Page 1 of 128 Defra Research Project GC0146 Development of co-ordinated in situ and ex situ UK Farm Animal Genetic Resources conservation strategy and implementation guidance Breeding Plans for Farm Animal Genetic Resources Review of Conservation Strategies Best Practice Guidance Glossary Technical Appendices Stephen J.G. Hall MA PhD Livestock Diversity Ltd. www.livestockdiversity.com Mention of an organization, system or procedure in this report does not imply a recommendation, endorsement, comparison, evaluation or criticism of any kind unless explicitly stated. Neither is it implied that any organization that is not mentioned is irrelevant to the topic under discussion. Examples unless otherwise stated are illustrative only. Page 2 of 128 Executive Summary The need for the project arises from the UK Government’s international commitments to the conservation and sustainable utilization of its farm animal genetic resources (FAnGR). This report complements the other elements of the project, which have focused on background policy and specific issues of animal identification and traceability. Its aims are To review current activities in UK FAnGR breeding and conservation; To generate a best practice document for stakeholders and policy makers. Breeding plans “The selective breeding of livestock in order to meet commercial requirements” 1. Breeding plans operate within political, economic and scientific-technical contexts and these are reviewed; 2. UK livestock are in the private sector and while decisions are made by individual breeders, who also own the information necessary to assess the genetic consequences, but the UK Government is responsible internationally for the effects of these decisions on FAnGR; 3. Breeding plans that fail to take account of genetic conservation can lead to genetic improvement in the traits under selection being accompanied by the avoidable loss of genetic variation in other traits which may be of value either now or in the future, as has been observed in the breeding of commercial dairy cattle; 4. A practical investigation of native mainstream and at-risk breeds, using new data and methods, has shown how breeding plans and conservation strategies coexist; 5. Methodologies developed for the planning and monitoring of breeding plans can readily be adapted to perform the same functions in conservation strategies. Conservation strategies “The planned mating of livestock in order to retain breed genetic variation” 1. The contexts of FAnGR conservation, and the relevant stakeholders, are reviewed, with the role of breed societies being considered in detail; 2. Conservation strategies must take account of the desire of many owners of at-risk breeds to develop their breeds along commercial lines; 3. New research is reported showing that while genetic variation is, in general, being conserved, there are important areas where particular attention is needed; 4. Ex situ conservation (principally, the storage of frozen semen) is reviewed and found to compare favourably with what is practised elsewhere in Europe, except in the case of poultry; 5. Emergent issues are highlighted, notably the conservation of traditional segments within commercial breeds and of poultry in general; 6. New research is reported on the monitoring of genetic variation by means of demographic variables, for breeds where computational approaches cannot be applied. Best practice guidance Best Practice Guidance is presented and the principles explained. The Guidance, which is for breeders, breed societies and the UK Government, is also available as a separate document. Page 3 of 128 Table of Contents 1 General Introduction ...................................................................................................................... 6 2 Breeding Plans for Farm Animal Genetic Resources ...................................................................... 7 2.1 The background to breeding plans ........................................................................................ 7 2.1.1 Economic context ............................................................................................................ 7 2.1.2 Scientific and technical context ...................................................................................... 8 2.1.2.1 Molecular biosciences ............................................................................................. 8 2.1.2.2 Conservation biology .............................................................................................. 9 2.1.2.3 Veterinary science ................................................................................................. 10 2.1.3 Legal context ................................................................................................................. 10 2.1.4 Social contexts .............................................................................................................. 11 2.1.5 Institutional organization and stakeholder bodies ....................................................... 11 2.1.5.1 Breed societies ...................................................................................................... 11 2.1.5.2 Umbrella organizations ......................................................................................... 12 2.1.5.3 Breeding companies .............................................................................................. 12 2.1.5.4 Industry platforms ................................................................................................. 12 2.1.5.5 Scientific research and knowledge transfer .......................................................... 13 2.1.5.6 Governmental bodies and levy boards ................................................................. 13 2.1.6 Institutional interactions ............................................................................................... 14 2.2 Practical breeding ................................................................................................................ 16 2.2.1 Interface with conservation strategies ......................................................................... 16 2.2.2 Principles applying to all species ................................................................................... 16 2.2.3 Breeding structures and global needs .......................................................................... 17 2.2.4 Crossbreeding ............................................................................................................... 17 2.3 Survey of breeding plans in practice ................................................................................... 19 2.3.1 Breed reviews................................................................................................................ 19 2.3.1.1 Cattle ..................................................................................................................... 20 2.3.1.2 Sheep ..................................................................................................................... 27 2.3.1.3 Goats ..................................................................................................................... 33 2.3.1.4 Pigs ........................................................................................................................ 34 2.3.1.5 Equines .................................................................................................................. 36 2.3.1.6 Poultry ................................................................................................................... 37 2.4 Breeding plans: summary of findings .................................................................................. 38 Page 4 of 128 3 Review of Conservation Strategies .............................................................................................. 40 3.1 The context of conservation strategies ............................................................................... 40 3.1.1 Policy context ................................................................................................................ 41 3.1.2 Regulatory context ........................................................................................................ 41 3.1.3 Overseas and international organizations .................................................................... 42 3.1.4 Institutional context ...................................................................................................... 42 3.1.4.1 Departmental Expert Committee on Farm Animal Genetic Resources ................ 43 3.1.4.2 Umbrella organizations ......................................................................................... 43 3.1.4.3 Breed societies ...................................................................................................... 44 3.1.4.4 Registration and publication of registers .............................................................. 45 3.2 National outcomes of UK FAnGR conservation ................................................................... 47 3.2.1 Maintenance of population numbers ........................................................................... 47 3.2.2 Conservation of within-breed variation ........................................................................ 47 3.2.3 The role of ex situ conservation .................................................................................... 50 3.3 Conservation practice at breed level ..................................................................................