Annex I - Description of Work

Transcription

1 SEVENTH FRAMEWORK PROGRAMME THEME 2 LowInputBreeds Food, Agriculture and Fisheries, and Biotechnology Grant agreement for: Collaborative Project Project acronym: LowInputBreeds Project full title: Grant agreement no.: Annex I - Description of Work Development of integrated livestock breeding and management strategies to improve animal health, product quality and performance in European organic and low input milk, meat and egg production. Date of preparation of Annex I (Final): 01 July 2009 Date of approval of Annex I by Commission: 01 July

2 ABSTRACT The proposed integrating project LOWINPUTBREEDS aims to develop integrated LIVESTOCK BREEDING and MANAGEMENT strategies to improve ANIMAL HEALTH, product QUALITY and PERFORMANCE in European organic and low input milk, meat and egg production through research, dissemination and training activities. The consortium includes 11 academic centres of excellence and 6 genetics/breeding companies (4 SMEs) in 11 European, 1 ICPC and 2 industrialised third countries. The proposed project has 4 main Science and Technology OBJECTIVES: 1. To DEVELOP and evaluate INNOVATIVE BREEDING CONCEPTS, including (a) genome wide and (b) marker assisted selection, and (c) cross-, (d) flower - and (e) farmer participatory breeding strategies, which will deliver genotypes with robustness and quality traits required under low input conditions. The project will focus on 5 LIVESTOCK PRODUCTION SYSTEMS (dairy cows, dairy and meat sheep, pigs and laying hens) and design SPECIES- SPECIFIC BREEDING STRATEGIES for different macroclimatic regions in Europe. 2. To INTEGRATE the use of IMPROVED GENOTYPES with INNOVATIVE MANAGEMENT approaches including improved diets, feeding regimes and rearing systems. This will focus on issues (e.g. mastitis and parasite control, animal welfare problems) where breeding or management innovations alone are unlikely to provide satisfactory solutions. 3. To IDENTIFY potential ECONOMIC, ENVIRONMENTAL, GENETIC DIVERSITY/PLASTICITY and ETHICAL IMPACTS of project deliverables to ensure they conform to different societal priorities and consumer demands/expectations and are acceptable to producers. 4. To ESTABLISH an efficient TRAINING and DISSEMINATION programme aimed at rapid exploitation and application of project deliverables by the organic and low input livestock industry

3 COST SUMMARY (copy of A3 form) LowInputBreeds Participant Organisation Estimated budget (whole duration of the project) Requested EC Number Short name Country RTD DM TR CO SU Management Other TOTAL TR contribution 1 UNEW UK 1,405,620 41, ,248 85,160 1,805, ,433,123 2 FiBL CH 1,385, ,752 62,499 1,584, ,118,487 3 INRA FR 495, , , ,500 4 WUR NL 1,026, ,000 25,312 1,055, ,977 5 UGöt DE 848, , , ,000 6 Ucat IT 216, , ,561 7 NAGREF GR 423, , ,520 8 vti DE 444, , ,000 9 UCPH DK 90, , , ULju SL 100, , , , UCLou BE 50, , , SG CH 50, , SBZV CH 50, , AGN CH 135, , IPG NL 627, , , , , PI ES 40, , ISA NL 276, , , INRAT TN ,000 20, , UL-NZ NZ 40, , UG-CAN CN 207, , UFV BR 32, , , Open Calls# * * * * * 0 * TOTAL 7,943, , , ,721 8,909,671 5,999,995 # new partners to be recruited via Open calls; * budget (120,000 total cost and 90,000 EU requested EU contribution) are currently included in coordinators (partner 1 UNEW) budget - 3 -

4 List of Beneficiaries Beneficiary Date No. Name Short Name Country Enter project Exit project 1 UNIVERSITY OF NEWCASTLE UPON TYNE UNEW UK 1 60 (Co) 2 FORSCHUNGSINSTITUT FUR FiBL CH 1 60 BIOLOGISCHENLANDBAU STIFTUNG 3 INSTITUT NATIONAL DE LA RECHERCHE INRA FR 1 60 AGRONOMIQUE 4 ASG VEEHOUDERIJ BV WUR NL GEORG-AUGUST-UNIVERSITAET UGöt DE 1 60 GOETTINGEN STIFTUNG OEFFENTLICHEN RECHTS 6 UNIVERSITA DEGLI STUDI DI CATANIA UCat IT NATIONAL AGRICULTURAL NAGREF GR 1 60 RESEARCH FOUNDATION 8 JOHANN HEINRICH VON THUENEN- vti DE 1 60 INSTITUT, BUNDESFORSCHUNGSINSTITUT FUER LANDLICHE RAUME, WALD UND FISCHEREI 9 Københavns Universitet UCPH DK UNIVERZA V LJUBLJANI ULju SL UNIVERSITE CATHOLIQUE DE LOUVAIN UCLou BE Swissgenetics SG CH Schweizer Braunviehzuchtverband SBZV CH applied genetics network AGN CH Institute for Pig Genetics BV IPG NL Pigture Iberica S.L. PI ES Institut de Sélection Animale BV ISA NL Institut National Reserche Agronomique de INRAT TN 1 60 Tunisie 19 LINCOLN UNIVERSITY UL-NZ NZ UNIVERSITY OF GUELPH UG-CAN CA Federal University of Viçosa (Universidade UFV BR 1 60 Federal de Viçosa) 22,23, 24 New partners to be recruited by OPEN CALLS * * Coord. = co-ordinator; ICPC = International cooperation partner country; * to be determined - 4 -

5 Table of Contents Contents List LowInputBreeds Page ABSTRACT 2 COST SUMMARY (copy of A3-form) 3 List of Beneficiaries 4 B1. Concept and project objectives, progress beyond the state-of-the-art, 11 S/T methodology and work plan B1.1 Concept and project objectives 12 B1.2 Progress beyond the state of the art Background Baseline description (where does the project work start) Description of performance/research indicators 17 B1.3 Science and Technology methodology and associated work plan 17 Overall and general description 17 Figure 1. Project management structure and organisation of the project workplan 19 Table 1.3a Work package list SP0 PROJECT COORDINATION 27 Background and overall approach 28 WP0.1 Project coordination and overall management SP1 IMPROVING PERFORMANCE, ANIMAL HEALTH & WELFARE, 37 ENVIRONMENTAL IMPACT AND PRODUCT QUALITY IN ORGANIC AND LOW INPUT DAIRY COW PRODUCTION SYSTEMS Main issues addressed under SP1 38 WP1.1 Development of WITHIN BREED selection systems to improve animal 43 health, product quality and performance traits; comparing genome-wide and traditional quantitative-genetic selection WP1.1.0 MANAGEMENT OF WP1.1 RTD ACTIVITIES 43 WP1.1.1 STAGE 1 Expanded phenotyping of Swiss Brown Cattle and parameter 46 estimation for traits required in organic and low input systems WP1.1.2 STAGE 2 Genotyping of Swiss Brown Cattle and estimation of genomic 49 breeding values WP1.1.3 STAGE 3 Design a genome-wide selection scheme for the Swiss Brown Cattle 52 subpopulation used in low input systems; quantification of genetic diversity impacts of GS WP1.2 Development of improved CROSS-BREEDING strategies to optimise the 56 Balance between robustness and performance traits; comparing cross-breeds with pure-bred Holstein Friesian genotypes WP1.2.0 MANAGEMENT OF WP1.2 RTD ACTIVITIES 56 WP1.2.1 STAGE 1 Effect of cross-breeding strategies on animal health and milk yield 59 and quality parameters in Holstein Friesian cattle WP1.2.2 STAGE 2 Effect of oil seed feed supplementation on animal health and milk 62 yield and quality parameters in pure and cross-breed Holstein Friesian cattle WP1.3 Design of optimised breeding and management systems for different macro- 64 climatic regions of Europe; model-based MULTI-CRITERIA EVALUATION with respect to performance, animal health and welfare, product quality and environmental impact WP1.3.0 MANAGEMENT OF WP1.3 RTD ACTIVITIES

6 Contents List LowInputBreeds Page SP1 continued WP1.3 continued WP1.3.1 STAGE 1 Model development and validation using existing data sets from 67 Northern-maritime, Northern-continental and alpine macro-climatic zones WP1.3.2 STAGE 2 Model adaptation and validation for additional macro-climatic 71 regions (Mediterranean, North Eastern Europe) SP2 IMPROVING PERFORMANCE, ANIMAL HEALTH, WELFARE AND 73 PRODUCT QUALITY IN ORGANIC AND LOW INPUT SHEEP PRODUCTION SYSTEMS Main issues addressed under SP2 74 WP2.1 Development of WITHIN BREED SELECTION systems to improve abiotic 79 and biotic stress resistance and performance traits; comparing marker assisted and traditional quantitative-genetic selection for functional traits. WP2.1.0 MANAGEMENT OF WP2.1 RTD ACTIVITIES 79 WP2.1.1 STAGE 1 Phenotyping of Sfakiano sheep for biotic and abiotic stress resistance 82 WP2.1.2 STAGE 2 Genotyping of sheep breeds used in different macro-climatic zones 85 of Europe (Greece, France and Switzerland) WP2.2 Development of improved endoparasite MANAGEMENT STRATEGIES 88 based on integrating (a) feed supplementation with tanniniferous forages with (b) strategic use of clean pastures and (c) the use of parasite tolerant breeds WP2.2.0 MANAGEMENT OF WP2.2 RTD ACTIVITIES 88 WP2.2.1 CONTROLLED STUDIES; Quantification of (a) condensed tannin 91 profiles in TR-forages and concentrate feeds, (b) in vitro and in vivo anthelmintic activity and (c) the potential contribution of non-tannin compounds to anthelmintic activity WP2.2.2 FIELD TRIALS (Mediterranean production systems); 95 Effects of (and interaction between) different (a) TF feeding regimes and (b) Sfakiano sheep genotypes on animal health, yield and product quality WP2.2.3 FIELD TRIALS (mountainous/alpine production systems); 97 Effects of (and interaction between) different (a) TF feeding regimes (b) grazing regimes and (c) sheep genotypes on animal health, yield and product quality WP2.3 Development of strategies to improve lamb meat and milk quality in SHEEP 100 production systems based on optimising (a) TF feed supplements (b) grazing regimes and/or (c) the use of stress tolerant breeds WP2.3.0 MANAGEMENT OF WP2.3 RTD ACTIVITIES 100 WP2.3.1 FIELD TRIALS and LABORATORY STUDIES Effects of (and interaction 103 between) using (a) robust breeds/genotypes, (b) TF-feed supplementation and (c) different grazing regimes on carcass and meat quality SP3 IMPROVING PERFORMANCE, ANIMAL HEALTH & WELFARE AND 109 PRODUCT QUALITY IN ORGANIC AND LOW INPUT PIG PRODUCTION SYSTEMS Main issues addressed under SP3 110 WP3.1 Development of a FLOWER BREEDING system to improve pig survival 115 and robustness related traits in small populations; comparing the performance of breeds from flower and conventional breeding systems WP3.1.0 MANAGEMENT OF WP2.1 RTD ACTIVITIES

7 Contents List LowInputBreeds Page SP3 continued WP3.1 continued WP3.1.1 Identification of the most suitable genotypes/breeds currently available/used 117 in low input production in different macro-climatic regions WP3.1.2 Development and implementation of a flower breeding systems (FBS) in 119 organic and low input production systems WP3.1.3 Identification of parameters associated with heat stress resistance in 122 Mediterranean flower breeding systems WP3.2 Development of MANAGEMENT innovations (gilt rearing and lactation 124 systems) on mothering ability of sows as well as pre- and post-weaning diarrhoea and losses of piglets WP3.2.0 MANAGEMENT OF WP2.1 RTD ACTIVITIES 124 WP3.2.1 Development of MANAGEMENT innovations (gilt rearing and lactation 125 systems) on mothering ability of sows as well as pre- and post-weaning diarrhoea and losses of piglets WP3.3 Effect of traditional, improved and standard hybrid PIG GENOTYPES and 128 FEEDING REGIMES on carcass, meat and fat quality in heavy pigs used for premium, regional pork products WP3.3.0 MANAGEMENT OF WP2.1 RTD ACTIVITIES 128 WP3.3.1 EXPERIMENTAL APPROACH 130 Effects of, and interactions between, (a) pig genotype and (b) dietary regimes on carcass, meat and processing quality characteristics WP3.3.2 SURVEY APPROACH 133 Effect of genetic, management and dietary factors on carcass and meat quality parameters in European low input production systems SP4 IMPROVING PERFORMANCE, ANIMAL HEALTH & WELFARE AND 135 PRODUCT QUALITY IN ORGANIC AND LOW INPUT LAYING HEN PRODUCTION SYSTEMS Main issues addressed under SP4 136 WP4.1 Development of FARMER PARTICIPATORY breeding systems to 141 improve productivity, health and welfare and egg quality related traits; comparing standard with farmer participatory breeding systems WP4.1.0 MANAGEMENT OF WP2.1 RTD ACTIVITIES 141 WP4.1.1 Selection and characterization of low input farm groups in 3 macro-climatic 144 regions in Europe for inclusion in a farmer participatory performance recording network (FP-PRN) and performance recording of currently used layer genotypes WP4.1.2 Design of breeding programme(s) for organic/ low input production systems 148 (based on data from WP4.1.1 and stakeholder consultations) and production of new genotypes for validation under WP4.1.3 WP4.1.3 Validation of performance of genotypes from organic/ low input specific 151 breeding programmes within the FP-PRN WP4.2 Effect of, and interactions between, laying hen genotypes, feeding regimes, 153 welfare-friendly moulting protocols and prolonged use of layers on performance, and animal health and welfare WP4.2.0 MANAGEMENT OF WP2.2 RTD ACTIVITIES

8 Contents List LowInputBreeds Page SP4 continued WP4.2 continued WP4.2.1 Effect of laying hen genotypes with contrasting pre-disposition for feather 155 pecking and feeding regimes on animal health and welfare parameters WP4.2.2 Effect of welfare-friendly moulting and/or prolonged laying period (to 158 extend the lifespan of laying hens) on animal health and welfare WP4.3 Effect of, and interaction between, laying hen genotypes and management 161 innovations on egg quality WP4.3.0 MANAGEMENT OF WP2.3 RTD ACTIVITIES 161 WP4.3.1 Effects of genotype choice and contrasting management regimes on sensory 163 and nutritional quality parameters of eggs from organic and free range systems EGG SAMPLES FROM WP4.1 WP4.3.2 Effects of management innovations (feeding regimes and husbandry systems 165 to prolong laying periods) on sensory and nutritional quality parameters of eggs - SAMPLES FROM WP4.2 WP4.3.3 Effects of layer genotypes and storing conditions on the shelf life of eggs SP5 HORIZONTAL ACTIVITIES 167 WP5.0 MANAGEMENT OF SP5 HORIZONTAL ACTIVITIES 173 WP5.1 Horizontal Activity 1 Economic and multi-criteria (e.g. environmental and 175 food quality) impact assessment WP5.2 Horizontal activity 2 Ethical impact assessments 178 WP5.3 Horizontal activity 3 Training of early stage researchers and agricultural 180 advisors/technologists WP5.4 Horizontal activity 4 Dissemination and technology transfer to stakeholder 183 communities Table 1.3b Deliverable Lists 187 Table 1.3d Project effort form 1 - Indicative effort per beneficiary per WP 215 Table 1.3e Project effort form 2 - Indicative effort per activity per beneficiary 216 Table 1.3f List of Milestones 218 Table 1.3g Tentative schedule of project reviews 243 B2. Implementation 245 B2.1 Management structure and procedures Project co-ordination/management 246 Project co-ordinator 246 Project co-ordination/management unit 246 Subproject managers 247 Workpackage managers 247 Figure Project management structure and organisation of the project workplan 248 Figure Timetable (in project weeks) for management actions and meetings 249 scheduled for a typical 18 months implementation period Decision making bodies/procedure 250 Subproject committees 250 Project Board 250 General Assembly

9 New beneficiaries/partners 251 Contents List Page B2. Implementation continued B2.2 Individual participants University of Newcastle upon Tyne (UNEW, UK) Forschungsinstitut für Biologischen Landbau (FiBL, CH) Institut National de la Recherche Agronomique (INRA, FR) ASG Veehouderij BV (WUR, NL) Georg-August-Universität Göttingen (UGöt, DE) Universita degli studi de Catania (UCat, IT) National Agricultural Research Foundation (NAGREF, GR) Johann Heinrich von Thuenen-Institut (vti, DE) Københavns Universitet (UCPH, DK) Univerza v Ljunljani (ULju, SL) Université Catholique de Louvain (UCLou, BE) Swissgenetics (SG, CH) Schweizer Braunviehzuchtverband (SBZV, CH) Applied Genetics Network (AGN, CH) Institute for Pig Genetics BV (IPG, NL) Pigture Iberica S.L. (PI, ES) Institut de Sélection Animale BV (ISA, NL/F) Institut National de la Recherche Agronomique de Tunisie (INRAT, TU) Lincoln University (UL-NZ, NZ) University of Guelph (UG-CAN, CA) Federal University of Viçosa (UVF, BR) 273 B2.3 Consortium as a whole Capacity of the LowInputBreeds consortium to achieve the project aim, objectives 274 and expected impacts; complementarity of participants Capacity of the consortium to ensure rapid technology transfer and exploitation 275 of LowInputBreeds RTD deliverables Capacity of the consortium to ensure efficient project management Sub-contracting Third parties Funding for beneficiaries from third countries Additional beneficiaries/competitive calls for partners 278 B2.4 Resources to be committed Costs of RTD activities Demonstration activities Project Management/co-ordination activities Other Activities 281 Table LowInputBreeds COST SUMMARY 283 Table Person months allocated to different LowInputBreeds activities

10 Contents List LowInputBreeds Page B3. Impact 285 B3.1 Strategic Impacts Contribution towards expected impacts listed in the work programme for topic 286 KBBE ANIMAL HEALTH AND WELFARE BENEFITS - potential impact in Europe 286 PRODUCT QUALITY BENEFITS - potential impact in Europe 287 ECONOMIC BENEFITS - potential impact at farm level 288 ENVIRONMENTAL AND MULTI-CRITERIA IMPACT ASSESSMENTS Contribution towards overarching objectives/expected impacts described in the 289 workprogramme for Theme 2 Food, Agriculture and Fisheries, and Biotechnology Steps that will be needed to bring about these impacts Need for a European (rather than a national or local) approach Account taken of other national or international research activities 293 B3.2 Plan for use and dissemination of foreground Training activities Dissemination activities Efficient management of Intellectual Property Rights (IPR) Ability to react to changes in societal priorities and consumer demands Reconciling the need for rapid dissemination and/or IPR-protection to optimise 295 exploitation and impact of project innovations B4. Ethical Issues 297 Table 4.1 Ethical Issues Table 298 B4.1 Studies on or involving animals and/or animal materials 299 B4.2 Ethical Impact assessments under WP B4.3 Studies on or involving humans and/or human materials 300 B4.4 Research involving plant genetic resources in developing countries: 300 benefit to local community B4.5 LowInputBreeds Ethical Committee 300 B4.6 Wider Societal issues 300 B5. Consideration of gender/equal opportunities aspects 303 B5.1 Equal opportunities/participation of women 304 B5.2 Gender action plan

11 SECTION B1. Concept and Objectives, progress beyond the state of the art, S/T methodology and work plan

12 B1. Concept and project objectives, progress beyond the state of the art, S/T methodology and work plan B1.1 Concept and project objectives LowInputBreeds Recent studies (e.g. the FP6 IP QualityLowInputFood; have indicated that livestock breeds (and breeding systems) developed for high input conventional production systems lack specific: (i) robustness traits required for optimum performance in organic and low input (e.g. extensive outdoor grazing and free range) production systems and (ii) product quality traits (including nutritional, sensory and animal welfare related quality parameters) that are demanded from the organic and low input sector. However, very little R&D has focused on developing breeding concepts, methods and programmes focused on the needs of organic and other low input systems. The scientific concept of the project is to improve animal health, product quality and performance of organic and low input production systems through R&D, training and dissemination activities focused on (a) the development of novel breeding concepts/strategies and (b) their integration with appropriate management innovations. The project will focus on 6 major livestock production systems (dairy cows, beef, dairy and meat sheep, pigs and laying hens). The LowInputBreeds consortium will pool expertise from 15 academic centres of excellence and 4 SMEs and 2 large livestock genetics/breeding companies in 11 European, 2 ICPC and 2 industrialised third countries (see Section 2 implementation for a detailed description of the consortium and expertise of individual partners). This multidisciplinary team will specifically target/address: productivity traits required to improve the competitiveness of low input production animal health and/or welfare issues including mastitis, gastrointestinal parasites, pig mortality and feather pecking that remain a serious challenge in low input systems. product qualities including nutritional and sensory quality of milk, meat, and eggs; reduction in veterinary medicine use demanded by consumers of organic and low input foods. ethical issues addressed will include (a) killing/disposal of spent laying hens and male chicks, (b) environmental impacts of outdoor production and (c) biodiversity (and other) impacts of molecular assisted breeding techniques that are or may become particular concerns among organic and low input food consumers and sector bodies. The Science and Technology (S&T) objectives of the project are: (i) to develop and to analyse innovative breeding concepts (e.g. genome-wide selection, cross-breeding, flower -breeding and farmer participatory breeding) for their ability to deliver genotypes with robustness and quality traits required under organic and low input production conditions. This will be based on livestock species-specific breeding strategies that are compatible with the (a) small size and greater diversity of production systems, (b) lack of breeding facilities/infrastructure in parts of the organic and low input sector and (c) specific breeding objectives prevailing in the organic and low input sector. This will be addressed in different macro-climatic regions (Northern maritime; North-East/Central; Alpine/mountainous; Mediterranean) under WPs1.1, 1.2, 2.1, 3.1, and 4.1. (ii) to integrate the use of improved genotypes with innovative management/husbandry approaches (e.g. improved diets, feeding regimes, rearing systems) suitable for organic and low input systems. This will focus on areas where breeding or management approaches on their own are unlikely to provide satisfactory solutions (e.g. control of mastitis and gastrointestinal parasites, animal welfare issues). This will be addressed in different macroclimatic regions (Northern maritime; North-East/Central; Alpine/mountainous; Mediterranean) under WPs 1.2, 1.3, 2.2, 2.3, 3.2, 3.3, 4.2 and 4.3.

13 (iii) (iv) LowInputBreeds to carry out economic, environmental, genetic diversity and ethical impacts assessments to quantify the performance of improved breeds/genotypes and management innovations against different societal and consumer demands. This will include the use of : multi-criteria evaluation models (to be developed under WP1.3 and 5.1) aimed at reconciling economic outputs with other gains expected by consumers and society and stakeholder workshops (under WP5.2 and 5.4) aimed at providing information and discussing concerns about ethical, environmental and biodiversity/plasticity impacts of new technologies (e.g. molecular marker assisted or genome-wide selection, welfarefriendly moulting, extended outdoor rearing periods). Both mechanisms are designed to (a) minimise the risk of innovations being rejected by stakeholder groups based on unfounded concerns/perceptions regarding risks and/or costs and (b) facilitate an understanding of different positions, conflict resolution, consensus building and prioritisation processes, where innovations may have both positive and negative impacts. to establish a training and dissemination programme aimed at facilitating rapid exploittation of results by the organic and low input industry. This will involve close collaboration with established technology transfer networks in Europe (see WPs 5.3 and 5.4). Fulfilling the above objectives will allow the proposed LowInputBreeds project to deliver against the expected impact of Call KBBE which is to stimulate organic and low input livestock production by enabling logical, regionally-adapted breeding strategies to be developed that are compatible with sustainable production, high product quality and organic principles. B1.2 Progress beyond the state of the art Background Until recently, very little R&D has focused on breeding livestock breeds/genotypes specifically for organic and/or low input (e.g. free range, pasture fed) livestock production systems. As a result the majority of such systems currently use either (a) breeds/genotypes/hybrids developed for high input production or (b) older traditional breeds. However, it is increasingly recognised that breeding priorities differ between high and low input systems. The LowInputBreeds project will therefore focus on developing (a) robustness (e.g. resistance to biotic and abiotic stress factors, survival of young animals, longevity, fertility), (b) product quality traits (including ethical qualities related to animal welfare and environmental impact related traits) that have a higher priority in organic/ low input compared to high input conventional systems Baseline description (where does the project work start) The need for breeding tools/concepts suitable for the organic and low input industry Commercial breeding companies and associations, which have driven cattle, pig and poultry breed development in the conventional sector, were until recently reluctant to develop specific breeding programmes for the organic and low input sector. This was mainly due to the: 1. high costs of developing and maintaining new breeding programmes and associated facilities (e.g. specialist production units for parent lines of cross and hybrid breeding systems), 2. relatively small market (in most EU-countries organic and low input systems account for less than 5% of production), 3. greater diversity of production systems in the organic and low input sector,

14 4. lack of appropriate breeding tools/concepts to improve the functional traits relating to robustness and product quality (which often have low heritability) desired by the organic and low input industry. The LowInputBreeds project will therefore focus on developing and/or improving a range of novel selection/breeding tools and concepts have been developed that may overcome these limitations. These include: 1. Farmer participatory breeding (FPB) systems used in Europe are based on farmers recording and reporting phenotype information and the use of such information in parent selection. FPB is widely used in bovine and small ruminant selection/breeding, but rarely applied in the pig and poultry sectors which mainly use cross and hybrid breeding schemes. This is primarily, because the use of specialist breeding units for parent lines has proved to allow more rapid breeding progress. As described above, the establishment of a separate breeding infrastructure for organic and low input (= free range ) poultry and pig production systems is currently not feasible. For the low input laying hens sector it is therefore proposed to develop a FPB concept under SP4, WP4.1. This will be based on the: establishment of a phenotype recording system in groups of farms using different combinations of layer brands/genotypes and production systems, data input from farmer and supply chain stakeholders (advisors, vets, customers) and design of breeding schemes for contrasting organic and low input systems, based on adapted proprietary algorithms/software developed by partners 17 ISA and 4 WUR. Under SP4-WP4.1 it is therefore proposed to develop FPB systems for organic and low input laying hen production in Northern maritime, mountainous/alpine and Mediterranean regions of Europe (see Section 1.3.4). 2. Flower breeding systems (FBS) have recently been developed by partner 15 IPG. They are designed to overcome two of the main infrastructure limitations that prevent the use of conventional cross-breeding systems in the low input pig sector: the need for (a) specialist cross-bred sow production units and (b) large pig breeding populations for selection. In contrast, FBS are based on: a central boar production and maintenance unit (for semen production), which is managed according to organic/ low input farming standards, 50 to 100 pig production units (= flower petals ) with 100% pure-bred sows, and selection based on on farm recording of (a) piglet survival and causes of death and (b) pig phenotyping data, using a farmer participatory approach. Such systems are thought to allow (a) significant breeding progress with relatively small populations and (b) the development of a wider range of self-contained breeding programmes focused on the specific combinations of production, animal health and welfare, and product quality traits required in different low input systems and macro-climatic regions of Europe. They are also expected to provide more rapid and appropriate breeding progress than in-housenucleus schemes started by some of the larger organic pig producers in the NL, DK and UK, which have so far had disappointing results. Under SP3-WP3.1 it is therefore proposed to develop FBS for low input pig production systems in Northern maritime and Mediterranean regions of Europe (see Section 1.3.3). 3. Cross-breeding (CB) has been used extensively in some European regions (e.g. the British Isles) to introduce robustness traits into high performance dairy cattle breeds and thereby reduce management cost. For example, cross-breeding of high productivity Holstein Friesian (HF) genotypes with smaller dairy breeds such as Jerseys, Shorthorns or Scandinavian Reds has been widely used in organic and low input (e.g. NZ type permanent grazing) systems in the UK and Ireland. Cross-breeding was associated with increased milk quality and decreased mastitis incidence (see Section WP1.2 and

15 However, significant differences in milk output per cow and diets between farms using cross-bred and HF genotypes were also reported and these are likely to have confounded results. Very little R&D has gone into comparing the effect of different dairy cross-breeding systems currently used on animal health status and milk quality parameters. It is also unclear (a) to what extent the maintenance of appropriate yield levels relies on maintaining a certain proportion of HF genetics in the cross-breeds and (b) how a sustainable cross-breeding scheme with a continuous exploitation of high levels of heterosis can be implemented in the dairy industry. Under SP1-WP1.2 it is therefore proposed to develop CB for organic and low input dairy cattle production systems in Northern maritime regions of Europe (see section 1.3.1). Results from WP1.2 will also be applicable in other regions where long grazing periods are used. 4. Molecular marker assisted selection (MAS) has been used successfully to improve specific characteristics in livestock breeds. For example, molecular markers have been used in conventional farming focused breeding programmes to (a) remove fishy egg taint due to a physiological defect in brown egg layer lines, (b) improve meat quality in pigs and (c) reduce the susceptibility of piglets against oedema disease caused by E. coli F18. Molecular markers linked to temperature stress, foot rot resistance, parasite resistance and product quality in sheep have been identified in NZ and Australia and are available via partner 19 UL-NZ. If there is heterogeneity for such markers in European sheep populations they may be used for within breed selection. This will be evaluated in Mediterranean and mountainous/alpine sheep production regions of Europe under SP2-WP2.1 (see Section 1.3.2). Since most resources under WP2.1 are focused on improving dairy sheep breeding in semi-arid regions of the Mediterranean (Crete, Greece), results will also be applicable in many non-european ICPC regions (e.g. Southern Mediterranean, Middle East and other world regions with semi-arid climates). 5. Genome-wide (or genomic) selection (GS) which has become feasible for some livestock species (e.g. cattle, pigs, poultry) through the availability of commercial arrays with up to 50,000 single nucleotide polymorphism (SNP) markers. These can be used for high throughput genotyping at relatively low cost. GS is described as having the potential to outperform classic phenotypic selection schemes, especially for functional or fitness traits that are difficult or expensive to measure and/or have low heritability. First practical applications indicate that GS provides accurate breeding values for functional and fitness related traits with low heritabilities. Under SP1-WP1.1 it is therefore proposed to evaluate and apply GS to within breed improvement of dairy cattle. A large Swiss Brown Cattle population managed under organic and low input farming conditions will be used as a model, since a unique set of detailed phenotyping data is already available for the population. This allows direct comparisons of GS with existing phenotype recording based selection systems (see SP1-WP1.1 in section below). SNP arrays may also be applied for other purposes such as (a) the identification of parents of progeny phenotyped at farm level and (b) more accurate monitoring of genetic diversity at the genomic level. Under SP3- WP3.1 it is therefore proposed to develop (and apply) a customised array for the identification of parent boars in flower breeding programme focused on improving heat stress resistance and other traits in pigs

16 The need to integrate breeding with innovative management strategies A range of important challenges in organic and low input (e.g. free range, pasture fed) livestock production systems are unlikely to be overcome by breeding alone. It is therefore important to (a) combine breeding with appropriate management innovations and (b) quantify genotype * environment (G*E) interactions. Such an integrated approach is needed in the following areas: 1. Endoparasite control and anthelmintic use Studies in Northern Europe have shown that tanniniferous forages (TF), the strategic use of clean pastures, and improved diet composition, may significantly reduce parasite infections in sheep and the need for anthelmintic treatments (see e.g. However, less R&D has focused on mountainous/alpine and especially Mediterranean regions. Under SP2, WPs 2.2 and 2.3 it is therefore proposed to (a) develop feeding, feed supplementation and management strategies for the control of endoparasites in sheep and (b) integrate such strategies with the use of sheep genotypes showing superior resistance to endoparasites. Work will focus on sheep production in Mediterranean (but also mountainous/alpine regions) of Europe and will therefore also be applicable in many non- European ICPC regions (e.g. other mountainous regions and/or regions with Mediterranean Climate where sheep are produced). 2. Udder, foot and gastrointestinal disease control and antibiotic use Recent R&D indicated that certain organic and low input systems have lower levels of mastitis and associated antibiotic use than high input conventional systems (see e.g. However, it remained unclear to what extent this was due to differences in breeds/genotypes and/or management parameters used. There is also limited information on the effect of both breed and management environments on mastitis in low input dairy sheep production. In pigs, outside rearing systems have resulted in lower levels of post weaning diarrhoea, but there is little information on G*E interactions with respect to gastrointestinal and other diseases in both pigs and poultry. Experiments under SP1-WP1.2 and SP2-WP2.2 are therefore also designed to identify interactions between (a) dairy cow and sheep genotypes and (b) feeding regimes and husbandry practices that reduce the incidence of diseases (especially mastitis and foot diseases). Similarly SP3-WP3.2 and SP4-WP4.2 have been designed to identify interactions between (a) pig and laying hen genotypes and (b) husbandry systems with respect to the incidence of gastrointestinal and other diseases (see Sections to 1.3.4). 3. Nutritional, sensory, welfare and ethical quality of livestock products Positive effects of forage intake on the fatty acid and fat soluble antioxidant composition of milk and meat from both ruminants and monogastric animals and eggs have recently been reported (see e.g. In contrast, the feeding of certain TF was associated with reduced carcass and sensory quality of meat. Also, diets used in organic production systems often have an imbalanced composition of amino acids and this was shown to exacerbate certain animal welfare problems (e.g. feather pecking and cannibalism in laying hens, tail biting and cannibalism in pigs). Experiments under SP1 (WP1.1 and 1.2), SP2 (all WPs), SP3 (WP3.1 and 3.3) and SP4 (all WPs) will therefore quantify the effect of integrating breeding and management innovations on product sensory and nutritional quality and/or animal welfare quality parameters recognised by consumers (see Sections to 1.3.4). In several livestock production systems male animals are killed and discarded shortly after birth/hatching (e.g. bull calves in dairy cattle production, male chicks in laying hen production systems). Also, spent laying hens are usually discarded after only one laying period, due to a lack of markets for their meat. This increases not only the cost of production, but may also seriously undermines consumer confidence in the ethics of low input livestock production

17 systems ( The development of welfare-friendly, organic veal production in the UK has demonstrated that such issues can be addressed. Under SP4-WP4.2 it is therefore proposed to integrate (a) novel layer genotypes with (b) appropriate management systems (e.g. welfare-friendly moulting systems) to prolong the use of laying hens and thereby indirectly reduce the numbers of spent hens and male chicks that are discarded (see Sections WP4.2 and WP5.2) Description of performance/research indicators The main performance/research indicators are: livestock phenotyping data sets that quantify levels of animal health, welfare and performance and product (milk, meat and egg) nutritional, sensory or processing quality, but also environmental and other impacts in different (a) genotypes of dairy cows, milk and meat sheep, beef-cattle, pigs and poultry, (b) management systems and (c) under contrasting macroclimatic conditions detailed analysis (including multi-criteria evaluations) that link animal health, welfare and performance and product (milk, meat and egg) nutritional, sensory or processing quality to breed/genotype, environmental and production systems parameters. genotyping data sets that improve genetic information/maps for selected livestock species (dairy cows and sheep and to a lesser extent pigs) and allows alleles, QTL and/or markers that are linked to desired (a) product quality, (b) performance and (c) robustness characteristics to be identified. These data sets will allow alleles, QTL and/or markers to be linked to specific morphological and physiological characteristics of livestock genotypes and will allow marker assisted selection/breeding approaches to be used more efficiently in the futures. data sets on the integrated use of breeding and agronomic/managment innovations that identify strategies to improve the overall performance, robustness, health, welfare and environmental impact of livestock in different crop production systems and macro-climatic regions. These data sets will also facilitate the development and calibration of multicriteria evaluation models which will allow a predictive/modelling based approach to the design of both livestock breeding and management strategies. training courses that successfully transfer state-of-the-art livestock breeding and agronomiuc knowledge, methodologies and skills developed as part of LowInputBreeds and already available in the consortium to Early Stage Researchers and technologists/agronomists. dissemination activities that successfully transfer state-of-the-art livestock breeding and agronomiuc knowledge and methodologies developed under LowInputbreeds (and other projects focused on improving organic and low input livestock production systems) to a wide range of user/stakeholder groups. See also Table 1.3f for a list of the main project milestones and means of verification, which describes in more detail when specific data sets and other performance/research indicators become available from individual SPs and WPs. B1.3 Science and Technology methodology and associated work plan Overall and general description The workplan to fulfil the Science and Technology (S&T) objectives of the project (see above) has been subdivided into 5 major subprojects (SPs) which are further subdivided into workpackages (WPs) (see Figure 1): Subproject 0 the project management/co-ordination (see Fig 1 and Sections and 2.1 below). This includes a description of risk identification/management procedures and contingiency planning

18 Subprojects 1 to 4, which aim at improving organic and low input dairy cow, sheep, pig and laying hen production systems respectively (see Fig 1 and Sections to below. Each SP is further subdivided into 3 major workpackages (WP) which target: (i) Development of innovative breeding strategies appropriate for the individual species (WPs 1.1, 1.2, 2.1, 3.1, 4.1) (ii) Detailed multi-criteria evaluations of ruminant breeding and production systems (using Dairy cows as a MODEL) with respect to economic/productivity, animal welfare, product quality and environmental outputs/impacts (WPs 1.3). Deliverables from WP3.1 will be used in activities under Horizontal Activity WP5.1, which will carry out multi-criteria impact assessments for all 6 production systems targeted under SP1 to 4. (iii) Integrating management innovations with novel breeds/genotypes (WPs 1.3, 2.2, 2.3, 3.2, 3.3, 4.2, 4.3) and/or (iv) Quantifying genotype * environment interactions (WPs 1.2, 2.2, 2.3, 3.3, 4.1, 4.2, 4.3) Subproject 5, which includes 4 HORIZONTAL ACTIVITES (WPs 5.1 to 5.4). Horizontal activities will support SP 1 to 4 in achieving (a) their specific objectives and (b) the overall expected impact of the project (see section 1.1. above). They will focus on: (i) Economic and multi-criteria impact assessments of breeding and management innovations developed under SPs 1 to 4 of the LowInputBreeds project; utilising deliverables from WP1.3 (WP5.1). (ii) Ethical impact assessments of innovations developed within the project (WP5.2), (iii) Training acitivites focused on Early Stage Researchers and Agricultural Advisors (WP5.3) (iv) Dissemination activities (project website, conferences and workshops) (WP5.4) Detailed descriptions of the activities under different SPs, WPs, and individual Tasks are given in sections to Each detailed SP-description includes an introductory section which describes the Background and overall approach and strategy used to fulfil the S&T objectives of LowInputBreeds addressed by the respective SP. Timing of workpackages and their components Gantt charts showing the timing of different WPs and Tasks are provided at the beginning of each SP description (Figures to 1.3.6). Work package list/overview See below for the (a) list of WPs (Table 1.3a) and (b) detailed descriptions of the activities proposed under different SPs, WPs, and individual Tasks (sections to 1.3.6). Deliverables list A list of all deliverables is provided in Table 1.3b after the detailed SP and WP descriptions. Efforts for the full duration of the project Summary effort tables/forms which shows person-months per beneficiary associated with each activity for the full duration of the project (Table 1.3d) and the indicative effort per activity type per beneficiary (Table 1.3e) are provided after the list of deliverables. List of milestones and planning of reviews A list of milestones and a time-table for project reviews are provided in Table 1.3f and Table 1.3g respectively, after the summary effort tables at the end of section

19 Figure 1. Project management structure and organisation of the project workplan General Assembly: one representative from each partner institution Project board: the co-ordinators and all SP-managers + 2 external specialists PPROJECT CO-ORDINATION TEAM SP0 Project co-ordination/management Administrative and scientific co-ordinators (Prof. C Leifert, UNEW; Dr. V. Maurer, FiBL) Financial manager (D. Whittock, UNEW), Secretary (L. Bell, UNEW); Statistical advisor (Dr. M. Eyre); Nutritional methodologies co-ordinator (Dr. C. Seal) SP1 Improving low input DAIRY COW production systems M: Prof. H. Simianer (UGöt, D) DM: Dr. P. Klocke (FiBL, CH) Workpackages# SP2 Improving low input SHEEP production systems M: Dr. H. Hoste (INRA, F) DM: Dr. S. Sotiraki (NAGREF, HE) Workpackages# SP3 Improving low input PIG production systems M: Dr. J. Merks (IPG, NL) DM: Prof. S. Edwards (UNEW, UK) Workpackages# SP4 Improving low input LAYING HEN production systems M: Dr. H. Spoolder (WUR, NL) DM: Dr. V. Maurer (FiBL, CH) Worpackages# WP1.1 Genomic Selection for robustness and product quality WP1.2 G*E (crossbreeds * diet) re milk quality & animal health WP1.3 Multi-criteria evaluation models Macro-climatic regions Northern maritime North-East/Central Alpine/mountainous Mediterranean WP2.1 MAS for biotic & abiotic stress resistance WP2.2 G*E (breed * diet / management) re endoparasites WP2.3 Improvement of milk and lamb meat quality Macro-climatic regions Alpine/mountainous Mediterranean WP3.1 Flower Breeding Systems for pig survival/health WP3.2 Improvement of rearing systems re pig survival & health WP3.3 Improvement of fresh and processed pork quality Macro-climatic regions Northern maritime North-East/Central Mediterranean WP4.1 Farmer participatory breeding for robustness and product quality WP4.2 G*E (hybrid * diet/management) re welfare & ethical quality WP4.3 Improvement of egg quality Macro-climatic regions Northern maritime Alpine/mountainous Mediterranean SP5 Horizontal Activities Managment M: Prof. C. Leifert (UNEW, UK) DM: Dr. H. Willer (FiBL, CH) WP5.1 HA1 Economic and multi-criteria impact assessment M: Prof. T. Dedeurwaerdere (UCLou, BE) DM: M. Benoit (INRA, F) WP5.2 HA2 Ethical impact assessments M: Prof. P. Sandøe (UCPH, DK) DM: H. Browning (Foods Ethics Council, UK) WP5.3 HA3 Training activities for early stage researchers and agricultural advisors/technologists M: Prof. C. Leifert (UNEW, UK) DM: Dr. V. Maurer (FiBL, CH) WP5.4 HA4 Dissemination activities (Project website, congresses and workshops) M: Dr. H. Willer (FiBL, CH) DM: G. Butler (UNEW, UK) G*E Genotype * Environment interactions = WPs focused on Integration of Breeding and Management Innovations M= Subproject or workpackage manager; DM = Deputy Subproject or workpackage manager # each main WP under SPs 1 to 4 is further subdivided into (a) one WP-management subworkpackage and (b) one or several RTD subworkpackages (see sections to below). See below for list of workpackages (Table 1.3a) and detailed descriptions of the S&T methodologies and workplans for WPs under SP1 to 5 (Sections )

20 Table 1.3a Work package list LowInputBreeds Work Package No Work package title Type Lead participant of activity No Short name Person- Months Start Month End month SP0 PROJECT CO-ORDINATION 0 WP0 Project coordination MGT 1 UNEW SP1 IMPROVING PERFORMANCE, ANIMAL HEALTH & WELFARE, ENVIRONMENTAL IMPACT AND PRODUCT QUALITY IN ORGANIC AND LOW INPUT DAIRY COW PRODUCTION SYSTEMS 1.1 Development of WITHIN BREED selection systems to improve animal health, product quality and performance traits; comparing genome-wide and traditional quantitative-genetic selection MANAGEMENT OF WP1.1 RTD ACTIVITIES MGT 2 FiBL STAGE 1 Expanded phenotyping of Swiss Brown Cattle and parameter estimation for RTD 2 FiBL traits required in organic and low input systems STAGE 2 Genotyping of Swiss Brown Cattle and estimation of genomic breeding values RTD 5 UGöt STAGE 3 Design a genome-wide selection scheme for the Swiss Brown Cattle subpopulation RTD 5 UGöt used in low input systems; quantification of genetic diversity impacts of GS 1.2 Development of improved CROSS-BREEDING strategies to optimise the balance between robustness and performance traits; comparing cross-breeds with purebred Holstein Friesian genotypes MANAGEMENT OF WP1.2 RTD ACTIVITIES MGT 1 UNEW STAGE 1 Effect of cross-breeding strategies on animal health and milk yield and RTD 1 UNEW quality parameters in Holstein Friesian cattle STAGE 2 Effect of oil seed feed supplementation on animal health and milk yield and quality parameters in pure and cross-breed Holstein Friesian cattle RTD 1 UNEW