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The Indigenous Farm Genetic Resources of Somalia: Preliminary Phenotypic and Genotypic Characterization of Cattle, Sheep and Goats The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats ILRI PROJECT REPORT ISBN: 92–9146–448–1 The International Livestock Research Institute (ILRI) works to improve food security and reduce poverty in developing countries through research for better and more sustainable use of livestock. ILRI is a member of the CGIAR Consor tium, a global research partnership of 15 centres working with many partners for a food-secure future. ILRI has t wo main campuses in East Africa and other hubs in East, West and Southern Africa and South, Southeast and East Asia. ilri.org CGIAR is a global agricultural research partnership for a food-secure future. Its science is carried out by 15 research centres that are members of the CGIAR Consor tium in collaboration with hundreds of partner organizations. cgiar.org The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats i The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats Anne Muigai1, George Matete1, Hussein Haji Aden1, Miika Tapio2, Okeyo Mwai3 and Karen Marshall3 1. Jomo Kenyatta University of Agriculture 2. Natural Resources Institute, Finland 3. International Livestock Research Institute January 2016 The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats iii © 2016 International Livestock Research Institute (ILRI) This publication is copyrighted by the International Livestock Research Institute (ILRI). It is licensed for use under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported Licence. To view this licence, visit http:// creativecommons.org/licenses/by-nc-sa/3.0/. Unless otherwise noted, you are free to copy, duplicate or reproduce, and distribute, display, or transmit any part of this publication or portions thereof without permission, and to make translations, adaptations, or other derivative works under the following conditions: ATTRIBUTION. The work must be attributed, but not in any way that suggests endorsement by ILRI or the author(s). NON-COMMERCIAL. This work may not be used for commercial purposes. SHARE ALIKE. If this work is altered, transformed, or built upon, the resulting work must be distributed only under the same or similar licence to this one. NOTICE: For any reuse or distribution, the licence terms of this work must be made clear to others. Any of the above conditions can be waived if permission is obtained from the copyright holder. Nothing in this licence impairs or restricts the author’s moral rights. Fair dealing and other rights are in no way affected by the above. The parts used must not misrepresent the meaning of the publication. ILRI would appreciate being sent a copy of any materials in which text, photos etc. have been used. Editing, design and layout—ILRI Editorial and Publishing Services, Addis Ababa, Ethiopia. Cover photo–ILRI/Peter Ballantyne ISBN: 92–9146–448–1 Citation: Muigai, A., Matete, G., Aden, H.H., Tapio, M., Mwai, O. and Marshall, K. 2016. The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats. ILRI Project Report. Nairobi, Kenya: International Livestock Research Institute (ILRI). ilri.org better lives through livestock ILRI is a member of the CGIAR Consortium Box 30709, Nairobi 00100, Kenya Box 5689, Addis Ababa, Ethiopia Phone: + 254 20 422 3000 Phone: +251 11 617 2000 Fax: +254 20 422 3001 Fax: +251 11 617 2001 Email: [email protected] Email: [email protected] iv The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats Contents Tables vi Figures vii Abbreviations viii Acknowledgments ix Executive summary x 1. Introduction 1 2. Background 2 2.1 Country background 2 2.2 Livestock production systems 4 2.3 Livestock marketing 4 2.4 Indigenous animal genetic resources of Somalia 4 3. Research methodology 8 3.1 Study sites and time period 8 3.2 Rapid assessment tool and sampling of households 8 4. Results and discussion 13 4.1 Purpose for keeping livestock 13 4.2 Livestock production system 13 4.3 Livestock ownership 14 4.4 Source of breeding stock 14 4.5 Breed preferences 14 4.6 Morphological characterization 15 4.7 Genetic characterization 16 5. Conclusions 19 The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats v 6. References 20 Appendix 1: Autosomal microsatellite and Y chromosome markers analysis 23 Appendix 2: Mitochondrial DNA analysis 24 Appendix 3: Candidate gene analysis 25 vi The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats Tables Table 1: The livestock breeds of Somalia: classification, distribution and breed characteriztics* 5 Table 2: Overview of breeds sampled 10 Table 3: Breeds and number of animals analysed 11 Table 4: Means ± standard errors of the morphometric measurements for mature Boran, Dauara and North Somali zebu cattle breeds1, 2 15 Table 5: Mean ± standard errors of the morphometric measurements for mature Somali goats and sheep breeds1 16 The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats vii Figures Figure 1: Agro ecological zones in the Horn of Africa including Somalia (Knips 2004) 3 Figure 2: Land use in Somalia (FAOSTAT 2012) 3 Figure 3: Livestock breeds in Somalia 7 Figure 4: Map highlighting sampling areas in Somalia and Kenya 9 Figure 5: Two dimensional plot representing the relationship between the first two principal coordinate axes (PCoA) using allele frequencies data from 15 microsatellite loci genotyped in the four Somali and two Kenyan reference cattle breeds 17 Figure 6: Two dimensional plot representing the relationship between two first principal coordinate axes (PCoA) using allele frequency data from 15 microsatellite loci genotyped in the for Somali Long-eared (SMLE), Somali Short-eared goat (SMSE) and four Italian reference breeds 17 Figure 7: Two dimensional principal coordinate axes (PCoA) plot, using allele frequency data from 15 microsatellite loci, representing the relationships between Somali Blackhead Persian and East and South African sheep breeds 18 viii The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats Abbreviations ADB African Development Bank AU African Union DAGRIS Domestic Animal Genetic Information System EDTA Ethylenediaminetetraacetic acid EU European Union FAO Food and Agriculture Organization of the United Nations FAOSTAT Food and Agriculture Organization Statistics platform IGAD Intergovernmental Authority on Development ILRI International Livestock Research Institute ISAG International Society for Animal Genetics PCR Polymerase chain reaction WB World Bank The indigenous farm genetic resources of Somalia: Preliminary phenotypic and genotypic characterization of cattle, sheep and goats ix Acknowledgments The International Livestock Research Institute (ILRI) and Terra Nuova are grateful to the European Commission and the Danish government for funding this study, which was a component of the project titled ’Improvement and diversification of Somali livestock trade and marketing‘. ILRI and Terra Nuova are very grateful to the livestock keepers of Somalia for readily collaborating with the project and availing their livestock for data and blood collection. ILRI and Terra Nuova would like to thank the following people for the roles they played during the project. In Somaliland, the then Minister of Livestock, the late Idris Ibrahim Abdi very kindly granted authorization to conduct the study. The following Institutions provided assistance for field work including the Ministry of Livestock, Commerce and Industry and Finance; the municipalities of Hargeisa, Burao and Gabiley and the Berbera Port Authority. The contribution of private institutions such as the Chambers of Commerce, Industry and Agriculture of Somaliland also provided great assistance. The Director of Veterinary Services Abdullahi Ahmed Hassan, the Berbera Port Veterinary Officer Ahmed Aibe Warsame, the Gabiley District Veterinary Officer Ahmed Hassan Bile and the Togdheer Regional Veterinary Coordinator Issa Nur Liban are gratefully acknowledged for their valuable assistance in undertaking the field work. In Puntland the Minister of Livestock, Agriculture and Environment Ibrahim Hared Ali Da’ar kindly granted authorization to conduct the study. The institutions which provided assistance for field data collection include the Ministry of Livestock, Agriculture and Environment, Commerce and Industry, Finance and Ports and Marine Resources; the municipalities of Galkayo and Las Anod; the Port Authority and the Chamber of Commerce, Industry and Agriculture. Valuable assistance was provided by the Vice Minister of Livestock, Agriculture and Environment Yassin Ali Abdulleh, the Director of the Animal Health Department in the Ministry of Livestock, Agriculture and Environment Mohamud Hassan Ismail, the Mudug Regional Veterinary Coordinator Mohamed Abdiqadir Hussein, the Galkayo District Veterinary Officer Abdirahman Mohamed Jama, the Bossaso Port Veterinary Officer Jama Mohamed Ali, the Technical Advisor in the Ministry of Livestock
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