Maize Lethal Necrosis (MLN): Progress in finding solutions to a new threat to maize in Africa

www.iita.orgA member of CGIAR consortium
Maize Lethal Necrosis (MLN):
23 November 2015
(R4D Week 2015)
Progress in finding solutions to a new threat to maize in Africa
Lava Kumar et al

A member of CGIAR consortium www.iita.org
23 November 2015, R4D Week 2015
Maize Lethal
Necrosis (MLN):
Progress in finding solutions to
a new threat to maize in Africa
Lava Kumar et al.
L.kumar@cgiar.org

Viral disease of maize

Maize streak virus (MSV) is an
endemic threat to maize in Africa
Leaf hopper (C. mbila)
• Widespread in Africa
• Transmitted by leafhoppers
• Causes severe yield reduction in
susceptible lines
• MSV resistant lines developed for
disease control

Outbreak of a new maize
disease in Kenya
• First outbreak in
September 2011 in Bomet
county in Kenya
• Necrosis, rapid decline
and premature death of
plants
• Rapid spread within and
between the fields
• Referred as ‘Bomet
Disease’

Outbreak of a new maize disease

Cobs from MCMV infected plants

• Yield losses vary from 30 to 70% depending on the
stage of infection
• In 2012, MLN outbreak in Kenya affected 77,000 ha ;
destroyed production worth US$52 million
• All the farmer adopted lines and hybrids are highly
susceptible

Maize chlorotic mottle virus
Sugarcane mosaic virus
The new disease identified as maize lethal necrosis
(MLN) caused by mixed infection of two viruses

The new disease identified as maize lethal necrosis
(MLN) caused by mixed infection of two viruses
SCMV
+
MCMV
Synergistic
interaction
• SCMV is known to be endemic and widespread in Africa. Not known to
be a threat to maize.
• MCMV is a new record in the continent; and the main contributor for
MLN outbreak.
• MCMV on its own can cause severe symptoms and yield losses.
• Both viruses have wide host range

Pedigree
Grain Yield (tha-1)
Optimal Conditions
Grain Yield (tha-1)
MLN
SYN(B)F2-5-8/CML539/CML442 7.6 2
SYN(B)F2-17-1/CML539/CML442 7.2 2.2
SYN(B)F2-14-3/CML539/CML442 7.1 1.8
SYN(B)F2-17-4/CML539/CML442 7.1 2.2
SYN(B)F2-19-4/CML539/CML442 7.1 1.6
SYN(B)F2-11-11/CML539/CML442 7.1 2.2
SYN(B)F2-5-5/CML539/CML442 7.0 2.9
SYN(B)F2-23-5/CML539/CML442 7.0 2.1
SYN(B)F2-22-3/CML539/CML442 7.0 1.4
SYN(B)F2-5-1/CML539/CML442 7.0 1.5
SYN(B)F2-5-4/CML539/CML442 7.0 1.1
SYN(B)F2-14-13/CML539/CML442 7.0 1.3
SYN(B)F2-9-1/CML539/CML442 6.9 1.5
SYN(B)F2-6-6/CML539/CML442 6.9 2.5
SYN(B)F2-12-2/CML539/CML442 6.9 1.1
SYN(B)F2-12-3/CML539/CML442 6.9 1.3
SYN(B)F2-17-3/CML539/CML442 6.9 2
SYN(B)F2-14-14/CML539/CML442 6.8 1.7
SYN(B)F2-7-1/CML539/CML442 6.8 2.2
SYN(B)F2-7-3/CML539/CML442 6.8 1.7
SYN(B)F2-11-8/CML539/CML442 6.8 0.4
Commercial Check 6.0 0.9
Mean 6.4 1.60
LSD (0.05) 2.3 1.33*
CV 18.8 41.85
Maize yield losses associated
with MLN-Babati
75%
reduction in
yield

2004
Thailand
2010
China
2012
1974
Peru
1976
USA1989
Mexico
MCMV distribution
MCMV has been identified in two MLN outbreaks
1. Kansas state USA (1980s)
2. Eastern Africa (since 2011)

Distribution in Africa
•Kenya (2012)
•Tanzania (2013)
•Uganda (2013)
•Rwanda (2013)
•Burundi (2013)
•South Sudan (2013)
•DRC (2014)
•Ethiopia (2014)
MCMV spread in Africa

• Delayed initial diagnosis
– Unfamiliar disease
– Lack of awareness
– Lack of diagnostic capacity
• Once established, difficult to control
• Limited control options (mainly regulatory
control)
– Multiple sources of inoculum
• Soil, residues and water
• Seed
• Vectors
Challenges to MLN control

IITA’s R4D focus on MLN
•MLN epidemiology (AfricaRISING and CRP): Causes and factors
contributing to disease spread
•Development of MLN diagnostics (BMGF, AfricaRISING and CRP):
Tools for reliable detection of causal viruses
•Breeding for MCMV resistance (CRP & BMGF): Evaluation of
maize lines for assessing host response to MLN causal agents and
finding promising lines for breeding
•Risk assessment & pre-emptive management (CRP): Determine
the spread risk potential and preparedness in Central and Western
Africa.
SARI
Sealian Agricultural
Research Institute

1. Understanding MLN Epidemiology
Sub-Humid District
(1610 to 2178 mts)
Semi-Arid Districts
(1261- 1527 mts)
Medium elevation
Studies in Tanzania

MCMV + SCMV
(MLND)
MCMV only
MCMV SCMV
SCMV+
MCMV MSV
51 (64%) 18 (22.5) 17 (21.5) 16 (20)
Viruses detected (N = 80 samples)
SCMV only
Incidence of MLN agents differ
First survey in 2013
•MCMV alone can cause severe symptoms

MCMV spread into DRC
• Only MCMV was detected in the MLN
outbreak in DR Congo.
• It is very likely that MLN-like severe
symptoms can result from MCMV infection
alone.
• Controlling MCMV is critical for MLN control

MLN surveys in 2015 in
Tanzania
Widespread and expanding; incidence between 5 to 70%

0.0
20.0
40.0
60.0
80.0
100.0
120.0
1
4
7
10
13
16
19
22
25
28
31
34
37
40
43
46
49
52
55
58
61
64
67
70
73
76
79
82
85
88
91
94
97
100
103
106
109
112
115
118
121
124
127
Manyara Dodoma Arusha
Babati
Percentincidence
Prevalence and incidence of maize lethal
necrosis in 2015 crop season (N = 116)
Kiteto Hanang Mbulu Simanjiro KKongwa AKondoa MCh Mo

MLN Virus MSV
Incidence of viruses
1 - 34%1 - 62%0 - 37%

MLN Virus MSV
Prevalence of viruses
10 - 100%51 - 100%0 - 100%

JX286709-MCMV (Kenya)
MCMV-DRC (KJ699379)
JQ982468-MCMV (Yunnan2)
KF010583-MCMV (Yunnan)
GU138674-MCMV (Yunnan)
EU358605-MCMV (USA)
X14736-MCMV (USA)100
99
84
63
0.002
MCMV diversity in East Africa
•Viral isolates from Kenya, Tanzania and DRC
are 99 – 100% identical to MCMV China isolates
•SCMV isolates were similar but greater
diversity observed in some locations
Africa

D02_Rm2COI_826285
E02_Rm3COI_826286
G04_RmECR1_826304
G11_RmECR2_826360
H11_RmECR3_826361
A05_RmAIbo_826306
B01_F11TTa_840483
D03_Rm4COI_826293
C02_Rm1COI_826284
F02_Rm3bCO_826287
HQ112195India-R maidis
F01_F12Tan_840487
G01_F9Tanz_840488
A01_F10Tan_840482
C01_F11BTa_840484
TANZF13COF
D01_F2Tanz_840485
GU457795RhoKorea-R padi
GU140277Canada-P nigronervosa
100
100
99
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.07
0.02
0.03
0.04
0.01
0.01
Rhopalosiphummaidis
Rhopalosiphumpadi
• Molecular analysis (COI gene-based taxonomy) confirmed R. padi
as common aphid vector of SCMV.
• Corn thrips, Frankliniella williamsi common vector of MCMV
MLN Vectors

Late planting in March
(High incidence)
Early planting in
January (no or low
incidence)
MLN disease cycle
Vectors
Maize growing period

MCMV Seed transmission
•Seed collected from infected plants for
seed transmission assay
•High rate of seed loss due to fungal
infection. Survived seed planted.
•Total 48 batches of 7 hybrids / lines; 500
seed tested per batch.
•11,527 of 24,000 planted seed germinated
(48% germination)
•No evidence of MCMV in the seed lots
tested
•MCMV seed transmission suspected for long range spread in Africa
•Previous reports indicated 0 to 0.33% rate of MCMV seed transmission
•MCMV can be detected in the seed

2. New diagnostics for MCMV
Scaling of new diagnostic tools developed in
AfricaRISING
•New diagnostics for MCMV
developed in 2013-14
•Recombinant polyclonal
antibodies against MCMV

• Single tuber Multiplex PCR for simultaneous
detection of all the major maize viruses
Improving diagnostics
10-1 -2 -3 -4 -5 -6 -7
Multiplex assay detected up to
10-3 dilution

New diagnostics
RT-
LAMP
Dilutions MCMV MSV
1 1:1000 + +
2 1:5000 + +
3 1:10000 + +
4 1:100000 + +
5 1:1000000 + +
6 1:10000000 + -
7 Buffer - -
8 Water - -
MSV
MCMV
• Reverse transcriptase/Loop-mediated isothermal amplification
(LMPA) assay.
• Further modified to develop UDG-LAMP to avoid contamination

• Established a MLN diagnostic Lab at Selian
Agricultural Research Institute (SARI), Arusha
• Pathology lab refurbished with essential equipment
• Training to staff
Developing diagnostic capacity

• 22 persons trained from Tanzania and
• Field and lab diagnosis | Insect vector identification
• Disease control
Developing diagnostic capacity

3. Breeding for MLN Resistance
• IITA initiated pre-emptive breeding for deploying MLN resistance
in cultivars and lines preferred in West and Central africa
• Evaluation CIMMY – KALRO MLN phenotyping facility at Naivasha,
Kenya

Initiation of pre-emptive breeding against the
spread of MLN to West and Central Africa
• 40 elite inbred lines screened and 3 promising inbred lines with
moderate resistance to MLN identified
• Used as partners to develop 22 bi-parental crosses in 2014
• The 22 bi-parental crosses were self pollinated in 2015 to
develop MLN resistant inbred lines
• Additional 33 bi-parental crosses involving other elite
inbred lines were successfully made in 2015
• Inbred lines with resistance to MLN introduced from CIMMYT
for crossing to expand the genetic base of resistance source
germplasm

0.0
1.0
2.0
3.0
4.0
5.0
6.0
Score1 Score2 Score3 Score4
MLNScores(1-5)
TZMI730 TZMI746
TZMI723 TZMI740
TZMI764 TZMI765
• Identification of MCMV resistant lines for use in crossing
Initiation of pre-emptive breeding against the
spread of MLN to West and Central Africa
TZMI723
TZMI730
TZMI746

•SCMV and MSV detected but not MCMV
•Aphids and thrips are widely distributed
• Baseline study for maize
viruses
• Assessment of risk to
seed production sector
• Awareness creation
about MLN
• Capacity development
of regulatory authority
• Understanding viruses
in perennial cereal
hosts (e.g. sugarcane)
Pre-emptive control

Unknown’s
•Rate of transmission
•Virus transmission through seed
•Inoculum survival
•Vector diversity and their role in spread
•Effect of environment and farmers practices
•Disease distribution in MLN affected countries
Knowledge gaps

MLN: Ebola of Maize
•MLN outbreak is a spoiler of maize revolution in Africa.
•Severely reduced maize production
•Crippled commercial seed industry in Kenya
•Forced re-strategising of maize improvement
programs (search for identification of high levels of
resistance to recovery maize production)
•Pre-emptive control (surveillance), preparedness and
emergency response plans are critical to save maize
from invasive threat.
Conclusions & Lessons

Acknowledgments
SARI
Sealian Agricultural
Research Institute

Maize Lethal Necrosis (MLN): Progress in finding solutions to a new threat to maize in Africa

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Maize Lethal Necrosis (MLN): Progress in finding solutions to a new threat to maize in Africa