5', J Zebu cattle of Kenya: Uses, performance, farmer preferences and measures of genetic diversity ILRI International Livestock Research Institute INTERNATIONAL L/VE5TOCK RESEARCH INSTITUTE tOTijr Kenya Agricultural Research Institute Zebu cattle of Kenya: Uses, performance, farmer preferences, measures of genetic diversity and options for improved use Animal Genetic Resources Research 1 J.E.O. Rege, A. Kahi, M. Okomo-Adhiambo, J. Mwacharo and O. Hanotte ILRI International Livestock Research Institute INTERNATIONAL LIVESTOCK RESEAXCH INSTITUTE Kenya Agricultural Research Institute Thl s One I I II II HS6H-2WA-EXK7 Authors' affiliations J.E.O. Rege, International Livestock Research Institute (ILRI), RO. Box 5689, Addis Ababa, Ethiopia A. Kahi, Department of Animal Science, Egerton University, P.O. Box 536, Njoro, Kenya M. OkomoAdhiambo, ILRI, P.O. Box 30709, Nairobi, Kenya J. Mwacharo, Kenya Agricultural Research Institute, KARI, Kiboko Research Centre, P.O. Box 5781 1, Makindu, Kenya O. Hanotte, ILRI, P.O. Box 30709, Nairobi, Kenya © 2001 ILRI (International Livestock Research Institute) All rights reserved. Parts of this docment may be reproduced without express permission for non-commercial use but with acknowledgment to ILRI. Cover photo courtesy of Clemens Wollny. ISBN 92-9146-094-X Correct citation: Rege J.E.O., Kahi A.K., OkomoAdhiambo M., Mwacharo J. and Hanotte O. 2001. Zebu cattle of Kenya: Uses, performance, farmer preferences, measures of genetic diversity and options for improved use. Animal Genetic Resources Research 1. ILRI (International Livestock Research Institute), Nairobi, Kenya. 103 pp. Table of Contents List of Tables v List of Figures vii Acknowledgements viii Foreword ix 1 Introduction 1 2 Background on African cattle 3 2.1 Origin and current classification of African cattle 3 2.2 Zebu cattle breeds of eastern Africa 4 2.2. 1 East African Zebu cattle 4 2.2.2 Kenyan zebu cattle 10 3 On-farm phenotypic characterisation of Kenyan zebu cattle 21 3.1 Objectives 21 3.2 Materials and methods 21 3.2.1 Data sources 21 3.2.2 Field data collection 24 3.2.3 Data classification 24 3.2.4 Data analyses 25 3.3 Results and discussion 25 3.3. 1 Uses of indigenous zebu breeds 25 3.3.2 Farmer preferences for breeds .- 28 3.3.3 Breeding systems and selection 29 3.3.4 Nutrition and feeding 31 3.3.5 Animal health and adaptation 31 3.3.6 Herd structures 34 3.3.7 Production and reproductive performance 35 3.4 Summary and conclusions 38 4 Molecular characterisation of Kenyan zebu cattle 41 4. 1 Objectives 41 4.2 Materials and methods 41 4.2. 1 Sampling and genomic DNA extraction 41 4.2.2 Determination of genotypes 42 4.2.3 Data analysis 42 4.3 Results 44 4.3. 1 Tests of Hardy-Weinberg equilibrium 44 4.3.2 Heterozygosity 45 4.3.3 Evidence for genetic introgression from non-zebu populations 46 4.3.4 Genetic relationships among populations 47 4.3.5 Principal Component analysis 49 4.4 Discussion 50 in 4.4. 1 Population structure and within-breed diversity 50 4.4.2 Extent of taurine introgression 51 4.4.3 Genetic diversity and relationships among breeds 51 4.5 Summary and conclusions 53 5 Breeding strategies for Kenyan zebu 54 5.1 Animal production systems 54 5.2 Goal traits in genetic improvement of Kenyan zebu 55 5.3 Open nucleus breeding schemes 58 5.4 Options for improved use of the Kenyan zebu 59 5.4. 1 Options for case 2 60 5.4.2 Options for case 3 63 5.4.3 Options for case 4 64 5.5 Development of a breeding programme 65 5.5. 1 Genetic design of a breeding programme 66 5.5.2 Structural design of a breeding programme: general considerations .... 68 5.5.3 Stakeholders and their potential roles 71 5.5.4 Proposal for a breeding programme in Kenya 74 6 Research priorities 80 7 References 82 Appendix I. Information collected and the classification applied 88 Appendix II 93 IV List of Tables Table 1. Classification, distribution and characteristics of some of the Large East African Zebus 5 Table 2. Classification, distribution and characteristics of some of the Small East African Zebus 6 Table 3. Performance characteristics of some representative East African zebu breeds/strains 10 Table 4. Climatic characteristics of the study areas 23 Table 5. Location of each survey and total number of questionnaires administered in each district 24 Table 6. Proportion (%) of respondents with preference for each characteristic, in each district 28 Table 7. Proportion (%) of respondents using a particular character as the basis for selection 30 Table 8. Age and sex structures of cattle herds in the study area 34 Table 9. Least squares estimates (means ± standard errors where applicable) for production and reproduction traits in each district 36 Table 10. Selected Kenyan zebu breeds/strains and the reference breeds of Bos indicus and Bos taurus types .• 42 Table 11. The analysed autosomal and Y-specific microsatellite loci 42 Table 12. Number of microsatellite loci showing deviations from Hardy- Weinberg equilibrium, average expected heterozygosity (and its standard error) and the total number of alleles observed across the autosomal microsatellite loci in each of the populations 44 Table 13. Average expected heterozygosity (He), gene differentiation (Gst) and the number of alleles observed at the autosomal microsatellite loci 45 Table 14- Mean frequencies of taurine and zebu-specific alleles observed at autosomal microsatellite loci and of indicine and taurine haplotypes at the Y-chromosome-specific microsatellite locus in the selected Kenyan zebu cattle and the reference breeds 46 Table 15. Standard genetic distances (Ds) (below diagonal) and genetic distances (DA)(above diagonal) observed among the cattle populations. ... 47 Table 16. The eigenvalues of the correlation matrix for the first three Principal Components (to which the percentage variance is proportional) and the breeds separated by each set of Principal Component analysis 49 Table 17. Function played by indigenous zebu breeds and the identified component traits 56 Table 18. A suggested list of breeding goal traits in the improvement of the Kenyan zebu breeds 57 Table 19. Economic values (v), phenotypic standard deviation (p), heritability (h2), genetic correlations (below the diagonal) and phenotypic correlations (above the diagonal) of the breeding goal traits 76 Table 20. The information sources for selection in the three pathways 78 Table 21. Predicted annual genetic gain for the breeding goal traits 78 VI List of Figures Figure 1 . Data and sample sources for the on-farm phenotypic and molecular characterisation 22 Figure 2. Functions performed by indigenous zebu breeds 26 Figure 3. Proportion of respondents using manure as fertiliser, fuel or for building 27 Figure 4. Proportion of respondents using a given breeding system 30 Figure 5. The most common cattle diseases occurring in each district 32 Figure 6. General degree of tolerance of the common cattle diseases in each district 33 Figure 7. Activities generated during data analysis 43 Figure 8. UPGMA tree with standard genetic distances (Ds): 17 populations, 17 loci 48 Figure 9. UPGMA tree with standard genetic distances (Ds): 12 populations, 17 loci 48 Figure 10. Principal Components graph of the first three Principal Components axis: 17 populations, 17 loci, and 213 alleles 49 Figure 11. Principal Components graph of the first three Principal Components axis: 12 populations, 17 loci, and 213 alleles 50 Figure 12. Two-tier open nucleus breeding structure with selection in nucleus and possibly in the participating herds, and downward and upward migration of genetic material 59 Figure 13. Diagrammatic depiction of a breeding plan to create a two-breed synthetic breed using participating herds 62 Figure 14. Potential key stakeholders in a breeding programme for the Kenyan zebu breeds 71 Figure 15. Outline of the structure of the breeding programme 77 vn Acknowledgements This report presents results from a set of research activities principally funded by the Kenya Agricultural Research Institute (KARI), through financial support from the European Union to the Agriculture/Livestock Research Support Programme (ARSP) Phase II project of KARI. The overwhelming support provided by the EU/KARI co-ordination office— Drs Romano M. Kiome and Helga Recke— was critical to the success of this work. The International Livestock Research Institute (ILRI) provided financial support to train KARI scientists in breed survey methodologies and backstopping for both the conduct of the survey and analyses of the survey data. Staff of the Department of Animal Production (DAP) of the University of Nairobi, Drs Reuben O. Mosi and Okeyo Mwai, were instrumental in the field blood sampling that provided the DNA analysed for the genetic characterisation. DAP also supervised an MSc project (of Dr Margaret Okomo), some results of which are reported here. ILRI funded Dr Okomo's MSc project, while KARI funded all the additional sampling and laboratory analyses. All laboratory work was done at the ILRI laboratory in Nairobi. Our special thanks to all the technical staff of Lab 7 (ILRI, Nairobi), and research assistants in the AnGR team (ILRI, Addis Ababa). We are also grateful to Mr CO. Ahuya, former KARI employee, for his efforts in the initial breed survey. Special thanks to the staff of KARI's Kiboko Research Centre, especially Mr Joseph Bii for his valuable contribution in the conduct of the survey, and also to Mr W.N. Mnene and Mr P.F.K. Kibet (the Centre Director) for their support. We also wish to thank the extension personnel who were instrumental during both the survey and blood sampling. Finally, and most importantly, we are immensely grateful to the farmers who gave us access to their herds and sacrificed their valuable time both during the survey and the sampling.