Presentation at the RTB Annual Review and Planning Meeting (Entebbe, Uganda, 29 Sep-3 Oct 2014)

1. Theme 3
Managing Priority Pest & Diseases of RTB Crops
James Legg & Theme 3 Team
RTB Annual Planning Meeting
September 29-October 3, 2014

2. Research Highlights
Overview
James Legg
Collaboration leads to progress in seed degeneration
Greg Forbes
A region-wide response to emerging pests in SE Asian cassava
Kris Wyckhuys
Banana bunchy-top disease: piloting containment and field recovery
approaches through learning alliance in sub-Saharan Africa
Lava Kumar
SPECIAL SEMINAR: The status of Foc TR4 in Mozambique and
proposed activities to prevent its spread in Africa. Wed 20.30
Altus Viljoen – Stellenbosch University

3. BANANA

4. Banana Xanthomonas Wilt (BXW)
Management through ‘Single Stem Removal’
Farm 1
Farm 2
Based on a detailed
understanding of the
epidemiology
1. Remove all stems
2. Rogue infected
stems re-growing
3. Apply basic crop
hygiene practices

5. A Brand New Threat to Africa’s Bananas
Fusarium oxysporum fsp cubense
Tropical Race4 (FocTR4):
Timeline of Rapid Response in Africa
02/13: First symptoms observed
06/13: Fungus identified as FocTR4
08/13: Recommendations to farm
09/13: Mozambique NPPO visit
10/13: Stakeholder meeting: Maputo
11/13: IPPC portal notified
11/13: Press release on outbreak
12/13: RTB funds for Mozambique
01/14: Research proposal developed
02/14: AC4TR4 formed (African
Consortium to combat Foc TR4)

6. Stakeholder Action Plans – TR4

7. 0 1 2 3 4 5 6 7 8
Wautersiella falsenii
Tatumella morbirosei
Staphylococcus auricularis
Sphingobacterium nematocida
Sphingobacterium anhuiense
Salmonella enterica subsp. indica
Ralstonia picke i
Pusillimonas ginsengisoli
Pseudomonas plecoglossicida
Pseudomonas nitri reducens
Pseudomonas geniculata
Providencia vermicola
Providencia thailandensis
Myroides odora mimus
Microbacterium testaceum
Leucobacter chromiireducens subsp. solipictus
Leifsonia shinshuensis
Leclercia adecarboxylata
Kluyvera ascorbata
Klebsiella variicola
Klebsiella pneumoniae subsp. rhinoscleroma s
Klebsiella pneumoniae subsp. ozaenae
Escherichia vulneris
Erwinia rhapon ci
Enterobacter soli
Enterobacter sacchari
Enterobacter hormaechei
Enterobacter asburiae
Enhydrobacter aerosaccus
Empedobacter brevis
Citrobacter youngae
Citrobacter werkmanii
Citrobacter freundii
Burkholderia cenocepaci
Bacillus aryabha ai
Alcaligenes aqua lis
Acinetobacter nosocomialis
Acinetobacter oleivorans
Acinetobacter baylyi
Achromobacter xylosoxidans
Frecuency
Over 500 isolates
0 2 4 6 8 10 12 14 16 18
Wickerhamomyces anomalus
Unknown
Trichoderma spirale
Trichoderma pinnatum
Trichoderma koningiopsis
Trichoderma asperellum
Sporothrix sp.
Pleosporaceae sp.
Penicillium janthinellum
Penicillium brevicompactum
Nigrospora sphaerica
Nigrospora oryzae
Microdochium spp
Gloeo nia temulenta
Fusarium oxysporum
Dothideomycete sp. 7654
Curvularia sp.
Colletotrichum gloeosporioides
Codinaeopsis
Cochliobolus geniculatus
Calonectria humicola
High diversity of bacteria and fungi found
in ex situ collection of banana wild relatives
fungi
bacteria
60
50
40
30
20
10
0
Bacillus spp B13+F
Bacillus spp P58+F
Bacillus spp B3+F
T. asperellum C36+F
Bacillus spp P52 +F
T. asperellum E6+F
T. asperellum End2+F
T. asperellum GM 15 +F
% Yellowing reduc on
% Rhizome discolora on reduc on
% Foc control Growth enhancement

8. http://www.pbs.org/wgbh/nova/next/nature/more-food-with-microbes/
0 1 2 3 4 5 6 7 8
Wautersiella falsenii
Tatumella morbirosei
Staphylococcus auricularis
Sphingobacterium nematocida
Sphingobacterium anhuiense
Salmonella enterica subsp. indica
Ralstonia picke i
Pusillimonas ginsengisoli
Pseudomonas plecoglossicida
Pseudomonas nitri reducens
Pseudomonas geniculata
Providencia vermicola
Providencia thailandensis
Myroides odora mimus
Microbacterium testaceum
Leucobacter chromiireducens subsp. solipictus
Leifsonia shinshuensis
Leclercia adecarboxylata
Kluyvera ascorbata
Klebsiella variicola
Klebsiella pneumoniae subsp. rhinoscleroma s
Klebsiella pneumoniae subsp. ozaenae
Escherichia vulneris
Erwinia rhapon ci
Enterobacter soli
Enterobacter sacchari
Enterobacter hormaechei
Enterobacter asburiae
Enhydrobacter aerosaccus
Empedobacter brevis
Citrobacter youngae
Citrobacter werkmanii
Citrobacter freundii
Burkholderia cenocepaci
Bacillus aryabha ai
Alcaligenes aqua lis
Acinetobacter nosocomialis
Acinetobacter oleivorans
Acinetobacter baylyi
Achromobacter xylosoxidans
Frecuency
Over 500 isolates
0 2 4 6 8 10 12 14 16 18
Wickerhamomyces anomalus
Unknown
Trichoderma spirale
Trichoderma pinnatum
Trichoderma koningiopsis
Trichoderma asperellum
Sporothrix sp.
Pleosporaceae sp.
Penicillium janthinellum
Penicillium brevicompactum
Nigrospora sphaerica
Nigrospora oryzae
Microdochium spp
Gloeo nia temulenta
Fusarium oxysporum
Dothideomycete sp. 7654
Curvularia sp.
Colletotrichum gloeosporioides
Codinaeopsis
Cochliobolus geniculatus
Calonectria humicola
High diversity of bacteria and fungi found
in ex situ collection of banana wild relatives
fungi
bacteria
60
50
40
30
20
10
0
Bacillus spp B13+F
Bacillus spp P58+F
Bacillus spp B3+F
T. asperellum C36+F
Bacillus spp P52 +F
T. asperellum E6+F
T. asperellum End2+F
T. asperellum GM 15 +F
% Yellowing reduc on
% Rhizome discolora on reduc on
% Foc control Growth enhancement

9. CASSAVA

10. Major Cassava Pest & Diseases
Cassava Mosaic Virus Disease (CMD)
CMD – Lake Zone, Tanzania
J. Legg - IITA
Cassava Brown Streak Disease (CBSD)
Whitefly Vector (Bemisia tabaci)

11. Cassava Green Mite and Damage

12. Cassava Green Mite Distribution Databases
M. tanajoa M. mcgregori M. caribbeanae M. planki

13. Cassava Green Mite Risk Maps
M. mcgregori M. tanajoa

14. Westwards Spread of EACMV-UG
EACMV-UG associated with severe CMD
Pandemic: > $ 1 billion annual loss

15. CMD resistance mapping using NGS
50
40
30
20
10
0
-Log10(P)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
a
50
40
30
20
10
0
0 30 60 90 120 150
IITA TMS
011412
IITA TMS
4(2)1425
Position (cM)
b
-Log10(P)
a. Genome-wide scan
for linkage between
CMD resistance and
6756 SNPs across 18
cassava linkage groups.
b. A detailed view of the
of linkage group 16
Rabbi et al. Virus Research 2014.
DOI: 10.1016/j.virusres.2013.12.028

16. Phytosanitation to Control CBSD
CBSD Clean Seed Systems Community Action
100
90
80
70
60
50
40
30
20
10
0
CBSD Incidence (%)
10 SRG
farmers
10 PRG
farmers

17. POTATO

18. Agro-ecology and IPM for potatoes
 Development of sustainable pest management strategies for low
and high input cropping systems e.g. for the Andean region based on
three new IPM technologies
Plastic barriers to control
Andean potato weevil
(organic farmers)
Attract-and-kill to control
potato tuber moths
(private sector)
Talco-Btk to control potato
tuber moths in store
(farmer associations)
Kroschel et al. (2009): Crop Protection 28: 466-476. Kroschel et al. (2012): Springer. UK, 419-450.
Kroschel & Zegarra (2013): Pest Management Science 69: 1205-1215.

19. Pest Risk Assessment
Temperature-dependent phenology modeling and GIS-based pest risk
assessments on global, regional and local scales under current and future
climates using the Insect life cycle model (ILCYM) software
(www.cipotato.org/ilcym).
Establishment Risk Index (ERI) for the potato tuber moth (PTM) >0.6 = success)
Andean region
2000 2050
ERI change
2000 to 2050
Mantaro valley, Peru
Current
temperature +1 ◦C
Data for more than 20 pests of RTBs, vegetables, maize and fruit crops are
included in a Pest Risk Atlas in collaboration with IITA and ICIPE.
(Kroschel et al., J. Agric. Forest Meterol., 2013, Sporleder et al. (2013): CABI Book publication, 412-427.

20. SWEET POTATO

21. The pan African sweet potato virome
SPVZ, SPVG, SPV2
SPCSV-WA
SPCSV-EA
SPCSV-EA/MZ
SPCSV-SA
SPMMV

22. Developing sensitive & robust
virus diagnostics
 Small RNA sequencing and assembly: towards
universal viral diagnostics and sequencing
 Tube-arrays for sensitive detection of all
viruses/pathogens of a crop at once (laboratory required)
 Field detection method with high sensitivity and ease of
use -> LAMP

23. YAM

24. Yam Biotic Constraints
Nematodes Beetles Scales Mealy bugs Termites Fungi & bacteria
Virus infection
•Different species and strains associated
with disease conditions in West Africa
•Pest risk assessment to identify major
pests & disease risks to yam in the
project target areas

25. Yam Virus Surveillance - 2013
Nigeria Ghana

26. Towards NextGen Diagnostic Tools
for on-site Testing
BMGF Complementary grant to NRI and IITA
Development of Low cost On-farm Robust
Diagnostic Toolkits for Yam Viruses
A complementary project funded by BMGF
Simple on-site test for yam virus diagnostics
• LAMP (Loop-mediated isothermal amplification)
• RPA (Recombinase polymerase amplification)
Simple on-site test for yam virus diagnostics
• Distinguishing integrated and episomal
badnavirus infections
Loop mediated isothermal
amplification (LAMP)

27. GCP-21 Meeting in La
Reunion – May 10-14, 2014
Agropolis/CIRAD/RTB
 Establishment of a pan-African Surveillance Cassava Network – PASCAN;
 Establishment of an International Cassava Transit site in La Reunion;
 Development of a Cassava Diagnostic Network in Africa - CDNA
 Development of a comprehensive educational and training plan for PASCAN and CDNA

28. Looking Forward
• Internal linkages. Under RTB 2.0
structure: strengthen linkages between
themes (esp. with 2 and 4) to develop
stronger more robust pest/disease control
• External partnerships. Expand these to
enhance coverage and impact
• ‘Global threat’ pests and diseases.
Identify and prioritize action to address
these

29. Acknowledgements
Fen Beed
Rachid Hanna
Soroush Parsa
Jan Kreuze
Eldad Karamura
Jürgen Kroschel
Kris Wyckhuys
Miguel Dita
Ismail Rabbi
Lava Kumar
Charles Staver
Greg Forbes
Claude Fauquet
Altus Viljoen
Kiddo Mtunda
Donors & Partners