General objectives

The project has the following scientific and technological objectives:

• Characterization of local sheep and chicken in Algeria, Morocco and Tunisia using advanced approaches to estimate phenotypic, genotypic and epi-genotypic diversity.
• Identification of genomic signatures of adaptation in local genetic resources.
• Establishment of selective breeding programmes to improve the sustainability and resilience of local farming systems, compatible with the preservation of diversity, and adaptation to harsh and changing environments.
• Assessment of the role of epigenetics in adaptation, to fill the existing gap in knowledge of the link between genotype and its phenotypic expression in different environments.
• Exploration of options to include epigenomic marks in breeding programs.
• Definition of the specific features and benefits of local sheep and chicken to develop approaches for in vivo conservation of local genetic resources.
• Development of strategies to add value to products from local genetic resources and promote their use.
• Development of a network of existing genebanks in the Southern Mediterranean region and cooperation with the European genebank network.
• Capacity building, knowledge transfer and dissemination of advances achieved by the project to the whole value chain and stakeholders.

To achieve these objectives, SCALA-MEDI will benefit from knowledge acquired and data produced by SCALA- MEDI Partners in ongoing and completed EU and National projects.

CMCC role

In SCALA-MEDI, CMCC will lead WP5 on Data Management, Harmonization and Validation. WP5 aims to: 

• Collect, compile, verify and manage project data in accordance with the Data Management Plan. 
• Make raw and processed data available in the appropriate formats for subsequent analyses. 
• Create bioinformatic pipelines for data processing and analyses. 
• Harmonize descriptors and ontology. 
• Carry out descriptive analyses and data quality control of molecular and phenotypic data. 
• Prepare datasets for transfer to public databases. 

The data management infrastructure for all the WPs will be created, including the performance of datasets quality control and the development of standardised pipelines and containers to assist the analyses. All raw data produced will be organized in a centralized project repository, based on Data Lake technology using descriptors and formats harmonized by SOP developed in WP2. Bioinformatic analyses will explore the integrity and structure of climatic, socio-economic, phenotypic and molecular data for quality control to identify and remove suspect and outlier samples and produce a clean dataset for subsequent analyses. Data management and processing will be overseen by the project data management committee (DMC). Specific WP5 tasks:

Task 5.1 – Pipeline creation for bioinformatic analysis 

Task 5.2 – Data organization and harmonization (Task Leader CMCC)

Task 5.3 – Descriptive evaluation of phenotypic and climatic data 

Task 5.4 – Descriptive evaluation of molecular data 

CMCC will also be involved in the following work packages and specific tasks:

• WP1 – Project Coordination and Management. Specifically:

Task 1.2 – Project monitoring

Task 1.3 – Administrative and financial support

Task 1.4 – Data management plan 

• WP2 – Data, phenotype and sample collection. Specifically:

Task 2.1 – Strategy and logistics 

Task 2.2 – Metadata and data standards 

Task 2.3 – Establishing remote phenotyping capability 

• WP3: Socio-economic background of local breeds and markets. Specifically:

Task 3.1 – Preparation of socio-economic questionnaires for value chain stakeholders 

• WP6: Biodiversity and Adaptation. Specifically: 

Task 6.2 Phenomics for adaptation to extreme environments 

• WP8: Decision tools for breeders and managers. Specifically:

Task 8.3 – Development of a phenotypic, genotypic and epigenetic enabled breeding decision tool 

• WP9: Technology transfer, training and dissemination. Specifically: 

Task 9.1. Preparation of a Dissemination and Exploitation Plan

Task 9.2 – Website design, population and maintenance. (Task Leader CMCC) Task 9.3 – Dissemination to the scientific community 

Task 9.4 – Transfer technology to stakeholders 

Task 9.5 – Communication to the society 

Task 9.6 – Training 

Task 9.7 – Exploitation Opportunities Report 

Activities

The work plan of the project is arranged in 9 work packages:

• Project Coordination and Management 
• Data, phenotype and sample collection 
• Socio-economic background of local breeds and markets
• Molecular data for biodiversity, adaptation and breeding 
• Data management, harmonization and validation 
• Biodiversity and Adaptation 
• Breeding programs for sustainable production 
• Decision tools for breeders and managers 
• Technology transfer, training and dissemination

Expected results

SCALA-MEDI will contribute to the impacts expected in the PRIMA call 2020, under the Topic 1.2.1 Sub-topic A. The project will optimise the sustainable use and conservation of local genetic resources from the Mediterranean region, focusing on adaptation to climatic conditions and consumer preferences. The expertise and data from previous EU projects will be extended to the genetic and epigenetic characterisation of local resources and their adaptation to different production environments in three North African countries, Tunisia, Algeria and Morocco. Tools and strategies will be developed to improve local breeds for sustainable production. Application of these tools will be demonstrated to farmers in diverse Mediterranean production systems. 

The application of the SCALA-MEDI strategies for breeding will increase the overall profitability of farming systems by developing adapted populations that can use local resources more efficiently and require lower inputs to survive harsh environments. Knowledge of breed adaptation will increase the value of some of the local breeds/populations. 

Climate change is a major risk for food security in Northern Africa. The improved resilience of sheep and chicken farming stemming from the SCALA-MEDI project will increase food security by ensuring sustainable production of local eggs, meat and milk. Establishing reliability in supply will ensure fair market prices for both producers and consumers, increasing accessibility to the high-quality protein that is fundamental for a balanced diet and enhanced human health.

Partners

1. Consiglio Nazionale delle Ricerche – Istituto di Biologia e Biotecnologia Agraria (CNR-IBBA) – Italy
2. Fondazione Centro Euro-Mediterraneo sui Cambiamenti Climatici (CMCC) – Italy
3. Agenzia Regionale per la Ricerca in Agricoltura – Sardegna (AGRIS) – Italy 
4. Nature4.0 BC SRL (NAT4) – Italy
5. University of Sciences and Technology of Oran “Mohamed Boudiaf” (USTO) – Algeria
6. University of Tlemcen “Abou Bekr Belkaid” (PPABIONUT) – Algeria
7. Technical Institute of Breeding /Tlemcen (ITELV) – Algeria 
8. National Research Institute for Agriculture, Food and Environment (INRAE) – France 
9. Institut de l’Elevage (SME) (IDELE) – France 
10. Institut National de la Recherche Agronomique (INRA-Maroc) – Morocco
11. Moroccan Poultry Federation (FISA) – Morocco
12. Association Nationale Ovine et Caprine (ANOC) – Morocco 
13. High School of Agriculture of Mateur (ESAM) – Tunisia 
14. National Agronomic Institute of Tunisia (INAT) – Tunisia 
15. Office de Développement Sylvo Pastoral du Nord-Ouest (ODESYPANO) – Tunisia
16. National Gene Bank of Tunisia (NGBT) – Tunisia

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