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Plant virome ecology in African farming systems: assessing food security “Alternate hosts for the viruses in weeds and non-maize crops” Plant virome ecology.

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Presentation on theme: "Plant virome ecology in African farming systems: assessing food security “Alternate hosts for the viruses in weeds and non-maize crops” Plant virome ecology."— Presentation transcript:

1 Plant virome ecology in African farming systems: assessing food security “Alternate hosts for the viruses in weeds and non-maize crops” Plant virome ecology in African farming systems: assessing food security “Alternate hosts for the viruses in weeds and non-maize crops” Francesca Stomeo / Mark Wamalwa Post Doctoral Scientist - Genomics, BecA- ILRI Hub (f.stomeo@cgiar.org) (http://hub.africabiosciences.org) – (http://www. Ilri.org) MLND Workshop, Nairobi 21-23 August 2013

2 Donor: Swedish Ministry for Foreign Affairs through SIDA Partners: BecA – ILRI Hub: Dr. Appolinaire Djikeng – Dr. Jagger Harvey Dr. Francesca Stomeo - Dr. Mark Wamalwa KARI: Dr. Douglas W. Miano / Dr. Gichuki FERA: Dr. Neil Boonham – Dr. Ian Adams UoN: Dr. Dora Kilalo Plant virome ecology in African farming systems: assessing food security Plant virome ecology in African farming systems: assessing food security

3 Project Overview Small Farming Systems  Small farms (2 hectares, FAO 2001) are estimated to produce four-fifths of the developing world’s food  They are home to approximately two-thirds of the world’s three billion rural residents  Key role in meeting the future food demands  Are not homogenous  Worldwide about half a billion farms are smaller than two hectares and they are getting smaller due to: growing rural population, urban growth, formal and informal barriers to rural- urban migration, distortionary land policies and climate change

4  Maize mixed farming system (maize plus pulses, banana, rice, sorghum, cassava, yams, minor crops like groundnuts, pigeon pea, vegetables, intercropped fruit trees and squash)  Continuous cropping; lack breaks; replicated in different AEZs  Great pathogens and vector diversity  Most studies tend to focus on single pathogens affecting a single crop  Small farm ecosystems: Complex mix of crop, non-crop plants Vectors and pathogens (Bacteria, Fungi, Virus)  Estimated $60 billion global annual losses due to crop diseases Project Overview Rationale

5 Project Overview Aims and Objectives  Multi pathogens detection – hosts and potential vectors  Emerging diseases  SSA small-scale (mixed) farming systems  Focus on maize (main staple food in East and Southern Africa, 20% gross farm outputs for small scale farmers)  3 different Kenyan AEZs (climate change)

6 Project Overview Sampling Strategy  Trans Nzoia/ Uasin Gishu Major maize zones Upper midland and Lower highlands 1800-200m asl  Bomet Rainfall bimodal throughout the year with peaks in May, Aug, Nov Maize grown on relay Lower highlands, Upper midlands and lower midlands Transition between the best maize growing areas and pastoralist grazing land where farmers are moving  Narok 500-1800mm rainfall; unreliable rains Occupied by pastoralists with a lot of uncultivated land Some areas too dry and soil shallows unable to support crop growth  3-4 farms randomly selected will be samples from each area  Selected crops (and vectors) to be sampled: maize and beans, grass and any other 3-4 (or more) crop species Trans Nzoia Narok Bomet

7 MLNMCMVSMV Project Overview Maize Lethal Necrosis Maize Chlorotic Mottle Virus Sugarcane Mosaic Virus New disease first identified in the autumn of 2011 South Rift region (Narok North, Narok South, Chepalungu, Sotik), Eastern Province (Embu, Meru and Kibwezi) and Central Province (Murang’a, Kirinyaga and Nyeri) of Kenya, Bomet Symptoms: leaf, stem and ears Mottling and chlorosis progressing to deformity and necrosis Foliar infection often associated with the leading growth with early formed leaves remaining green For plants with foliar or stem infection, grain filling was shown to be markedly reduced

8  NGS sequencing (MiSeq) Total RNA/dsRNA/small RNAs (viral diversity) DNA 16S rRNA gene Metagenomics (Plants, Soils, Vectors)  Bioinformatics analysis Plant Virus Database/Pipelines Explore viral diversity through automatically constructed time-measured phylogenies Viromes comparison Project Overview Methods

9 Project Overview Outputs  Confirmation of known diseases/pathogens  Pathogen Discovery / Emerging diseases  Host range and vector information  Risk analysis based on AEZs and dynamics of disease spread/climate change  Policy makers, donors and researchers

10 Preliminary Analysis and Results First Sampling Trans Nzoia Narok Bomet December 2012 Bomet County Consent Form, Questionnaire Botanist Two Farms were sampled Pilot Sampling Mixed cropping system (maize, cabbage, pumpkin, Irish potato, grasses, etc.) The MLND has been a threat to the farm. As a result the farmer decided to plant maize only in a small area The farmer uses commercial seeds and he does not control the disease Mixed cropping system The diseases present are: Northern Leaf Blight, Common Rust, Maize Streak Disease The farmer uses his own plant materials and he does not control the diseases. Bomet Farm 1 Bomet Farm 2

11 Sample TypeNumberDescription MAIZE96 SYM - 3 ASYM SORGHUM51 SYM - 4 ASYM PUMPKIN8 1 SYM - 7 ASYM (6 PROB ASYM) SUGARCANE55 ASYM (4 PROB ASYM) SOLANUM TUBEROSUM94 SYM - 5 ASYM SWEET POTATO55 ASYM (4 PROB ASYM) PHASEOLUS VULGARIS6 3 SYM (1 FUNGAL DESEASE) - 3 ASYM CABBAGE22 SYM NAPIER GRASS44 PROB ASYM CROTON MEGALOCARPUS (TREE)11 ASYM LANTANA CAMARA22 ASYM WEED111 SYM - 10 ASYM Bomet Farm 1 Sample TypeNumberDescription MAIZE10 6 SYM (1 RUST) - 4 ASYM (1 PROB ASYM) TEA55 ASYM (5 PROB ASYM) ONION65 SYM - 1 ASYM IRISH POTATO22 PROB ASYM CLIMBING BEAN22 PROB ASYM PUMPKIN11 ASY KALES52 SYM - 3 ASYM NAPIER GRASS44 PROB ASYM WEED1212 PROB ASYM MAIZE10 6 SYM (1 RUST) - 4 ASYM (1 PROB ASYM) TEA55 ASYM (5 PROB ASYM) ONION65 SYM - 1 ASYM Bomet Farm 2 Preliminary Analysis and Results First Sampling Total: 67 4 Soil samples and 3 Vectors (2 aphids, 1 whitefly) Total: 47 4 Soil samples and 6 Vectors (5 aphids, 1 beetle) Visual Characterization!

12 Preliminary Analysis and Results - NGS Bomet Farm 1 RNA Extraction Libraries Prep Illumina TruSeq RNA Kit No mRNA! No Pools! Quality control Trimming Assembly of ORF FERA – June 2013 – MiSeq Sequencing Sample TypeSample ID Sample Status MaizeM1Symptomatic MaizeM2Symptomatic MaizeM3Asymptomatic MaizeM5Symptomatic SorghumS1Symptomatic SorghumS2Asymptomatic PumpkinP1Symptomatic PumpkinP3Asymptomatic SugarcaneSC1Asymptomatic SugarcaneSC2Asymptomatic Solanum Tuberosum ST7Asymptomatic Solanum Tuberosum ST8Symptomatic Sample TypeSample ID Sample Status Phaseolus VulgarisPV3Asymptomatic Phaseolus VulgarisPV3Symptomatic CabbageC1Symptomatic Lantana CamaraLC1Symptomatic Amaranthus HybridusW6Asymptomatic Weed (Acantachaceae) W1Symptomatic GyanadropisW3Asymptomatic Datura StramoniumW7Asymptomatic MegalocarpusCM1Asymptomatic Napier GrassNG4Asymptomatic Sweet PotatoSP1Asymptomatic Sweet PotatoSP2Asymptomatic

13 Preliminary Analysis and Results -NGS M1 - SymptomaticM2 - Symptomatic Maize MCMV

14 M3 - Asymptomatic M5 - Symptomatic Maize MCMV SCMV MLND = MCMV + SCMV?

15 Sorghum S1 -Symptomatic S2 -Asymptomatic MCMV SCMV MCMV MYDV

16 Sweet Potato SP1 - AsymptomaticSP2 - Asymptomatic MCMV

17 Sugarcane SC1 - Asymptomatic SC2 - Asymptomatic MCMV

18 Napier Grass NG4 - Asymptomatic Weed 1 - Symptomatic Weed MCMV SCMV MCMV

19 Maize Chlorotic Mottle Virus Genome Coverage ST, PV, W (Potato, Beans, Weeds)

20 Sugarcane Mosaic Virus Genome Coverage

21 Community Reconstruction and Sample Diversity

22 Community reconstruction and sample diversity

23 Discussion  The results show greater estimates of viral richness  MCMV and SGMV detected  High coverage  Is the combination of the two viruses (MCMV and SGMV) a paramount requisite for the appearance of the Maize Lethal Necrosis?

24 Future Activities  Deep Data Analysis / Paper Writing  Second Run FERA  TruSeq RNA MiSeq Sequencing  Second sampling September 2013  RNA (smallRNA) Seq, MiSeq, BecA – ILRI Hub  16S Metegenomics  Vectors Sample NameSample TypeSample Status M1MaizeSymptomatic M2MaizeSymptomatic M3MaizeSymptomatic M6MaizeSymptomatic M7MaizeSymptomatic M9MaizeSymptomatic M4MaizeAsymptomatic M8MaizeAsymptomatic O1OnionSymptomatic O2OnionSymptomatic O4OnionSymptomatic O5OnionSymptomatic O6OnionSymptomatic O3OnionAsymptomatic K2KaleSymptomatic K3KaleSymptomatic K4KalesAsymptomatic T1TeaAsymptomatic T4TeaAsymptomatic IP2Irish potatoAsymptomatic CB1Climbing BeanAsymptomatic P1PumpkinsAsymptomatic NG3Napier GrassAsymptomatic W5WeedAsymptomatic Bomet Farm 2

25 ABCF Fellow: Jane Wamaitha M., PhD, NAIST, Japan Understanding the genomics of Maize Lethal Necrotic Virus and other potyviruses Based at Kenya Agricultural Research Institute- NARL, Biotechnology section Concept note submitted to Africa Biosciences Challenge Fund (ABCF) - 2013 Capacity Building Related Activities

26 Acknowledgment Appolinaire Djikeng Mark Wamalwa Neil Boonham Ian Adams Douglas W. Miano Dora Kilalo Joyce Njuguna Jagger Harvey Martina Kyalo BecA Hub Team! Swedish Ministry for Foreign Affairs through SIDA


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