Category Archives: Genetics

John Vercoe Conference: Animal breeding for poverty alleviation

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The John Vercoe Conference and seventh Peter Doherty Distinguished Lecture will take place at ILRI headquarters in Nairobi 8-9 November 2007.
 


The International Livestock Research Institute (ILRI) Board of Trustees is pleased to announce the John Vercoe Conference and the seventh Peter Doherty Distinguished Lecture. The conference theme is ‘Animal breeding for poverty alleviation – harnessing new science for greater impact’.

The John Vercoe Conference will be inaugurated by the Kenyan Minister of Science and Technology, Hon. Noah Wekesa and thereafter, followed by the presentation of a keynote paper by Achim Steiner, Executive Director of the United Nations Environment Programme (UNEP).

Further topics include:

  • Case studies of breeding programs within developing countries (Christie Peacock, Farm Africa, UK)
  • Breeding program design issues for small-holders (Ed Rege, ILRI)
  • New opportunities for reproductive technologies in developing countries (Johan van Arendonk, Wageningen University, Netherlands)
  • New DNA-based technologies and their prospects for developing countries (Julius van der Werf, University of New England, Australia / Brian Kinghorn)
  • How animal breeding relates to other interventions to reduce poverty (Ade Freeman, ILRI)

The conference will be held at ILRI headquarters in Nairobi on 8-9 November 2007. For further information and to register for the conference, go to the John Vercoe Conference website at: https://www.ilri.org/johnvercoeconference
 

Genebank community wins science partnership award

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Research centres are honoured for their work to preserve the diversity of the world’s key food and forage crops.

Twelve centres of the Consultative Group on International Agricultural Research (CGIAR) recently won the CGIAR’s Outstanding Partnership Award for their management of genebanks and effective stewardship of plant genetic resources they hold in trust for the world community.

The Partnership’s genebanks are vital for achieving food security and protecting plant genetic diversity and represent the most important international effort to safeguard the world’s agricultural legacy. ILRI and the other 11 centres of the CGIAR hold more than 600,000 samples of crop-plant diversity. These include wild relatives and more than half of the global total of farmer-created varieties, which are a rich source of sought-after characteristics.

Base genebanks are used for long-term security storage of original germplasm collections. They act as a repository of materials that have been reasonably characterized and which may or may not have current interest or use by plant breeders. Collected materials are preserved until such time as there are enough resources available for them to be characterized and evaluated. Active genebanks are used for current research and distribution of seeds, with all seeds in active collections freely available in small quantities to all research workers and distributed both directly and through networks.

Jean Hanson, a plant geneticist working at the Addis Ababa campus of the International Livestock Research Institute (ILRI), said, ‘This Outstanding Partnership Award recognizes almost 20 years of collaboration between staff of the CGIAR genebanks, first as an ad hoc working group and community of practice and later as the formal steering committee for the CGIAR System-wide Genetic Resources Programme.

‘Partnerships involving staff of 12 CGIAR centres are rare. This award recognizes an active and collegial partnership that has stood the test of time and changes in staffing and funding within the CGIAR genebank community.’

This Outstanding Partnership Award, announced at the CGIAR’s Annual General Meeting in Washington, DC, in December 2006, recognizes the teamwork that provided stewardship of global public goods central to the CGIAR’s work and also provided leadership to the whole plant genetic resources community. While discharging its duties as custodians of the CGIAR in-trust collections, the Partnership has advanced research in the many scientific disciplines providing leadership for germplasm conservation and use, raised awareness world-wide of the importance of genetic resources to development, and represented the CGIAR in important international fora, from the Earth Summit, held in Rio in 1992, to the first meeting of the Governing Body the International Treaty for Plant Genetic Resources for Food and Agriculture, in 2006.

Collective action by the Partnership generated common policies and practices with which to administer the CGIAR collections under legal agreements governing their in-trust status. Employing these common policies and practices has ensured the highest standards in germplasm conservation and dissemination of that germplasm and related information. Achieving these two objectives demanded combining conservation and information science with smart legal and policy know-how, skillful negotiation and tactful diplomacy.

To secure the in-trust collections, the Partnership took an open, self-critical approach to meet the highest international standards. The Centres continue their work to take conservation technology forward by convening meetings to explore methodologies; publishing guidelines on field and in vitro genebank management and regeneration and other topics; scoping new areas for action, such as research on underutilized species and holistic approaches to agricultural biodiversity; and tackling research bottlenecks such as difficulties in storing clonal material. The Partnership has also conducted upstream research, examining the application of molecular genetics to genebanking, which led to wider developments such as the CGIAR initiation of a Generation Challenge Program.

Pulling technical, economic, policy and information components together, this Partnership helped materialize a vision of a co-ordinated global system for the conservation and use of plant genetic resources. This Partnership is providing coherent leadership of a global genetic resources system underpinning food security for humanity into the future.
Last October, world leaders in agricultural research signed agreements to guarantee long-term access to some of the world’s most important collections of agricultural biodiversity by placing all their ex-situ genebank collections under the International Treaty on Plant Genetic Resources for Food and Agriculture. The agreements require commercial users to share benefits with the global community. Eleven centres belonging to the Consultative Group on International Agricultural Research (CGIAR) were party to the agreements, which will allow breeders and other researchers to tap the collections for solutions to some of the world’s most pressing development problems, including drought, desertification and food and nutritional security. ‘World’s Most Diverse Forage Collection Comes under New Treaty’. (https://newsarchive.ilri.org/archives/452)ILRI maintains both an active and base genebank at its principal campus in Addis Ababa, Ethiopia. As part of its commitment to maintaining the collection as a global public good, ILRI claims no ownership nor seeks any intellectual property rights over the germplasm and related information. ILRI conserves its diverse forage collection to make it and relevant information freely available to scientists and the national agricultural research systems of developing and other countries.

CGIAR Genebank Community
The genebanks of the CGIAR Centres
01  International Center for Tropical Agriculture (CIAT), Colombia (represented by Daniel Debouck)
02  International Potato Center (CIP), Peru (represented by Willy Roca)
03  International Maize and Wheat Improvement Center (CIMMYT), Mexico (represented by Thomas Payne)
04  International Center for Research in the Dry Areas (ICARDA), Syria (represented by Jan Valkoun)
05  World Agroforestry Centre (ICRAF), Kenya (represented by Tony Simons)
06  International Centre for Research in the Semi-Arid Tropics (ICRISAT), India (represented by CLL  Gowda)
07  International Institute for Tropical Agriculture (IITA), Nigeria (represented by Dominique Dumet)
08  International Livestock Research Institute (ILRI), Kenya (represented by Jean Hanson)
09  Bioversity International, Italy (represented by Laura Snook)
10  International Rice Research Institute (IRRI), Philippines (represented by Ruaraidh Sackville Hamilton)
11  West African Rice Development Association (WARDA), Benin (represented by Ines Sanchez)

Related organizations
12  United Nations Food and Agriculture Organization (FAO), Italy (represented by Linda Collette)
13  International Food Policy Research Institute (IFPRI), Washington, DC (represented by Melinda Smale)
14  CGIAR Systemwide Genetic Resources Programme (SGRP) Secretariat, Italy, (represented by Jane Toll)

Building African bioinformatics skills and expertise locally

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Specialists at a new-age computing facility are seeking partnerships with international universities to develop world-class bioinformatics capacity in Africa – and Africa's first generation of bioinformaticians.
 
One of the great recent successes of African biosciences was mapping the genetic code of a parasite known as Theileria parva. This single-celled parasite is transmitted to cattle by biting ticks and causes East Coast fever, which kills a million cattle a year in 11 countries of Africa and is responsible for up to half of all deaths of calves kept by pastoralists there. Much of the work that contributed to this world-class scientific breakthrough, published in the prestigious journal Science, was undertaken in Africa by scientists at the International Livestock Research Institute (ILRI), in Nairobi, Kenya, in partnership with scientists at The Institute for Genomic Research (TIGR), based in the Maryland, USA.

Working with ILRI, scientists at TIGR first sequenced the genome of the T. parva parasite. Most of the subsequent work in annotating the sequence by identifying genes and assigning gene functions was performed by two bioinformatics specialists at ILRI— South African Etienne de Villiers and Kenyan Trushar Shah—using ILRI’s new high-performance computing facility at its Nairobi laboratories.

de Villiers, Shah and colleagues are hoping to build on this breakthrough to strengthen bioinformatics capacity in Africa. They are forming partnerships with leading universities worldwide with the aim of offering post- and under-graduate training in bioinformatics in and for Africa until African universities begin offering masters and doctoral degrees in this new discipline.

Genomics is the molecular characterization of all the genes in a species. It is concerned with sequencing and mapping all of the genes—together known as the genome—that make up a given species, and from this information, establishing what makes the species and the individuals within the species unique. Those working in genomics are interested to discover, for example, how genetic make up is responsible for making some species and individuals susceptible to disease while otheres tolerate or resist the same disease. The prospect of discovering such important biological factors makes genomics one of the most exciting fields in science today. Developments are rapid and new insights are being gained daily.

Bioinformatics is a combination of computer, information and biological sciences. Bioinformatics takes advantage of new computing and information technologies and exploits these to help scientists answer complex biological questions. Specialist databases and tools are used to manage the huge amounts of complex biological data being generated by genomics.

 High-performance computing in and for Africa
The high-performance computing facility on ILRI’s campus in Nairobi provides local scientists with access to state-of-the-art technologies to enable them to conduct extensive and large-scale genomics research fast and cost-effectively for the first time. The facility has been established in Nairobi to serve the bioinformatics needs of ILRI and the eastern and central African scientific community. It is being managed as a shared facility by a new regional science platform called ‘Biosciences eastern and central Africa’ (BecA), whose hub is at ILRI’s Nairobi laboratories.

Etienne de Villiers explains that, ‘Exploitation of the latest genome technologies requires scientists skilled in bioinformatics and with access to high-performance computing infrastructure. The strategy behind high-performance computing is “divide and conquer”. Dividing a complex problem into smaller component tasks, that can be worked on simultaneously by computer, saves time, physical and human resources and money.

‘Bioinformatics is a relatively new specialist area. We need to raise awareness of the field here in Africa and expose people to its potential. The West has spent millions of dollars sequencing the genomes of humans, animals, plants and parasites and the resulting data are freely available on the internet. This is a vast body of knowledge that local scientists can use to solve their specific problems or to answer research questions. All scientists in Africa need to make use of these data are a computer, good internet access and bioinformatics skills.’

Raising awareness and building capacity in Africa
ILRI/BecA training courses and research projects are already taking advantage of the high-performance computing facility, which was commissioned in January 2005. In association with the Swedish University of Agricultural Sciences and the Linnaeus Centre for Bioinformatics, in Uppsala, Sweden, ILRI and BecA recently ran a three-day training workshop that introduced 30 scientists and students from eastern and central Africa to the field of bioinformatics.

BecA scientist Trushar Shah says that ‘bioinformatics is a new and dynamic field that young African scientists should be getting involved in, whether as a specialist or a user exploiting the technology to help answer a complex research question. Our recent short training course was very successful and we are organizing a further course in April 2007.’

 

African bioinformatics skills and expertise

Participants at the Bioinformatics introductory course, August 2006
 

Home grown strategies and interim partnerships
de Villiers is an advocate of home-grown strategies that take into consideration local needs to build capacity in Africa. ‘One of our primary goals is to grow the number and competence of bioinformatics developers and users in the east and central Africa region. To do that, we have to be responsive to local needs. We are raising awareness of the importance and utility of bioinformatics, providing introductory training for early-career scientists, and giving skilled bioinformaticians in the region ready access to advanced tools, support and expertise. We are also considering the longer term and how best we can contribute to building bioinformatics skills and expertise throughout Africa.

‘Local universities are working hard to build capacity but at the moment are unable to award degrees in bioinformatics. Our thrust now is to explore partnerships with leading bioinformatics institutes to enable us to make undergraduate and postgraduate training possible. We are working to link up with universities with well-established training programs in bioinformatics to offer East and Central African students masters and doctoral degree training in bioinformatics, possibly through distance learning.
 
‘We are also planning to link up with universities and institutes that can host these students for a few months so they can gain practical experience in the applications of bioinformatics. This way we are also training future local trainers.’

de Villiers was recently made Extraordinary Lecturer at the Bioinformatics and Computational Biology Unit of Pretoria University, in South Africa. This appointment enables him to supervise students from eastern and central Africa who are affiliated with the high-performance computing facility and wish to pursue higher degrees in bioinformatics through Pretoria University.

New tools to improve utilisation of farm animal genetic resources in developing countries

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The International Livestock Research Institute (ILRI) has recently launched important new information and training resources designed to improve utilisation of the full spectrum of animal genetic resources available in developing countries.


 improve utilisation of farm animal genetic resources
DAGRIS project team leader Tadelle Dessie among cattle in the Ghibe Valley of southwestern Ethiopia.

Throughout the developing world, rapidly increasing populations and changing lifestyles will continue to cause massive increases in demand for foods of animal origin. Key to meeting that demand – and to preventing widespread hunger and malnutrition – are the unique genetic resources found in thousands of locally adapted indigenous breeds of livestock. However, lack of accessible information on these breeds and a shortage of teachers and researchers specialising in animal genetic resources are currently major constraints. The result: in developing countries very few people are appropriately trained in animal breeding and genetics and many genetic conservation and livestock improvement programmes are unsuccessful; globally, a third of the world’s 5,000 breeds of livestock are at high risk of extinction and more than 700 have already been lost.
 
The Domestic Animal Genetic Resources Information System (DAGRIS) is a database which aims to assemble and make readily available in the public domain information – drawn from both formal publications as well as the ‘grey’ literature – on the origin, distribution, diversity, use and status of local breeds. Starting with African breeds of cattle, sheep and goats and recently adding pigs and chicken from Africa and Asia, it hopes to eventually expand its coverage to include geese, ducks and turkeys and also Latin America and the Caribbean. To further enhance capacity at the national level, ‘Country DAGRIS’ will also be established with local partners supported by ILRI to better meet their specific research and development needs. DAGRIS is available both on-line and via CD-ROM, and will be regularly updated as more information becomes available. Click here for a two page brief on DAGRIS.

The Animal Genetics Training Resource (AGTR) is a unique, ‘one-stop’, user-friendly, interactive, multimedia resource, targeted at both researchers and scientists teaching and supervising graduate and post-graduate students in animal breeding and genetics. It consists of core modules, case studies from developing countries, exercises, tools, a library and has links to many other information sources on and related to animal genetic resources, including DAGRIS. It covers established as well as rapidly developing areas, such as gene-based technologies and their application in livestock breeding programmes. Today’s university students are tomorrow’s researchers, lecturers, animal breeders and policy makers: by increasing the capacity of their teachers, AGTR aims to better equip them to rise to the challenge of effectively utilising indigenous animal genetic resources to achieve sustainable food and nutritional security.

For more information visit dagris.ilri.cgiar.org  and agtr.ilri.cgiar.org.

Biosciences for development

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Today the spotlight is on European partners in livestock biosciences for development.
European donors and research institutions working in partnership with ILRI and other CGIAR Centres to speed up agricultural development in poor countries will be highlighted at a breakfast meeting at the 2005 World Bank Sustainable Development European Forum entitled ‘Managing Ecosystems and Social Vulnerabilities in the 21st Century: Towards a More Secure World’, to be held in Paris on 14-15 June 2005. The Forum provides an opportunity to update European bilateral donors on the strategy and work program for the World Bank’s Environmentally & Socially Sustainable Vice Presidency. A significant portion of the agenda is reserved for in-depth, issues-based break-out sessions.

Examples of ILRI projects with European partners are summarized below.

Saving Africa’s unique indigenous cattle breeds critical to its poorest people
In 1998, with funding from Ireland Aid and other European donors, the Africa-based International Livestock Research Institute (ILRI) teamed up with Trinity College, Dublin, to analyse the genetic diversity of indigenous African cattle populations. This project completed molecular diversity datasets from the two centres, unravelled the genetic make-up of African cattle and identified priority cattle breeds for conservation or utilization for the benefit of the farmer communities. The project also helped nations develop strategies for conserving these animals and broadening their use. The project supported evidence that the African continent was a likely center of origin of cattle pastoralism. The latter award-winning research, published in the leading research journal Science, raised awareness of the genetic wealth of Africa’s indigenous cattle populations. African countries are now taking steps to conserve, characterize and make better use of them.

A public-private partnership for technological innovation against a lethal African cattle disease
The East Coast fever vaccine project is an initiative funded by the UK’s Department for International Development (DFID) to design and disseminate a bio-engineered vaccine against a parasite that kills cattle across eastern, central, and southern Africa. A complex set of partnerships between public and private sectors across several continents, including the International Livestock Research Institute (ILRI), in Kenya, the Ludwig Institute for Cancer Research, in Belgium, and the University of Oxford, UK, has played an important role in moving the science forward. The multinational veterinary pharmaceutical company Merial, headquartered in France, is helping to produce the vaccine for trial and will be responsible for the delivery of the vaccine among poor countries. A high degree of complementarity exists between the major partners. ILRI has reached an advanced state of research on the protozoan parasite that causes East Coast fever, bovine immunology and the economic impacts of the disease. Merial produces the vaccine candidates and has been working with Oxford on novel delivery system with potential spin-offs for other human and veterinary vaccines. The project is an example of conceiving and funding a ‘system of innovation’ within the CGIAR, one which cuts across research institutions in new ways, building capacity across the widest possible spread of partners, including NARS.

Conserving a unique genetic resource and way of life among Ankole pastoralists in East Africa
In late 2003, with funding from Austria, scientists from the Africa-based International Livestock Research Institute (ILRI) and the BOKU University of Natural Resources and Applied Life Sciences, in Austria, launched a project to identify indigenous selection criteria and genetic diversity in African longhorn Ankole cattle. The results of this project will improve and sustain the livelihoods of poor Ankole cattle keepers in the four East African countries where these unique cattle are found: Uganda, Burundi, Rwanda and Tanzania. Specifically, the project is facilitating community-based delivery of technical interventions that are genetically improving this breed to meet the needs of their pastoral owners. In the process, the project will help the pastoral communities sustain their environment and culture as well as the genetic diversity of their breed. Indigenous knowledge of animal husbandry and breeding are being captured, as well as selection criteria used by the pastoralists to assess intangible values of their unique Ankole genetic resources.

Development of a second-generation anti-tick vaccine
In late 2004, the Swiss Centre for International Agriculture (ZIL) began funding a project conducted jointly by the Swiss Tropical Institute (Basel), Pevion Biotech (Bern), and the International Livestock Research Institute (ILRI, Nairobi), to develop an anti-tick vaccine to control ticks and tick-borne diseases of tropical cattle. Current tick-control methods rely on regular treatments of animals with acaracides, which kill the ticks. Development of an anti-tick vaccine is one of the most promising alternatives to chemical control, being much safer for the environment and human health. The only commercial vaccine against ticks currently on the market, based on a hidden tick-gut antigenic molecule, requires a series of inoculations to boost the vaccine’s effectiveness. This project is developing a novel antigen-delivery system for use in cattle using virosomes. The aim is to improve the efficiency, handling, user friendliness and cost of the existing vaccine for smallholder farmers. The technology platform developed for the new vaccine may be applied in future against a range of livestock diseases.