapping population for YMV
• Virus-free seed systems
www.iita.org

54. Soybean virology
• Baseline studies to assess the impact of
virus diseases on soybean
• Evaluation of improved varieties and
breeding lines against
widespread/economically important
viruses.
• Monitor seed stocks and eliminate virus
contaminated seed.
H Tefera, C Fatokun,
T Imbor, R Adesida and P Ogunsanya
•TL2 and Core funds
www.iita.org

55. Baseline studies in Nigeria
Virus Abbreviation Genus Vectors
1 Bean pod mottle BPMV Comovirus Beatles
2 Black eye cowpea mosaic BICMV Potyvirus Aphids
3 Cowpea aphid-borne mosaic CABMV Potyvirus Aphids
4 Cowpea mottle CMeV Carmovirus Beatles
5 Cowpea yellow mosaic CYMV Comovirus Beatles
6 Cucumber mosaic CMV Cucumovirus Aphids
7 Cowpea severe mosaic CpSMV Comovirus Beatles
8 Cowpea mild mottle CPMMV Carlavirus Whiteflies
9 Southern bean mosaic SBMV Sobemovirus Beatles
10 Tobacco streak TSV Nepovirus Nematodes
11 Soybean mosaic SMV Potyvirus Aphids
12 Soybean chlorotic blotch* SbCBV Begomovirus Whiteflies
13 Soybean mild mottle* SbMMV Begomovirus Whiteflies
14 Cassava mosaic virus** CMD Begomovirus Whiteflies
*New viruses; **New report Ezeri et al., 2009
www.iita.org

56. www.iita.org

57. 2.7
2.5
3.4
3.9 3.8
3.3
3.4
3.3 3.7
4.2
3.2 4.1
3
4.5
4
www.iita.org

58. Virus incidence in various states
120
100
% infection
80
60
40
20
0
Ba u
a
A d un a
Ka a
e
yo
hi
o
Ka o
a
er
pl a
as CT
a
gi
ea
b
w
n
aw
nu
rn
in
ar
uc
Ko
ig
O
ra
Ka
ra
F
ts
Bo
Kw
d
Be
at
N
am
Ta
sa
N
State
•Virus incidence exceed 50% in 13 of the 15 states (87%) surveyed
www.iita.org

59. Relative abundance of viruses in Nigeria
CpSMV
BICMV
SMV
CpSMV
TSV
Virus
BPMV
SBMV
CMeV
CYMV
CMV
CABMV
CPMMV
0 20 40 60 80 100 120
Proportion
Imbor et al., 2010
www.iita.org

60. Relative abundance of viruses in
latent infections
0.7 CMeV
1.5 BPMV
1.5 CABMV
virus
2 CYMV
4 TSV
9 CMV
CPMMV 99
Total = 166 100
0 20 40 60 80 100
% infection
www.iita.org

61. Distribution of viruses in Nigeria
Agro-ecological zone State Viruses present Total
Derived Sav Benue CPMMV,CABMV,CMV,CYMV, SBMV, BPMV, CMeV, TSV, SMV 9
Taraba CPMMV, CMV, CYMV, BPMV, CMeV, TSV,SMV 7
Kogi CPMMV 1
Oyo CPMMV, CMV 2
FCT CPMMV, CMV, BPMV, CMeV, TSV, CpSMV,SMV 7
Nassarawa CPMMV, CMV, BPMV,SMV 4
Sud/Sahel/N.G.Sav Katsina CPMMV 1
Kano CPMMV, CABMV, CMV 3
Kaduna CPMMV, CMV, BPMV 3
Sud/ South G.Sav Adamawa CPMMV 1
Niger CPMMV 1
Borno CPMMV 1
Kwara CPMMV, CMV 2
Mid-Altitude, Sud/D.
Sav Plateau CPMMV, CABMV, CMV, BPMV 4
Bauchi CPMMV 1
www.iita.org

62. New whitefly-transmitted
begomoviruses in soybean
[Legumoviruses]
•Soybean chlorotic blotch virus (SbCBV)
•Soybean mild mottle virus (SbMMV)
•Begomoviruses (legumogroup)
•Novel types within features of both new
world and old world begomoviruses
Alabi et al., 2010
www.iita.org

63. Novel features
CRA CRB
AC4
(2117…2410)
AV1
(260…1021)
SbCBV
SbCBV
2647 bp BV1
2708 bp AC5 BC1
(373…1158)
AC1 (701…995)
(1219…2310)
(1479…2567)
AC3
(1018…1431)
AC2
(1163…1579)
First bipartite legumoviruses
that lack AV2 gene;
IR
V2
(1…507)
C4
SbMMV
(2198…25)
2768 bp V1
C1
First monopartite legumovirus
(299…1072)
(1563…2612)
C3
(1069…1473)
C2
(1187…1624)
www.iita.org

64. 96 AYVV AJ558120
100 CoTSV DQ875869
57 SbCLV AB050781 68 SiYMYuV DQ875873
77 AYVHuV DQ866124
SiGMV AF0841
TbLCYnV AJ512761 80
86 AbMV X15984
ToLCMYV AF327436
ToMHV Y14875
StaLCuV AJ810156
80
EpYVV AB007990 Asia 100 ToMoTV
ToMoV
AF012301
AY965901
VeYVV AM182232 97
BDMV M88180
81 66 PepLCV AF134484
61 ToLCSinV AJ508783
69 TYLCCNV AJ319675 79
89 CdTV AF101478
ToLCTWV DQ866125 55
95 ToLCVV DQ641705 SiGMCRV X99551
67
AYVSLV AF314144 SiGMHV Y11098
99
92 ChiLCV DQ6759 100 SiYVV Y11100-1
ToLCBDV AF188481 CLCrV AF480941
86 99
AEV AJ437618 DesLDV DQ875871
99 85
CYVMV AJ507777 PYMPV Y15033
99
85 PaLCuV Y15934 100 PYMV D00941
100
ToLCNDV DQ169056 India 73 BGMV
TGMV
M88687
K02030
100 ICMV Z24758
SLCMV AJ579307 99 SiMMV AJ5573
100 ToRMV AF291706
New World
CLCuBV AY7050
55
Old World
BYVMV AF241479 97 SiMoV AJ5574
100 OYVMV AJ0021 100 ToYSV DQ336351
100
CLCuGV AF155064 70 BGYMV AF173556
100 100 55
CLCUGV EU024120 MaYMFV AY044136
HoLCrV AY036009 56 MaMPRV AY044134
ACMV X17095 DiYMoV AF170101
TLCuKV EU350585 MeMV AY965899
92 75 TbLCZV AF350330 TYMLCV AY508994
85 ToCSV AF261885 99 PHYVV AY044163
75 88 ToYLCrV AY502935 RhGMV DQ356429
59 ChaYMV AJ223191 100 CabLCuJV DQ178609
66 61
93 OYLCrV EU024119 CabLCuV U65530
76
86
ToLCMLV AY502936 Africa 55 61 PepGMV AY928517
ToLCArV DQ519575 76 RhGMSV DQ6673
100 TYLCMalV AF271234 82 BCaMV AF110190
TYLCMLV FM212660 EuMV DQ3189
97 EACMCV AF112354 CuLCrV AF327559
91 82
EACMV AJ717542 MCLCuV AF4790
75 56 EACMMV AJ0060 97 SLCV M182
SACMV AF155806 100 SMLCV AF421553
100 EACMKV AJ717580 ToCMoV AF491306
97 EACMZV AJ717562 ‘Legumovirus’ CoGMV DQ641689
Africa
CPGMV AF029217 100 CoYVV AY727904
SbCBV GQ472985 100 SLCCNV AF509742
100 SbCBV GQ472987 98 SLCPHV AB085794
100
SbMMV GQ472984 100 LYMV AF5097
98
DoYMV AY309241 ToLCGV AY190291
100
99 KuMV DQ641690 100 ToLCNDV DQ169057
Asia
66 RhYMV FM208848 ICMV Z24759
99
100 MYMIV AY049772 SLCMV AJ579308
100
96 HgYMV AJ627904 ClCMV DQ641693
100 MYMV AJ421642
95 PepLCIV AB2678
CoYVV AY727903 100
100
CoGMV DQ641688 Jute 100
100
TYLCKaV
TYLCTHV
DQ169055
X63016
DiYMoV AF1168 100 HgYMV AJ627905
100 100 PepGMV AY928516 100
New World
97 MYMV AJ867554
Old World
SLCV M183 100 MYMIV AY049771
100
60
BGMV M88686 Americas 99 KuMV DQ641691
BDMV M88179 RhYMV FM208848
56
81 CdTV AF101476 ACMV X17096
100 ToMoV AY965900 100 SbCBV GQ472986
91 SiGMV AF049336 99
100 SbCBV GQ472988
SPLCESV EF6741 WmCSV AJ2653
SPLCGV AF326775 95
EACMCV AF112355
100 SPLCCaV EF6742 100 EACMV AJ704949
99
68
SPLCLaV
IYVV
EF67
AJ132548
Sweet potato 100 EACMZV AJ704942
100 EACMKV AJ704965
61
100
SPLCV
BSCTV
AJ586885
U02311
66 SACMV
BSCTV
www.iita.org
AF155807
U02311

65. Search for resistance to CPMMV
TGX 1448-2E TGX1903-1F TGX1951-4E
TGX1440-1E TGX1903-3F TGX1954-1F
TGX1485-ID TGX1904-4F TGX1955-4F
TGX1740-2F TGX1904-6F TGX1956-1F
TGX1830-20E TGX1908-8F TGX1961-1F
TGX1835-10E TGX1910-14F TGX1963-3F
TGX1844-18E TGX1932-1F TGX1965-7F
TGX1844-4E TGX1935-3F TGX1971-1F
TGX1869-31E TGX1937-1F TGX1972-1F
TGX1871-12F TGX1945-1F TGX1987-10F
TGX1876-4E TGX1949-7F TGX1987-14F
TGX1889-12F TGX1950-7F TGX1987-43F
TGX1895-33F TGX1951- 3F TGX1987-57F
TGX1895-50F TGX1987-62F
TGX1987-8F
•47 elite lines evaluated in screenhouse
•No immunity, variation in susceptibility
•Activity in progress
www.iita.org

66. Soybean reaction to CPMMV
250
200
No. of seeds
150
100
50
0
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43
Control Accessions
(8 plants per accession)
Susceptible check
www.iita.org

67. Disease of unknown etiology
• Virus-like disease of
unknown etiology.
• Extreme reduction in
leaf lamina, stunting of
plant and thickening of
stems.
• African soybean dwarf?
www.iita.org

68. New soybean disease in
Southern Africa
•Incidence of soybean phyllody was high in Mozambique (15-25%)
Virus disease incidence was very low in Southern Africa
•Low incidence
•CPMMV and SMV detected in few fields
www.iita.org

69. Next steps
• Evaluation of soybean genotypes for resistance to
abundant viruses (CPMMV, SMV, CMV, BPMV, CABMV)
• Characterization of soybean phyllody
• Diagnostics for common soybean viruses
• Characterization of new soybean infecting viruses
www.iita.org

70. Cowpea virology
Focus:
• Evaluation of germplasm
(landraces / improved varieties)
for resistance to viruses
[adding value to drought and striga
resistance; earliness etc.]
• Breeding for multiple virus
resistance
• Establishment of virus-free cowpea
seed stocks
C Fatokun, B Ousman
K Ogunsola, R Adesida, P Ogunsanya
Core and TL2
www.iita.org

71. Important viruses of
cowpea in West Africa
Virus Abbreviation Genus Vector
1 Blackeye cowpea mosaic BlCMV Potyvirus Aphids
2 Cowpea aphid-borne mosaic CABMV Potyvirus Aphids
3 Cucumber mosaic CMV Cucumovirus Aphids
4 Cowpea mottle CMeV Carmovirus Beetles
5 Cowpea mosaic CPMV Comovirus Beetles
6 Southern bean mosaic SBMV Sobemovirus Beetles
7 Cowpea mild mottle CMMV Carlavirus Whiteflies
*All these viruses are seed transmitted
Viruses of minor importance (sporadic incidence):
Bean pod mottle virus; Peanut mottle; Sunn-hemp mosaic;
Cowpea golden mosaic; Cowpea severe mosaic virus
www.iita.org

72. Distribution of cowpea infecting
viruses in West Africa in 2008
www.iita.org

73. Cowpea virus diversity and distribution
1978 samples from 166 sites from 5 countries (2008-09)
Ghana and Togo
45
(N=639)
40
Nigeria (N=833)
35
%Infection
30
25
20 Benin and Mali
(N=899)
15
10
5
0
CAbMV
CAbMV
CAbMV
CPMMV
CPMMV
Mixed infect
CPMV
CPMMV
CPMV
BlCMV
BlCMV
CPMV
Mixed infect
SBMV
SBMV
CMV
CMV
CMeV
BlCMV
CMeV
SBMV
CMV
CMeV
Mixed infec
• Present situation is not significantly different from a decade ago.
• Virus equation remains same: CABMV > BlCMV > CPMV > SBMV > CMoV > CMV
www.iita.org

74. Cowpea viruses in
southern Africa
• Severe incidence in
Mozambique
• Detected: BlCMV,
CpSMV, CMV, CABMV,
SBMV
• Evidence of new
strains / species
www.iita.org

75. Screening elite lines for
virus resistance
www.iita.org