6.1 Animal Genetic Resources
6.2 Development of Disease-Resistant Livestock
6.3 Disease Control and Diagnosis
6.4 Epidemiology and Disease Control
6.5 Ruminant Feed Resources
6.6 Interactions Among Genetics, Health, Nutrition and Feed Supply
6.7 Assessment of the Direction and Quality of the Programme
The Biosciences Programme is working at "paving the way" for a more productive tropical animal agriculture with a portfolio of new technical change products. In this programme, the sciences of genetics, genomics, immunology, parasitology, biotechnology, and nutrition are utilised to determine how to reduce animal losses by controlling key diseases, and to improve animal performance by improving nutrition with adapted feed resources. Details about the Biosciences Programme are in Appendix I.
6.1.1 Current Strategy
6.1.2 Achievements
6.1.3 Future Plans
6.1.4 Assessment
[Characterisation, conservation and use of animal genetic resources (Project 1)]
An essential step in any global strategy for the conservation of animal genetic resources is the development of methods of defining and documenting the available livestock and measuring their diversity and genetic relationships. Once such systems are in place the collection of information on a global scale can be initiated with the advantage that the data are comparable. The aims and objectives of this project arc to identify the characteristics of livestock breeds as well as define biodiversity and identify unique populations where conservation measures are required.
The research is aimed at defining the characteristics and extent of diversity in indigenous ruminants (cattle, sheep, and goats) by analysing phenotypes and defining genetic relationships using microsatellite markers. Considerable investment has been made in methodologies for collecting data as well as identifying appropriate genetic markers. The initial focus has been on cattle in sub-Saharan Africa with extensive involvement of NARS, analysis of existing published and unpublished data, and a collaboration with Trinity College Dublin. The research contributes to the identification of characteristics of livestock breeds that are useful in Project 2. Current and future strategies are aimed at extending and developing the same approaches for sheep and goats within Africa, as well as extending these approaches to Asian cattle. The research activities are appropriately focussed on Africa in the short term to assess effectively the methodologies and markers before expanding the analysis to Asia. The approaches and methodologies are of global significance.
A series of significant achievements have been made and these include:
1. Compilation of data on the geographic distribution, physical characteristics and performance of indigenous cattle, sheep and goats together with the creation of a Domestic Animal Genetic Resources Database.2. Development of methodologies to collect data on breed characteristics that can be applied elsewhere and can be analysed comparatively and pooled.
3. Identification and validation of a set of cattle microsatellite markers for genotyping.
4. Development of microsatellite markers for sheep and goats.
5. Identification of a Y chromosome specific marker that distinguishes Bos taurus and Bos indicus crossbreds.
As the focus of the research has been to develop methods of data analysis and the analysis and cataloguing of diversity, the main impacts are likely to be forthcoming in terms of defining breeds with increased disease resistance, and for assuring genetic diversity of domestic livestock for future use. Impacts have primarily been in terms of publications, advice on data analysis for breeding programmes being undertaken by NARS, and in worldwide recognition of the uniqueness of African germplasm from the cattle genome. .
· On-farm phenotypic characterisation methodology to be fully available and validated for use by NARS.· Domestic animal genetic resources database to be fully developed and available.
· Microsatellite markers for sheep and goats to be established and used to define the African breeds.
· Initiation of work on the genetic relationships in Asian cattle.
This is a well-conceived project which readily integrates with a global mandate. The methodologies, data and the database constitute unique resources that will be accessible by NARS and ARIS and will provide invaluable information for breeding programmes, conservation strategies and future research projects. The high degree of integration with project 2 is commended. It is important that the project maintains the focus on African breeds to fully validate methodologies and tools before applying these to other breeds elsewhere in the world. This is a high priority project but it seems to have a relatively low profile internationally; this should be addressed. The relationship of this project to the FAO conservation of genetic resources programme should be clarified and it is suggested that ILRI should play a more significant role in this programme. This project involves a high level of involvement, especially through the NARS-ILRI livestock networks in eastern and southern Africa, in the collection of data and will ultimately be of benefit through the definition of breeds suitable for production.
6.2.1 Current Strategy
6.2.2 Achievements
6.2.3 Future Plans
6.2.4 Assessment
(Project 2)
[Genetic resistance to trypanosomosis in cattle and mice;
Genetic resistance to gastro-intestinal parasitism in small ruminants]
This genomics research is aimed at developing and testing genetic markers for resistance to trypanosomosis in cattle and helminthosis in sheep, and to incorporate this information into breeding programmes to improve net productivity, indigenous sheep and goat breeds in Africa and Southeast Asia are also being evaluated for resistance to gastrointestinal parasites; and integrated endoparasite control strategies are being developed. These complementary efforts are appropriately supported by research with laboratory mice to facilitate gene discovery through DNA-sequence comparisons between species. Once identified, genome regions influencing disease or parasite resistance can be incorporated into selection programmes using marker assisted introgression.
Research activities, involving top-flight scientists from several collaborating institutions, have been 1) to establish an F2 resource population of cattle resistant to trypanosomes, 2) to establish nucleus flocks and backcross sheep families and a mouse population in which to search for markers and genes, 3) to evaluate breeds and their crosses under parasite challenge and dietary alternatives, and 4) to develop appropriate statistical methods for marker assisted introgression and to quantify infection and productivity responses in a repeated measures design.
Three unlinked quantitative trait loci (located on different chromosomes) for trypanotolerance have been located in mice, which are the first narrow QTL definitions associated with an important disease in a mammalian genome. Three QTL marker-regions for trypanotolerance have been identified in cattle, which is a milestone towards developing a DNA-based diagnostic test for this trait. Better-adapted (parasite resistant) breeds of sheep and goats were shown to be at least twice as productive as the susceptible genotypes. This was an important step in valuing adapted animal genetic resources. Milestones meriting commendation include 1) the location of multiple QTLs for disease resistance in cattle, 2) that identification of candidate genes for disease resistance is imminent in mice, and 3) the establishment of resource populations of resistant cattle and sheep.
· Continue the search and mapping of disease resistance genes, including comparative mapping of cattle QTL regions with mouse and human.· Design a breeding plan for marker assisted introgression of loci determining trypanotolerance in crossbred cattle.
· Continue evaluation of endoparasite resistance and development of unique animal resources for genetic research, and test integrated control strategies for sheep and goats.
The Panel commends researchers for the "cutting edge" science of this project, which has attracted to ILRI's agenda world class scientific collaborators from numerous outside institutions. These outstanding efforts to integrate molecular and quantitative genetics techniques are at the forefront of mammalian genomics research. They hold promise for reducing losses by adding to breeding options some of the major genes affecting these important maladies, which should also enhance management options (health control, nutrition) to improve productivity in the target environments. Further assessment of interaction with management alternatives is encouraged. The Panel suggests that all candidate helminth-resistant genetic material (breeds, genes or markers) be comparatively evaluated, preferably at two locations. At least, a reference breed's germplasm that is common to both locations (i.e., transferring it by embryos or semen) should be incorporated into the research design to enable comparisons.
Progress in ruminant genetics research at ILRI is currently constrained by two factors. First, it has been slowed in both projects by the delay in refilling the co-ordinator position for Project 2, which was vacated in April 1998. Efforts should be redoubled to fill this vacancy. Second, important synergies and research progress are being sacrificed because the collaborating scientists in the two genetics projects are divided between the campuses; this also reduces the efficiency of resource use. Repeated feedback from ILRI scientists confirmed these assessments.
To ensure research quality and productivity by having project co-ordinators and their research teams work together on a daily basis and thereby achieve cross-fertilisation of ideas, catalyse critical thinking, and design cutting-edge research and research proposals, the Panel recommends that Project 1 (Characterisation, conservation and use of animal genetic resources) and Project 2 (Development of disease resistant livestock) be managed at the Nairobi campus.
The Panel urges that ILRI move swiftly to continue establishing itself as a leader in genomics research on the livestock diseases that are important in developing countries, and to solidify linkages with key institutions. This would require greater investment and a larger core of researchers in this area. Besides shifts in existing resources, ILRI should approach other key genomics research institutions, like the Agricultural Research Service of the US Department of Agriculture. The ARS is increasing funding for genomics research, and has recently established a new centre for Bioinformatics and Comparative Genomics to analyse genebanks resulting from various gene-sequencing projects using rapid DNA sequencing.
6.3.1 Current Strategy and Approaches
6.3.2 Achievements
6.3.3 Future Plans
6.3.4 Assessment
[Molecular basis of pathogenesis and disease resistance (Project 3), Immunology and vaccine development (Project 4). Improving livestock productivity through development of sub-unit vaccines (Project 5), Development and application of diagnostic tools in disease control and surveillance (Project 6)]
This research is primarily strategic but with downstream goals and is essential if biological control measures are to be developed. The work focuses on different aspects of disease control, but primarily on the development of vaccines and improved diagnostic tools using modem molecular and immunological approaches with Theileria parva (ECF) and T.congolense/T.brucei as the prime target parasites. Additionally more basic research on both parasite and host genes involved in immunosuppression, pathogenesis and host resistance are being undertaken together with fundamental studies on immune mechanisms.
A number of strategies for defining antigens capable of inducing a protective response have been taken based on rational considerations of likely target antigens (Theileria sporozoite surface antigens, Theileria macroschizont molecules identified by sequence analysis, the flagellar pocket antigens of trypanosomes and genome analysis of T. brucei) and on assay systems derived from the protective mechanisms (CD8+ cytotoxic and CD4+ T-cells recognising Theileria macroschizont antigens). Once such antigens have been identified, the genes encoding them are sequenced, expressed in a variety of recombinant expression systems and these products are used in laboratory and, ultimately, in field-based vaccine trials.
The strategies for developing diagnostic assays for T. parva, T. mutans, Babesia bigemina and Anaplasma marginale have been based on identifying conserved immunodominant antigens (either in-house or through collaboration), cloning and expressing the genes encoding such antigens and then developing ELISA based assays. In addition standard approaches for PCR based diagnosis and the use of polymorphic markers for strain identification in Theileria have been undertaken. Similar strategies have been taken to diagnose trypanosome species, although a DNA based ELISA format has replaced the antigen based ELISA. Strategies have also been developed to produce methods for identifying drug-resistant trypanosomes with a specific focus on isometamidium.
A diverse set of strategies has been undertaken to identify parasite molecules mediating immunosuppression, pathogenesis, parasite cell death and novel chemotherapeutic targets as well as a collaborative project aimed at identifying the basis for resistance in Cape buffalo and eland to trypanosomosis infection. The common theme to these sub-projects is to identify molecules of either host or parasite origin that modulate the growth and pathogenic consequences of trypanosome infection.
These are considered in relation to sub-sections outlined in 6.3.1, namely: vaccines/immune mechanisms, diagnostics/molecular markers and modulation/pathogenesis of infection. In general significant achievements have been made with the development of diagnostics, the single antigen vaccine against T. parva, the delineation of immune mechanisms and the identification of congopain as a mediator of trypanosome pathogenesis. Furthermore, the receipt of the Chairman's Award for Best Outstanding Young Scientist is a credit to the programme. The remaining areas show promise but are at an early stage, which makes it difficult to assess their potential impact at the present time.
The sporozoite antigen, p67, from T. parva was identified as inducing a protective response under laboratory conditions at the time of the last EPMR review of ILRAD (1993). Achievements since that time have been to test extensively the p67 antigen using a variety of delivery systems, and show that >70% protection can be achieved with a LD70 challenge under laboratory conditions. A single field trial resulted in 25% protection; this lower level may reflect the unanticipated adverse conditions experienced during the trial. Since the demonstration by ILRI scientists that cytotoxic T-cells generated against the macroschizont stage of the parasite can confer protection, it is clear that the identification of the parasite antigens involved is a high priority. A number of candidate antigens have been isolated.
The prospect for a vaccine against trypanosomosis is debated among the scientific community in terms of feasibility. In collaboration with scientists from France and Belgium, it has been shown that an antigen (congopain) can reduce the pathogenic consequences of infection while a crude sub-fraction of trypanosomes can induce 100% protection against infection in mice. More recent studies have begun to identify the mechanisms of immune suppression in T. congolese infections and have demonstrated clear differences in responses between trypanotolerant and susceptible breeds of cattle. The potential impact of these findings is high, but further research effort is needed to assess this fully.
Serodiagnostic tests for four tickborne diseases have been developed and fully validated in both Africa and Asia. ELISA based kits are currently being distributed to NARS. A set of PCR based diagnostics have been developed for the three main trypanosome species infecting cattle as well as dot blot assays for their detection in tsetse flies. The PCR assays for T. brucei and T. vivax have been converted to an ELISA format. In collaboration with scientists from Glasgow, an ELISA based kit for measuring isometamidium levels in cattle has been developed and validated as a rapid indirect test for the occurrence of drug resistance. The whole range of tests will have significant impact as both research tools in epidemiological studies as well as for routine diagnosis, although the latter may require the development of pen side tests and formats suitable for use by NARS.
A series of molecular reagents have been developed in both T. parva and T. brucei which have been used to develop a detailed restriction map of T. parva, provide a series of markers to define strains of T. parva and initiate the characterisation and identification of drug resistant T. congolense. Additionally some 4,000 expressed sequence tags have been sequences as part of the WHO trypanosome genome project and will be used by the worldwide trypanosome research community for basic research and drug discovery.
Collaborative research with labs in The Netherlands and Scotland has been directed at identifying the molecular basis for cell death of trypanosomes. These projects are essentially at a descriptive phase, but have identified a number of key molecules likely to be involved including a 'secreted' factor causing trypanosome cell death
This is a large programme composed of four separate, but interrelated projects leading to a significant number of future aims and plans, which can be summarised as follows:
Vaccines and vaccine development
There are three component plans, firstly to test the existing p67 Theileria vaccine and develop/identify further antigens to include in a multi-component vaccine; secondly to develop further immunological approaches for defining immune mechanisms, protective antigen identification and antigen delivery for vaccines against ECF and trypanosomosis as well as and collaborative evaluation of a vaccine against cowdriosis; and thirdly to define protective and anti-'disease antigens' for the development of a trypanosome vaccine.
Diagnostics and markers for drug resistance
Further development of tickborne disease and trypanosome diagnostics to include simpler tests and markers for drug resistance and strain identification These will provide the tools for epidemiological analysis, vaccine trial monitoring and more effective diagnosis.
Pathogenesis and disease resistance
The research plans are somewhat diverse and include investigation of the mechanisms of trypanosome cell death, the basis for wild game disease resistance and the identification of molecules mediating immunosupression in trypanosome infections.
This is a broad-ranging portfolio of projects clearly aimed at developing a range of different control strategies against both tickborne diseases and trypanosomosis. The projects have evolved since the last ILRAD EPMR away from basic molecular and biological research towards more applied goals. It is critical that ILRI maintains a strong base in biotechnology and basic research and the expertise to partner new initiatives in the genomics of parasites so that they are in a position to exploit the fruits of gene discovery in the post genomics era. In this context, such expertise will be critical in exploiting the information derived from the proposed T. parva genome-sequencing project, however it is important that the research resulting from such information is of high quality and is focussed.
As the research portfolio has shifted towards more downstream objectives (vaccines and diagnostics) the quality of output has to be judged by different criteria to those largely based on purely scientific considerations. The CCER (1996) report largely endorsed the current projects but provided limited comment on the quality of the work although it suggested the need for consultation in the area of trypanosome diagnostics. The report also recommended expansion into vector-parasite interactions and the coverage of further diseases. The Panel does not endorse this view as there is a need to focus both the resources and the science. The output of the research has been reasonable and Project 6 has developed an array of PCR and ELISA based diagnostics that is commended although consideration needs to be given to the most suitable formats for routine use.
Vaccines are clearly an ideal approach to the control of trypanosomosis and theileriosis as well as other tickborne diseases. However, vaccine research is high-risk, long-term and resource-intensive with organisms as complex as parasites. The issues that face the future development of this research area are several fold and these need to be addressed with urgency if successful delivery of new control measures is to be achieved
In the MTP (1998-2000, table A2) an ex ante impact assessment of vaccines against ECF and trypanosomosis suggests that these will take a further 6 and 10 years research respectively (assuming a 50% probability of success) and both have a high benefit to cost ratio. Considering the ECF vaccine, it seems unlikely that the single (p67) antigen is going to provide full protection under field challenge, highlighting the need to focus on further candidate antigens. The slowness in undertaking the field trials of the p67 vaccine are a major criticism as well as the lack of a major effort to identify additional antigens to other stages of the parasite. The available evidence strongly suggests that a vaccine is feasible albeit in a longer timeframe than 6 years from 1996 when the analysis was undertaken. The Panel suggests that this project area needs to be critically evaluated in terms of its focus and strategies with the development of stringent criteria for making ' go/no go' decisions on particular antigens and approaches so as to avoid resources being expended on nonproductive lines. Furthermore, it is critically important that the p67 ECF vaccine is tested extensively in field trials as soon as possible. Reorganization of the project structure is suggested in order to integrate the disciplines of immunology and molecular biology under a single leadership
The relative value and feasibility of different approaches to the control of trypanosomosis needs to be evaluated either internally or by external consultation given the questions surrounding the feasibility of developing a vaccine against the bloodstream stage of the parasite where natural immunity is rare in contrast to the situation with theileriosis. What are the relative merits of vector control, chemotherapy, or the development of a transmission blocking vaccine? How feasible is it to deliver a vaccine, with the available resources, in a ten-year time frame? To suggest that there is a 50% probability of success is optimistic at this stage of the research.
Consideration needs to be given as to when the research on diagnostic tools has achieved its goals and can be concluded. A number of tests have been successfully developed for tick borne diseases and for defining Theileria strain diversity. Is this an end point? Clearly further research is warranted on developing species specific tests for trypanosomes that can be used in both the vector and the host with subsequent use in epidemiological analyses. Evaluation is required of the future need for diagnostic tests and whether effort should be put into diagnosis of other diseases of relevance outside Africa. Similar considerations apply to the development of tests to detect drug resistant trypanosomes as well as the issues of the cost and the relevance of the need.
The research on disease resistance and pathogenesis has some promising and interesting data in the areas of disease resistance, molecules mediating pathogenesis and immunosuppression, the mechanisms of trypanosome cell death and a new potential target for chemotherapy. The research on congopain (anti disease antigen) should be followed through to a definitive evaluation of its efficacy so as to determine its practicality as a product. There is too large a portfolio of projects and too great a breadth of topic to make substantial progress in any one area. On this basis it is suggested that the research areas be prioritised and a number sidelined so that this project area has a high probability of making a significant impact.
Because the slow pace and past unrealistic timescales have led to a lack of credibility in the area of ILRI vaccine research, the Panel recommends that the research on vaccine development (ECF and Trypanosomosis) be critically reviewed with the aim of clearly defining a strategy and programme for developing further antigens for the ECF vaccine and evaluating whether a vaccine against trypanosomes is a viable prospect
6.4.1 Current Strategy and Approaches
6.4.2 Achievements
6.4.3 Future Plans
6.4.4 Assessment
[Epidemiology and disease control (Project 7)]
This project starts from the premise that control strategies and technologies are often inadequately or incorrectly applied because of a poor understanding of disease epidemiology and the need to define the relative merits of available control options under different situations. Thus it critically underpins the animal health area and is an important source of information for determining priorities in the Biosciences Programme. The initial focus was on vector borne haemoparasites but this has been broadened, as a result of external funding, to include studies of heartwater and rinderpest.
The prime focus of the project is on the epidemiology of vector borne diseases of ruminant livestock and the effect of different control interventions. Four main strategies are being undertaken: 1. The development of a theoretical framework based on conceptual models, mathematical models and geo-referenced databases supported by experimental and field epidemiology (tickborne diseases and trypanosomosis) The framework will focus on the use of vaccine technologies in the case of tick borne diseases and chemotherapy in the case trypanosomosis. 2. Evaluation of the intervention technologies through clinical field trials. 3. Generic impact assessment techniques are being developed to apply to other diseases in relation to regional trade. 4. Investigation of the pathways for delivery of animal health-technologies in systems where veterinary provision is now largely in the hands of the private sector.
A considerable proportion of the research will be carried out in collaboration with a number of ARIs. The aim is to provide improved disease management and control strategies to improve income generation and alleviate poverty. The project has good and extensive links across the Biosciences project portfolio.
The achievements can be divided into three areas: heartwater, rinderpest and trypanosomosis/East Coast Fever. Projects have been completed on rinderpest and heartwater and have provided important and valuable analysis of the economic impacts of the Pan African Rinderpest Campaign and an evaluation of the infection dynamics of heartwater in different production systems in Zimbabwe. This has led to a detailed impact assessment of heartwater and the development of a model to evaluate the effect of different control options and their economic viability. This study is currently being extended to the SADC region (5 countries), in collaboration with the University of Florida, as well as identifying field sites for the evaluation of an inactivated tissue culture vaccine.
In the area of trypanosomosis, an expert system for evaluating chemotherapy options has been developed, a belief network approach to create a cattle disease diagnosis system achieved and a detailed study of trypanocide resistance in Uganda completed. A similar approach to that taken for developing the chemotherapy options has been taken to develop an expert system for the control of ticks and the management of cattle to minimise the impact of tick borne diseases.
It is clear that this project is highly productive and has developed a series of tools that both allow the analysis of the impact of different control strategies as well as putting these into effect to define the impact of specific control programmes. The continued development of these systems will be enormously valuable in advising other areas of the Biosciences programme in terms of the relative value of different control technologies.
Essentially these are to carry on the strategies and approaches outlined in 6.4.1 and extending the approaches described into the evaluation of delivery and adoption pathways for new disease control technologies.
This project is of good quality and has produced a reasonable output both in terms of good scientific publications as well as advice, impact analysis and methods for evaluating different control strategies. The Panel commends the progress in this project and supports its continuation. This project illustrates how interaction between projects can provide added value. It is strongly suggested that the area of trypanosome control strategies should be extended to consider the relative importance and likely impact of different control methods and evaluate whether investment in trypanosome vaccine research is warranted.
6.5.1 Current Strategy
6.5.2 Achievements
6.5.3 Future Plans
6.5.4 Assessment
[Feed utilisation improvement for improving livestock productivity (Project 8);
Rumen microbiology for feed utilisation enhancement (Project 9);
Characterisation and conservation of forage genetic resources (Project 10)]
This set of closely related topics is aimed at alleviating the nutritional bottleneck on ruminant productivity with better diets comprising crop residues and forages, including multipurpose trees and shrubs. Primary topics include 1) strategic dietary supplementation to improve digestion rate, feed intake and microbial protein supply, which involves assessing feed nutritive value to identify better-quality dietary ingredients, 2) utilising exotic rumen microbes, based on their fermentation and detoxification properties, to overcome anti-nutritional factors in forages from trees and shrubs, and 3) to characterise and evaluate forage germplasm to identify adapted genotypes for feed use. A related objective is to conserve forage diversity and disperse disease-free seeds from superior cultivars.
Animal productivity increases with dietary improvement using forage legumes have been quantified; and whole-farm responses to management of nutrient transfers from multipurpose trees for feed and mulch and from manure have been measured. Forage germplasm resources, especially Cynodon species and accessions of Sesbania sesban have been morphologically characterised; and molecular characterisation revealed high differentiation among populations of S. sesban. Nutritive values and genetic marker information have been combined to identify high grain-yielding sorghum and millet genotypes with higher quality residues for feed. This was an inroad towards optimising varietal inputs for more productive crop-livestock systems; farmers were rejecting higher grain-yielding varieties because of low feeding quality of residues. These achievements portend greater net economic returns by managing nutrient flows in fanning systems.
Rumen microbes that tolerate the anti-nutritional factors in Acacia angustissima were successfully transferred to animals with unadapted rumen ecologies, thus enabling them to avoid mortal toxicity when first introduced to this forage.
Collaborative contributions with ecoregional efforts in nutrition management and nutrient cycling resulted in ILRI's notable publication (1995), Livestock and Sustainable Nutrient Cycling in Mixed Farming Systems of sub-Saharan Africa.
· Characterise and evaluate feeding value of tropical forages to improve nutritional status and productivity of ruminant livestock using standard chemical methods and near-infrared spectroscopy.· Improve animal performance through dietary supplementation strategies using tree forages.
· Collaborate with plant breeders to improve nutritive quality of sorghum and millet residues using QTL markers.
· Evaluate tannin-degrading capabilities of rumen microbes to improve nutritional status, including their molecular characterisation.
· Identify plants with anti-protozoal activity to reduce bacterial predation and potential reductions in nutrient flow from the rumen. Identify the anti-protozoal agents in Sesbania sesban and Enterlobium cyclocarpum, and quantify the effects of rumen defaunation on animal productivity.
Adjustments in research focus are needed to increase the likelihood of reducing nutritional restrictions on the productivity of ruminants and farming systems. Farm-level impacts in various crop-livestock systems would be enhanced by shifting emphasis to systematic evaluation (chemically, near-infrared spectroscopy, in situ, in vitro) of the nutritive values of optional plant germplasm and their interactions across locations, including inhibition by secondary compounds (e.g., assaying for tannins). A global feed resources library, or database, containing this information and results from screening studies (including plant QTL markers) would enable study to identify promising dietary options for alternative farming situations (and to quantify the expected differences between them). Such a database would also help determine the best-bet forage grasses, herbaceous and tree legumes (where collaboration with ICRAF would be mutually beneficial), and crops for cultivation in different agroclimatic conditions (e.g., soils, rainfall and temperature). Better understanding the mechanisms controlling dietary supply and utilisation of nutrients, using animal trials to evaluate them, would help determine nutritional recommendations for farmers after modelling appropriate feeding value adjustments (discounts) on the predicted supplies of protein and energy and expected animal performance.
Furthermore, the effectiveness of the microbiology work is compromised by quality of the Debre Zeit facilities: the existing laboratory is rudimentary and difficult to keep clean. Also, this small staff is scientifically isolated, which further impairs ILRI's capacity to efficiently pursue some of the current objectives (e. g., the search for detoxifying microbes, their molecular sequencing, and whether they are likely to be maintained in the ecology of the rumen after inoculation). Because of these limitations, certain microbiology questions on the research agenda requiring substantial facilities and a larger core of researchers should be carried out externally.
The Panel also urges that continuing microbiology work in support of nutritional evaluation (e.g., inhibition by tannins) be relocated at the Nairobi campus, where the facilities better match experimental requirements.
To integrate a systematic global evaluation of forages, crop residues and other feeds with the nutritional evaluation of dietary options to increase animal productivity and net economic returns, the Panel recommends merging Projects 8, 9 and 10 (Feed utilisation improvement for improving livestock productivity; Rumen microbiology for feed utilisation enhancement; and Characterisation and conservation of forage genetic resources) into a cohesive Ruminant Nutrition Management Project.
Thus fused and reoriented, it would better complement the regional research efforts and the smallholder dairy project (Project 19), the Systemwide Livestock Programme, and the respective networks of NARS. It would also enable linkages with the research on molecular characterisation of rumen microbes that is recently underway at the Nairobi campus. The Panel's recommendation would enable ILRI to fully capitalise on its research capacity if collaborating scientists were located at a single location.
This section is to remind readers of the kinship between biological science and system science applications to agriculture. Like the dynamic agricultural systems containing them, many factors affect the productivity of ruminants and their herds and flocks. Also, there are important, sometimes large, interactions among genetic, health, and nutritional factors in the environmental milieu of agriculture across agroclimates and farms. Although there are several kinds of interactions, depending upon the resources and information available to farmers, those with dietary nutrient supply are fundamental because gene products require a balanced substrate of nutrients and a healthy environment to be fully expressed. Insufficient or unequal nutrient supplies signal unequal payoffs from other factors and the livestock system as a whole. As a result, it should be recognised that the effects from every technical factor of the life sciences are ultimately manifested as utilisation, stocks and flows of nutrients across all system scales (e.g., animal, herd or flock, farm, landscape).
Increased gene frequency for disease or parasite resistance (or, alternatively, the use of vaccines or chemotherapy) improves the environmental health backdrop of animal performance. However, the corresponding reductions in mortality and morbidity translate directly into greater total requirements for nutrients to support more, and healthier, surviving animals (i.e., greater collective "appetite" demands by more animals in larger holdings). Consequently, this favourable intermediate outcome exacerbates nutritional limitations. Unless dietary supplies are improved to match the increased collective nutrient demand, there may not be any net increase in productivity, or economic benefit, if the gains portended by reduced disease are cancelled by equal, or maybe greater, losses among less well-fed and more immunologically compromised animals. Hence, synergies among constituents of the biological system are essential to productivity and net economic gains in farm households, here illustrated by an unfavourable interaction between health status and nutrition status. Although loss reduction is necessary to improve the performance of animals and livestock systems constrained by disease, it is insufficient for achieving the desired final outcomes. Because factor interactions have important effects on the performance of animals and herds (flocks), they underscore the need for cross-location synthesis of outcomes and impacts, and the strategies for achieving them.
Overall, ILRI's work in the Biosciences has many elements of good quality, although it requires greater focus in order to achieve a substantive output of high quality. Specific project areas are weak and have been identified in the preceding sections together with suggestions and recommendations for their improvement. The direction of the projects on animal genetic resources and the development of disease resistant livestock (sections 6.1 and 6.2) are very appropriate and although the projects are highly focussed and productive, the Panel considers that co-ordinators' posts should be filled without delay. The group of projects considered under disease control and diagnostics (section 6.3) contain some of the core skills in molecular biology and immunology that underpin the development of new technologies; these are essential for ILRI so that it can capitalise on the new opportunities presented by Biotechnology and Genomics. The current directions are broadly appropriate but require further focus so as to reduce the large number of aims and objectives. An important area is the development of vaccines, and the strategies, approaches and feasibility need to be critically evaluated, as well as fully evaluating the current ECF vaccine candidate in field trials. The area of epidemiology (section 6.4) has appropriate goals and is undertaking well focussed and relevant research; however, care must be taken to avoid that external funding driving the work into too many diverse areas. Adjustments are needed in the ruminant feed resources area (section 6.5) in order to increase the probability that this work leads to a reduction in the constraints on ruminant productivity, and the effectiveness of the microbiology work needs to be assessed. While the overall direction is an area of high priority, the research needs to be re-focussed around clear-cut achievable aims with high impact. In conclusion the Panel believes that it is important to do fewer things very well rather than do a wide range of things poorly.
The evaluation system (Chapter 11) was used here to obtain an approximation of overall scientific quality for each research project. Two factors were used to explain variations in the quality and quantity of outputs; these were research focus (relevance and feasibility of high priority objectives) and critical mass of available human and other resources for maintaining or improving research quality. To report the results of this analysis it is simplest to consider the Biosciences Programme's projects in three groups: projects land 2; projects 3-7; and projects 8-10. In the first group the quality scores exceeded the Panel's threshold definition of good science defined in section 11.2, and the focus was excellent, although critical mass was identified as a problem in terms of maintaining this output and improving quality. The second group equalled or exceeded the ranking of good science, but overall were below average on focus while having sufficient critical mass. The third group fell below the quality rating of good science and showed average or well below average levels of focus with one project (9) being considered to have a low critical mass. Clearly these problems need to be addressed to improve output and quality.
As shown in Chapter 5, the Panel suggests structural alterations of the research programme. On the basis of the rationale provided in Chapter 5, projects land 2 would form the Animal Genetics and Genomics Programme, projects 3-7 would form the Disease Control Programme and projects 8-10 would join the new Production Systems and Animal Nutrition Programme.
As shown in Chapter 5, the Panel suggests structural alterations of the research programme. On the basis of the rationale provided in Chapter 5, projects 1 and 2 would form the Animal Genetics and Genomics Programme , projects 3-7 would form the Disease Control Programme and projects 8-10 would join the new Production Systems and Animal Nutrition Programme.
