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Assessing Food Security through Plant Virome Ecology in African Farming Systems

This project aims to assess food security in small-scale farming systems in Africa by studying the virome ecology of plants. The project focuses on the identification of alternate hosts for viruses in weeds and non-maize crops. The research will be conducted in different regions of Kenya and will utilize next-generation sequencing techniques to detect and analyze viral diversity. The project is funded by the Swedish Ministry for Foreign Affairs through SIDA.

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Assessing Food Security through Plant Virome Ecology in African Farming Systems

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

  2. Plant virome ecology in African farming systems: assessing food security • 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

  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. Project Overview Rationale • 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 • 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

  5. Project OverviewAims 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 OverviewSampling Strategy • Trans Nzoia/ UasinGishu • 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 Bomet Narok

  7. Project Overview Maize Lethal Necrosis • Maize Chlorotic Mottle Virus • Sugarcane Mosaic Virus MLN MCMV SMV • Symptoms: leaf, stem and ears • Mottling and chlorosisprogressing 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 • 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

  8. Project Overview Methods • 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

  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 Bomet Farm 1 • December 2012 • Bomet County • Consent Form, Questionnaire • Botanist • Two Farms were sampled • Pilot Sampling Trans Nzoia Bomet Farm 2 Bomet Narok

  11. Preliminary Analysis and Results First Sampling Bomet Farm 2 Bomet Farm 1 Visual Characterization! Total: 67 4 Soil samples and 3 Vectors (2 aphids, 1 whitefly) Total: 47 4 Soil samples and 6 Vectors (5 aphids, 1 beetle)

  12. Preliminary Analysis and Results - NGS FERA – June 2013 – MiSeq Sequencing • Bomet Farm 1 • RNA Extraction • Libraries Prep • Illumina TruSeq RNA Kit • No mRNA! • No Pools! • Quality control • Trimming • Assembly of ORF

  13. Preliminary Analysis and Results -NGS Maize M1 - Symptomatic M2 - Symptomatic MCMV MCMV

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

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

  16. Sweet Potato SP1 - Asymptomatic SP2 - Asymptomatic MCMV MCMV

  17. Sugarcane SC2 - Asymptomatic SC1 - Asymptomatic MCMV MCMV

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

  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 Bomet Farm 2 • 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

  25. Capacity Building Related Activities 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

  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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