Agri-Aqua Labs

A. [2018]: Understanding the genome of farmed animals, its expression and translation into traits (RIA)

For the purpose of sub-topic A, the terms 'animal' and 'farm' apply to both terrestrial and aquatic animals. Research activities should generate experimental data to map out what part of farmed animal genomes are active (whether coding or regulatory), and under which circumstances, characterise the resulting phenotypes and assess how phenotypes are affected by genetic and epigenetic changes. Bioinformatic analyses should support identification of these functional and structural elements in genomes, and enable the development of tools for genotype to phenotype prediction. Work should also help to develop or extend terminologies (ontologies) to describe, represent and standardize annotation. Proposed projects should target one or more farmed animal species with high-quality genome assemblies (in particular cows, chicken, pigs, sheep, salmon and other relevant species), focussing on specific tissue panels, and address correlations between normal and abnormal situations. They may target different physiological and developmental stages and different breeds within the same species, where this brings added value to the understanding of the genotype to phenotype relationship. As regards genome annotation, the proposed projects should use FAANG[[http://www.faang.org/index]] metadata standards and core assays and coordinate with other projects in order to minimise overlaps. The data should be submitted to relevant European biological data archives in accordance with these standards to ensure they are available to the whole community (EMBL-EBI[[http://data.faang.org]]). The proposed projects should develop and test, where appropriate, innovative tools to measure related phenotypes, including intermediate phenotypes. Activities may include biomarkers and their proxies, as well as sensors, together with ways to record related phenotypes at population level (whether reference populations or not). Proposals should include a task to cluster with other projects financed under this topic.

B. [2019]: Looking behind plant adaptation (RIA)

Proposals shall advance our understanding of the ability of plants to (pre)adapt to specific – often extreme - conditions or to react to sudden changes in their environment.

They will look into the specific mechanisms (genetic, epigenetic, physiological, morphological, metabolic…) and dynamics that underlie adaptive processes of crops and how these responses are modulated by the type and severity of conditions/stresses. In studying adaptation of crops to single or multiple abiotic conditions, work shall also establish potential fitness trade-offs. Proposals are expected to improve capacities for modelling plant adaptation responses in order to better predict changes in plant performance and inform crop improvement and crop management strategies. While taking advantage of findings from (semi) model crops, work shall focus on crop plants and relevant agronomic conditions.

Proposals should foresee a task for joint activities with other projects financed under this topic.

C. [2020]: Plant energy biology (RIA)

Proposals will advance our understanding of the plant energy system in terms of elucidating specific mechanisms as well as the complex processes and interactions that determine overall energy efficiency in plants.

More specifically work will allow to better understand and determine

• (some of) the various components, processes and interactions of plants’ energy system and their regulation - from energy capture to its conversion, transport, photoassimilate partitioning and use
• the metabolic reactions underlying particular functions of plants’ energy system
• responses of the energy system to abiotic changes (e.g. CO₂ concentration, light, temperature, water, salinity)
• the basis of naturally occurring variation of selected components of the energy system
• the overall energy efficiency in plants at various levels: cell – whole plant – canopy (including leaf anatomy and canopy structure)
• trade-offs between the efficiency of the energy system and the plant's susceptibility to or tolerance to biotic stresses

The above listed elements provide a framework for action from which proposals can choose a particular scope and approach in line with the broader objectives of the call.

While capitalising on knowledge resulting from work in model species, proposals should also work in crop species taking into account relevant agronomic conditions.

The Commission considers that proposals requesting a contribution from the EU of up to EUR 6 million for sub-topic A, EUR 5 million for sub-topic B and EUR 5 million for sub-topic C would allow this specific challenge to be addressed appropriately. Nonetheless, this does not preclude submission and selection of proposals requesting other amounts.

Agriculture and aquaculture are increasingly knowledge-intensive sectors that need to be supported by advances in basic science domains in tandem with translational research. This nexus between basic and applied research requires specific openings for testing ideas and their potential application in plant and animal production, both terrestrial and aquatic.

Recent developments in genomic selection have revolutionised animal breeding and resulted in significant gains in production efficiency of animals. However, our understanding of the biological mechanisms underpinning traits remains limited. Most phenotypes, in particular for traits related to health, biological efficiency and robustness, are complex and a major goal of biological research is to use genome information to predict such complex outcomes.

In the area of crop production, there is a fundamental interest in deciphering the dynamic responses of plants as they (pre)adapt to local conditions or adjust their growth and development to changes in the environment within their plasticity range. These adaptive traits are all the more important as plants are sessile and therefore require effective strategies to deal with uncertainty and to tolerate rather than avoid stress. Understanding the different adaptation strategies, and the circumstances that favour one strategy over another, is vital for understanding how annual or perennial crops perform in a given environment or under changing conditions. It will also help to assess how plants may respond to future environmental changes. Food and other plant-based products are the result of plants' capacity to harvest light and convert it into chemical energy to build energy rich organic compounds and ultimately biomass. Energy efficiency is central to plant yield and robustness. The various components of the complex plant energy system as well as their interactions (in spatial and temporal terms) need to be better understood as a basis for crop improvement, crop management and adaptability of crops to changing environments.

Results of funded activities will help to create knowledge hubs in their respective domains and develop specific pathways to feed biological insight into agricultural (husbandry, crops) and aquaculture practices.

In the short to medium term work will:

• deliver comprehensive genome annotation maps of high quality in the targeted farmed animal species/tissues (sub-topic A);
• progress in understanding genotype per environment interactions and deciphering the mechanisms by which some effects induced by environment/stressors can be transmitted across generations (sub-topic A);
• pave the way for subsequent use of annotated genomes to improve precision breeding in farmed animal production, by linking genome to phenotype and improving means to measure/record phenotypes (sub-topic A);
• contribute to international cooperation on genome annotation (sub-topic A);
• provide insight into the range of mechanisms that underpin plant responses (from single cell to whole plant) to specific and/or multiple environmental changes (sub-topic B);
• deliver more accurate models for the prediction of crop adaptation in response to environmental stresses (sub-topic B);
• translate knowledge on the adaptive plasticity of plants and complex genotype by phenotype interactions into crop improvement and management strategies (sub-topic B).
• allow to better understand the key mechanisms, interactions and control of the various components of plants’ energy biology system as well as their inherent trade-offs at the subcellular and whole plant level (sub-topic C)
• help to better assess plant responses to abiotic changes (sub-topic C)
• elucidate energy related traits to feed into breeding and crop management strategies at the level of individual plants and the canopy (sub-topic C)
• advance knowledge on the relationship between photoassimilate partitioning, plant growth and agronomic yield (sub-topic C)

In the long term activities will enhance the sustainability of farmed animal production (sub-scope A). They will allow making more solid assertions on how crops will respond and can possibly better adapt to changing environments, also by means of enhancing plant energy efficiency to optimise productivity of plants.