Biosciences eastern & central Africa (BecA) Hub International Livestock Research Institute (ILRI), Nairobi, Kenya

Biosciences eastern and central Africa (BecA)

BecA Hub: Core activities1. Research

Core competencies and research programs in agriculture: crop, animal health and microbial sciences

2. Capacity building and training3. Research and Technology-related services4. Focal point for the agricultural research community in

eastern and central Africa5. Promotion of product development and delivery

Laboratory facilities for the HubSeven laboratories to provide for livestock, crop and microbial research and training.

Laboratory upgrade and construction:

BecA Hub Core competencies• Genomics/Metagenomics• Functional genomics • Bioinformatics • Genetic engineering• Diagnostics • Molecular breeding (marker development and

application)• Proteomics• Vaccine technology/Immunology• Vectors (e.g. ticks)• Mycotoxins

Bios

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18(+) supported countries: UniversitiesNat’l Ag Research Systems (NARS)Research Institutions

Nodes:University of Buea, CameroonEthiopian Institute of Agricultural ResearchSokoine University of Agriculture, TanzaniaNational Agricultural Research Organization, UgandaKigali Institute of Technology, Rwanda

Rural Development Administration of the

Republic of Korea

Partnerships

2009

2011

and more…

• Syngenta Foundation for Sustainable Agriculture (USD 5M; 2009-14)

• The BecA-CSIRO partnership is part of the Australia/Africa Food Security Initiative (AUD$ 14M; 2009-13): AusAID

• The Bill & Melinda Gates Foundation core support to BecA Hub (USD 2M, 2011-14)

• The Swedish Ministry of Foreign Affairs/SIDA (USD12M, 2012-2015)

• In addition to many other investors supporting our partners, graduate students, etc.

Current BecA Hub Major Funding Agreements

SFSA Partnership

Staff salaries

Capacity buildingWorkshops

Technical support to Hub

Institutional Support

African Biosciences Challenge Fund (through

salaries/core support)

Core support

Emphasis: providing affordable

access to African users, promoting African –led

projects at Hub, and product development

SFSA BecA Hub

BecA-CSIRO Partnership

AusAID CSIRO

Capacity building through

African Biosciences Challenge Fund

• Courses and workshops

• Visiting Scientists• Institutional Capacity

Building

Research Projects

PPR

ASF

CBPP

Aflatoxin

Mushrooms

Amaranth

Domestic caviesAn

imal

hea

lth R

&D

Food & Nutrition Science

BecA Hub

Core supportCSIRO/Australian scientific collaboration, co-investment and partnership management

BMGF Partnership

Key staffing/core support

GenomicsBioinformaticsCrop Breeding

Capacity building through

African Biosciences Challenge Fund

• Courses and workshops

• Visiting Scientists• Institutional Capacity

Building

BMGF BecA Hub

Research ProjectsGoat improvement

Swedish Partnership

Molecular diagnostics: crop and animal diseases

Plant tissue culture & virus indexing

Ministry for Foreign Affairs SIDA BecA Hub

Bioinformatics platform enhancement

Capacity building through

African Biosciences Challenge Fund

• Courses and workshops

• Visiting Scientists• Institutional Capacity

Building

Core support

staffing

Research

ILRI Biotech Research

Major fociAnimal healthLivestock geneticsPathogen discovery

Research includes:CBPPBREAD projectsASFPPRECF AVID

ILRI Biotech Theme Research

Hosted Institution Crop Research

BecA Hub

Research with PartnersHighlights

CAAREA: Activities to dateCapacity and Action for Aflatoxin Reduction in Eastern Africa (CAAREA)

Potential Intervention Points:Pre-harvest: varieties (eg, KARI 170 to date) Insect damage/resistanceBiocontrolDryingStorageBinding clay

Aflatoxin research – critical gaps

Capacity and Action for Aflatoxin Reduction in Eastern Africa (CAAREA)

CAAREA objectives1. Establish mycotoxin diagnostics platform at BecA

2. Characterize Aspergillus flavus from around Kenya and Tanzania (maize and soil): as source of inoculum, resolve key population biology/pathosystem questions, etc.

3. Test modeling as a potential predictive tool and to contextualize findings across Kenya, Tanzania and the region.

4. Identify maize germplasm resistant to aflatoxin accumulation in specific environments (field trials and postharvest experiments), including GxE(xM).

5. National breeders leading field trials will affect subsequent changes to Kenyan and Tanzanian maize breeding programs.

Projected impact:

In Kenya alone, it is estimated that over 5.6 million people in drought prone areas in Eastern and coastal lowlands alone will directly benefit from maize varieties with reduced mycotoxin accumulation.

In Tanzania, not only does maize provide 60% of daily dietary calories and about 50% of protein, but it is also a cash crop for 85% of the current Tanzania’s the population which is estimated at about 41 million.

Platform will extend the impact by enhancing capacity to address mycotoxins in the region.

Capacity and Action for Aflatoxin Reduction in Eastern Africa (CAAREA)

Kenya:BecA Hub at ILRI: Jagger Harvey (Project Leader, Research Scientist); Benoit

Gnonlonfin (postdoc); Samuel Mutiga (Cornell PhD student); Eric Magembe; Vincent Were

KARI: James Gethi and team, National Maize Research CoordinatorUniversity of Nairobi: Sheila Okoth

Tanzania:ARI: Arnold Mushongi, National Maize BreederOpen University of Tanzania: Said Massomo

Australia:Ross Darnell, biometrician, CSIROMary Fletcher, natural product organic chemist, QAAFI/Univ. QueenslandGlen Fox, NIR expert, QAAFI/Univ. QueenslandDarren Kriticos, ecological modeler, affiliated with CSIRO and Harvest Choice

USA:Rebecca Nelson, Cornell University Michael Milgroom, Cornell UniversityPhil Pardey, University of Minnesota, Harvest Choice

Other linked scientists:Yash Chauhan, DEEDI (APSIM modeling for predicting aflatoxin risk)Stephen Trowell, CSIRO (electronic nose development as a potential aflatoxin detection method)

CAAREA partners

Justification: Domestic cavies and other short cycle alternative livestock have great potential to contribute to addressing food security challenges in developing countries.

Objectives:1. Characterize current production systems & establish cavies production innovation platforms.2. Generate and integrate genetic diversity data with other breeding information to design a sustainable

cavies production system.3. Improved feed system for higher cavies productivity.4. Information dissemination and capacity building.

Partners:ILRI/BecA Hub: Appolinaire Djikeng (PI), Mwai Okeyo, Francis WamonjeCIAT (International Center for Tropical Agriculture)Cameroon: University of Dschang and Min of Livestock, Heifer Prog International, Farmers’ VoiceDRC: Universite Evangelique en Afrique, Women for womenAustralia: CSIRO

Pathway to impact: Improved husbandry practices will be disseminated for a sustainable cavies production linked to market and consumption.

Harnessing husbandry of domestic cavies for alternative and rapid access to food and income (Cameroon and Eastern DRC)

Justification: Income generation.

Objectives:1. Collect and characterize wild edible mushrooms.2. Domesticate them on agro-wastes (eg, sisal, rice straw).3. Nutritionally profile domesticated varieties.4. Farmer training.

Partners:University of Dar es Salaam Prof. Amelia Kivaisi (PI)Kenya Industrial Research and Development Institute (KIRDI)University of BurundiCSIROBecA Hub at ILRI

Pathway to impact:Existing mushroom domestication and training programs at each institution will be expanded to include these indigenous varieties.

Domestication of wild edible mushrooms in E. Africa (Nat’l Program-Led)

Justification: Amaranth is popular (vegetable & grain) in many African countries.

Objective:Reduce food and nutrition insecurity in rural communities of SSA by increasing amaranth production & transforming its leaves and grain products into a variety of shelf stable, nutritious, highly acceptable and marketable products.

Partners:Jomo Kenyatta University of Agriculture and Technology

Dr Daniel Sila (PI)Sokoine University of AVRDC (Tanzania)CSIROBecA Hub at ILRI

Pathway to impact:Stakeholder consultations & training through established extension activities at the African institutions will be used. Amaranth is very popular in these countries.

Amaranth (Nat’l Program Led)

PPRDevelopment of Improved Control Interventions for Peste des Petits Ruminants (PPR)

Justification: PPR is an important disease of small ruminants with challenges in vaccine delivery (cold chain,…).

Objectives:

1: To thermostabilize existing PPR vaccineNigeria 75/1 strain - OIE recommendedWidely used in Africa

2: To pilot vaccine delivery models

Partners:BecA-ILRI BiotechAu-IBARAustralia

Pathway to impact:

Research embedded in development (ILRI and AU-IBAR) and piloting of vaccination/new institutional models will help ensure delivery of an improved vaccine.

LOCATION: well positioned to co-operate with regional and international partners.

CAPACITY: build a critical mass of scientists by training and engaging them in a wide range of research activities.

SCIENCE: focused on research that can address pressing constraints for Africa’s smallholder farmers.

The BecA Hub: A key driver for Agricultural transformation

Research-related services at the BecA Hub and their impact on research and capacity building

1. Research

2. Research-related services

3. Capacity building and training

4. Focal point for the agricultural research community in eastern and central Africa

5. Promotion of product development and delivery

BecA Hub: Core activities

Presentation outline

I. The Central Core Unit

II. The SEGOLIP Unit

III. The Genomics platform

IV. The Bioinformatics platform

V. Other platforms

Current services• Laboratory cleaning and waste management• Glassware cleaning and sterilization services• Preparation of culture media and buffers • Mol Biol grade water, custom made solutions

Staff (10)• 01 Manager• 03 Tech Lab Ass• 06 Lab cleaners

I. Central Core Unit

Users/customers• BecA Hub staff and all African researchers using the Hub• ILRI Biotech (media/buffers and packaging of the ITM vaccine)• Hosted institutions (IITA, CIMMYT, CIP)

• Kenya Agricultural Research Institute (KARI)• Kenya Medical Research Institute (KEMRI)• Institute for Primate Research (IPR)• Universities (Univ of Nairobi, JKUAT, KU, MMU, Egerton Univ)• icipe• Other CG centers based in Nairobi • Syngenta Flowers

• Makerere University, Uganda• MARI, Tanzania

I. Central Core Unit (Cont’d)

Expansion to other users/customers)• Other institutions in the region (Hub activities’ expansion)

Other services under consideration (include)• Molecular biology reagents (nucleic acids extraction reagents,

DNA size standards)• Enzymes (i.e. Taq DNA polymerase)

I. Central Core Unit (outlook)

II. SEGOLIP Unit

Staff 04 technical staff Extensive lab experience

Current Servicesa. DNA sequencing

Sanger sequencing (capillary – low to medium throughput)

Pyrosequencing (next generation – high throughput)b. Genotyping

Full genotyping 01 (DNA extraction, PCR, fragment analysis)

Full genotyping 02 (PCR, fragment analysis)Partial genotyping (fragment analysis)

c. Oligonucleotides

BananaBeans

CassavaCowpea

EucalyptusMaizeMilletsNapier grass

OcimumPassion

fruitPigeon pea

RiceSorghum

StrigaSugar cane

Sweet potato

TefYam

Arthropod vectors BuffaloChicken

CowGoatPigs

SheepMice

Wildlife

BacteriaFungi

ParasitesViruses

II. SEGOLIP Unit (Cont’d)Supporting a wide range of research projects

II. SEGOLIP Unit (Cont’d)Supporting a wide range of programs

1. Generation Challenge Program (GCP): 2011 Work Order• 09 countries (South Africa, The Philippines, Kenya, Ghana, Ethiopia,

Uganda, India, Burkina Faso, Mexico)• 10 crops (maize, rice, sorghum, cowpea, chickpeas, cassava, sweet

potatoes, beans, finger millet, pearl millet)

2. Projects at the Hub facilities• Support (services and training) to all ABCF fellows, AWARD fellows,

graduates students and other visiting scientists projects• ILRI Biotech Theme • Hosted CGIAR crop centers

3. Other users (African NARS, universities, international research institutes and regional programs, USA, Latin America, Middle East and Asia)

II. SEGOLIP Unit (Cont’d)supporting various breeding programs in Africa

1. Characterization of sorghum germplasm collection focusing on biotic and abiotic stresses (Kassahun Bante – Jimma University, Ethiopia)

2. Stress Tolerant Rice for Africa and South Asia (STRASA) project: Development and delivery of improved rice varieties that are tolerant to five major abiotic stresses; drought, submergence, salinity, iron toxicity and low temperature (Negussie Zena – Africa Rice Center)

3. Cassava breeding in Uganda (Robert Kawuki, NARO, Uganda)

4. Genotyping of sorghum BC4F1 population associated with striga resistance (Rasha Ali – University of Khartoum, Sudan)

5. Genetic diversity to support a goat breeding program in Cameroon (Felix Meutchieye – University of Dschang, Cameroon)

6. Genetic characterization of Senegalese trypanotolerant N’Dama cattle (Mame Diouf – ISRA, Senegal)

II. SEGOLIP Unit (Cont’d)A steadily increasing demand

*

Institutions using genotyping servicesserving institutions within and out of Africa

Number of Samples

Institutions

# Data 2010 – Aug 2011# Full genotyping 01

1 sample = 1 library = 1 plate500 mb/run1/2 cassava genome1/8 human genome

IV. The Genomics platformOpportunities for genomics and metagenomics research

ABI 3130-xl ABI 3730-xl ABI 3500-xl

Next generation sequencing:

454 GS pyrosequencer

Capillary sequencing

Genomics (microbial and other organisms)1. Large genomes re-sequencing (Cassava)2. Viral genomics (African Swine Fever, Rift Valley Fever, blue tongue

virus, equine encephalitis virus)3. Functional genomics (small viral RNAs in cassava)

Metagenomics4. Pathogen discovery, tracking and surveillance of zoonotic diseases

(e.g. RVF)5. Microbiome analysis; environmental metagenomics (e.g. aquatic

environment)

IV. The Genomics platform (Cont’d)Highlights of applications

Completed and ongoing projects 1. Re-sequencing of the cassava genome

# 06 next gen sequencing runs => 1.4 billions bases => ~ 1.5x coverage of the cassava genome# Ongoing data analysis (BecA Hub/IITA, Univ Arizona)

2. Deep sequencing to support a study on soil management (Study on the interaction between resident and inoculated mycorrhizal communities) – TSBF-CIAT# ¼ next gen sequencing run with 36 multiplexed samples# Ongoing data analysis (BecA Hub, TSBF-CIAT)

IV. The Genomics platform (Cont’d)Major outputs

3. Pathogens genomes sequencing projects(61 viral genomes sequenced so far with 14 deposited @

Genbank)

# Rift valley fever virus (16 sequenced and ongoing analysis)# New castle disease virus (03 sequenced and deposited @ Genbank)# African swine fever virus (02 sequenced and ongoing analysis)# Equine encephalitis virus (05 sequenced and ongoing analysis)# Blue tongue virus; collection 1970 – now (24; ongoing sequencing)# Ndumu Virus (07 partially sequenced) // also found in pigs (discovery !!)# Other viruses: Dugbe virus (01), semliki virus (02), bunyamwera (01); deposited @ Genbank

IV. The Genomics platform (Cont’d)Major outputs

V. The Genomics platform (Cont’d)Highlights of forthcoming projects

Genomics:# Genome sequencing of napier stunt disease pathogen, phytoplasma (icipe, ILRI) # Genomics of Novel Respiratory Adenovirus isolates (CDC, Kenya)# Genomic characterization of hMPV isolates in of Kenya (Walter Reed, Kenya)# Heredity and Human Health in Africa (H3 Africa – sequencing and genotyping support), Wellcome Trust and NIH# Development of new markers (Enset, etc..)

Metagenomics: # Microbial community in selected environments of Nairobi city district (Univ Notre Dame, ILRI) # “Viromes” of selected African farming systems; assessing food security risks (BecA, KARI, FERA)# Heredity and Human Health in Africa (H3 Africa – sequencing support)

• Linux cluster• 32 CPUs (AMD 64-bit)• 128 Gigabyte RAM

• >10 terabytes disk storage• Grid computing • Parallel applications:

> Genome assembly (Newbler, MIRA, Celera, velvet, CAP3. …)

> Genome annotation (glimmer, …) > Phylogenetic analysis (Beast, Mr

Bayes)> Other sequence analysis tools

(BLAST, clustalw, HMMER, R)

BecA/ILRIIRRI – PhilippinesICRISAT – IndiaCIP – Peru

IV. The Bioinformatics platform

Bioinformatics Group LeaderDr Etienne de Villiers

IV. The Bioinformatics platform (Cont’d)Selected outputs

1. Research support# Genomics approach to the identification of virulence genes of CBPP# Genomics approach to the development of vaccines and diagnostics of camel Streptococcus agalactiae (to support camel milk marketing through improved control of mastitis)# Cassava genome project# Molecular markers development# Diagnostic development (ex. Passion fruit)

2. Capacity building# Since 2006: 15 bioinformatics courses (~ 391 participants from African institutions)# Established a Regional Student Group (RSG) affiliated with The International Society for Computational Biology (ISCB) in 2007

1. Diagnostics platform (from sequence to impact): exploiting genomic data

Animal and zoonotic diseases

Crop pathogens: Viral diseasesBacteria Ralstonia solanacearum (Endemic disease - keep this out of

local seed)Dickeya solani (European disease - keep this out of the region)

VI. Other platformsExpanding our research and capacity building

and services opportunities

2. Mycotoxin and nutrition analysis platformInfrastructure: Atomic Absorption Spectrophotometer Gas chromatograph – Mass Spectrophotometer (GC-MS)HPLC system comprising UHPLC solvent systemFourier Transform Near Infrared (FT-NIR) spectrometer

Applications/measurements: Mycotoxins, sugars, vitamins, carotenoids, phenolics, fatty acids and amino acids, trait analysis (crops and animals)

VI. Other platformsExpanding our research and capacity building

and services opportunities

3. Online data integration and analysis platforms

iPlant Collaborative (Cyberinfrastructure to support plant biology research. # Sustainable access to high performance computing, interoperable software analysis, and large data sets

ibp (Integrated breeding platform: public web-based one-stop shop for information, analytical tools and related services to design and efficiently conduct molecular-assisted breeding experiments)

VI. Other platforms (Cont’d)Expanding our research, capacity building

and service opportunities

Strategies for new equipment and technologies acquisition

Strategies for new equipment and technologies acquisition(Some challenges!!!)

Equipment replacement plan# < 100 000 USD (Grants)# > 100 000 USD (special donations)# Capital expenditure ???

BecA Hub Lab asset distribution

Biosciences eastern & central Africa (BecA) Hub International Livestock Research Institute (ILRI), Nairobi, Kenya

http://hub.africabiosciences.org

Thank you

The BecA Hub Capacity Building Programme

“Biosciences are seen as one of the major engines of growth in the world in fields such as …. agriculture. Africa lags behind in biosciences. The two key problems are lack of sufficient funding from governments and shortage of skilled expertise.”

NEPAD www.nepad.org/humancapitaldevelopment/abi

• Strengthen capacity of individuals and institutions to harness the latest biosciences technologies to improve agriculture in Africa

• Support African scientists efforts to lead and sustain biosciences research in Africa

Objectives

• Promote access to world-class research and training facilities at the BecA Hub

1. Research placements• Graduate students• Visiting scientists

2. Individual/small group training3. Training workshops4. Conferences5. Institutional capacity building6. Linkages, information, creating awareness

of BecA Hub

Building biosciences capacity for improving African agriculture

Growing numbers using the Hub

Graduate students, visiting scientists and short term trainees

•1-5 trainees• 1-4 weeks• Customised training• One or more technologies

Individual/small group training

• Hosted by the BecA Hub– 2007-2011: 42 training workshops– Examples (2011):

• Basic Laboratory Health and Safety (ILRI, BecA)• Marker Assisted Breeding (ICRISAT)

• Annual practical training workshops organised by BecA Hub, under ABCF 1. Science paper writing2. Introduction to molecular biology and bioinformatics3. Advanced bioinformatics4. New for 2012: Laboratory management & equipment

maintenance

Training workshops

Science Writing Workshops: 2009 - 2011

• Applications: 703 (2009), 560 (2011)• 64 participants from 15 African countries (27 women, 37 men)

• Outputs (2009, 2010): 24 papers submitted, 15 published

• 2009: BMGF funding; training by Scriptoria• 2010, 2011: AusAID funding; training led by CSIRO

“I had been struggling for one year with my introduction, but I finished it in one afternoon.”

Anne Akol, Senior Lecturer, Makerere University, Uganda

Molecular Biology and Bioinformatics Workshop 2011

• 21 participants (6 women, 15 men) • 10 African countries

•Research discovery processTissueDNAPCRCloning SequencingSequence analysis

BLAST

Advanced bioinformatics workshop 2011:Next Generation Sequencing for Africa

• 24 participants (18 men, 6 women) from Africa

•13 tutors from Kenya, Europe, USA

• EMBO Global Exchange Lecture Course: Next Generation Sequencing data analysis

•4 collaborations initiated- RVFV (VRI-Sudan, ILRI-BecA)- Finger millet SNPs (KU-Ke, U Liverpool)- Trypanosome MDR (SUA-Tz, U Liverpool)- Drought stress in banana (Makerere U-Ug, BecA)

• Major focus– Post graduate research

projects (up to 3-4 yrs)– Students registered at many

universities

– Visiting scientist placements (up to 6 months)

– Employees from NARIs and Universities

Building capacity through research

ABCF: African Biosciences Challenge Fund

• Syngenta Foundation for Sustainable Agriculture (SFSA)

• BecA-CSIRO partnership funded by the Australian Agency for International Development (AusAID)

• The Bill & Melinda Gates Foundation (BMGF)

• Ministry for Foreign Affairs, Sweden, through the Swedish International Development Cooperation Agency (SIDA)

Making the ABCF possible

ABCF Research Fellowships

• Large demand for use of BecA Hub: inadequate funds• Enable African scientists access Hub facilities and services, for

high quality research addressing African agricultural problems• Researchers from national research institutes and African

universities• 3-6 months at the Hub• Competitive basis or targeted ‘fast track’

ABCF Research Fellows

Charles MasembeDepartment of Zoology, Makerere University, Uganda

Pig diseases and food security: Next-generation DNA sequencing of African swine fever virus (ASFV) in Uganda

Selamawit Bedane (Haramaya University, Ethiopia)

Sisay Alemu (Holetta Agricultural Research Center, EIAR, Ethiopia)

Molecular characterization of enset from Ethiopia using banana microsatellite markers

Dia HassanCentral Veterinary Research Laboratories, Khartoum, Sudan

Theileria parva genotyping to support control of East Coast fever, an emerging disease in South Sudan

ABCF Research Fellows

Dora KilaloDepartment of Plant Science and Crop Protection, University of Nairobi

Passion fruit woodiness disease diagnostics

ABCF Research Fellows

Alexander BombomDepartment of Agricultural Production, Makerere University

Molecular characterization of maize-sorghum hybrids

Félix MeutchieyeUniversity of Dschang, Cameroon

Molecular characterization of Cameroon indigenous goats and sheep

Building capacity of African institutes

• National Agricultural Biotechnology Centre, Holetta, Ethiopia

• Gulu University, Uganda

• Mikocheni Agricultural Research Institute (MARI), Tanzania

Raising awareness

• Burundi• Cameroon• Ethiopia• Rwanda• Sudan• Tanzania• Uganda• Nigeria

• Conferences in many countries• BecA workshops• Website• Printed materials• We host over 1500 visitors per year

38 institutes and organisations in 8 countries visited in 2011

BecA alumni: Where are they now?

IRRI

Research

Capacity building

Research related services

Integration of research, capacity building and research-related services

For a better delivery of the BecA mission

Acknowledgements

• Australian Agency for International Development (AusAID)/CSIRO• Bill & Melinda Gates Foundation (BMGF)• Ministry for Foreign Affairs, Sweden, through the Swedish International

Development Cooperation Agency (SIDA)• Syngenta Foundation for Sustainable Agriculture (SFSA)• NEPAD/AU• Canadian International Development Agency (CIDA)• Google Foundation• Rockefeller Foundation• Gatsby Charitable Foundation• Doyle Foundation• The Kenyan Government• and many others

Thank you

IRRI