Gene2Farm work packages

WP1. Novel statistical models, for genome selection, software development and testing,  led by Theo Meuwissen

The main goal of this WP is to develop statistical theory needed to optimise the use of genomic data for the improvement of cattle genetics in many different situations. The applications will focus on small populations, with a transfer of information between populations. The use of different density of genome data, from low density SNP panel to the whole genome will also be tested within this WP. Another important tasks are the optimization of mating schemes and the incorporation of new phenotypes.


WP2. Genome information and SNP panels, led by Giulietta Minozzi.

This WP will identify key animals to sequence using pedigree and molecular information. Once identified, key animals in various breeds will be (whole genome) sequenced. Using the whole genome sequence data, SNP and other variation will be identified within or among breeds. Un-ascertained sequence data will provide a clear genome structure (LD allele distribution, CNVs, etc), and SNPs that mark haplotype blocks (tag-SNPs) will be identified. Furthermore, inter-changeability of SNP panel information will be explored and an optimised marker panel design strategy within and across breeds will be set up.


WP3. Phenotypes for cattle improvement and management, led by Giorgios Banos

This WP will assess the current phenotyping practices and the needs among SME participants. Will develop standardisation procedures for trait measurements across different breeds and assess the possibilities for the application of on-farm automated data recording in genome based selection programmes. In addition, will identify and characterise opportunities for routine phenotype collection of novel traits and will evaluate expanded options for data recording at the abattoir.


WP4. Population structure, led by Miguel Toro

Tasks in WP4 include the estimation of effective population size and the exploration of population structure.  Variations in population structure within breeds between geographical locations will be defined and relationships and genetic distances between breeds will be examined. Footprints of selection and differentiation between populations will be detected, examining the conservation of haplotypes within and between populations. These objectives will allow to establish optimal marker densities for establishing predictors during the training phase, also defining parameters of a minimal SNP panel to be able to input haplotypes within and between breeds. This effort will provide the background information to impute missing genotypes more accurately.


WP5. Integration and provision of tools, led by Alessandra Stella

WP5 will translate the research and tool development work undertaken in early work packages into a series of user friendly software tools, genomic assays, procedures required to address the breeding needs of the modern cattle industry. In addition, will provide the protocols in a user friendly package that can be adopted by the industry. Protocols to apply the products of the project in an appropriate way in a commercial setting will be produced.


WP6. Application of statistical models to different situations in specific breeds, led by Trygve Roger Solberg

This WP will bring together all modules of the next generation genomic selection package and ensure inter-operability in specific situations. Will carry out testing in specific industry led situations, and will review and validate performance and make necessary modifications.


WP7. Training, Knowledge Transfer and Sustainability, led by Toine Roozen.

This WP will create the project Web Site and establish an education programme for industry participants. Will organize training of industry participants in the applications of the tools developed in the project and establish a “industry club of interest” to ensure durability of a support network


WP8. Project management, led by John Williams

This WP will ensure that the project runs efficiently and delivers objectives fully and on time, will facilitate communication between partners, deliver reports to the European Commission and provide financial management. In addition, will track progress and changes in the state of the art, and where appropriate update objectives. IP will be identified and correctly managed. Finally, this WP will manage all project dissemination activities.




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