Adaptations to dietary shift in aquaculture: characterization and enhancement – AGREENFISH

Global aquaculture has expanded continuously over the last 30 years to meet the increasing demand of fish for human consumption, which can no longer be met by fisheries captures. The growth of aquaculture has generated an increasing demand of raw materials for aquafeeds. However, the volume of fish meal (FM) and fish oil (FO), the traditional major ingredients of aquafeeds produced from feed-grade fisheries, remained stable over the last 20 years. This has forced a shift from marine resources towards plant products as ingredients for fish feed. The proportion of FM and FO in fish feeds has been reduced by one third as a result of recent research efforts. Nevertheless, trials using highly substituted (little or no FM and FO) plant-based diets highlighted physiological bottlenecks.
These limits in the adaptive capacity of the fish to the unavoidable changes in dietary formulations urged us to explore a new paradigm: “adapting the fish to the new diets”. Having now demonstrated genetic variability for such adaptation in rainbow trout, we propose to take advantage of the existence of divergent genotypes to (i) decipher the mechanisms underlying the differences in short and long term adaptive response to plant-based diets and (ii) find markers of short or long term adaptation of fish to plant ingredients which will enhance the efficiency of future selection for fish adapted to new diets. This is the core of the AGREENFISH project.
Using rainbow trout as a model of fish relying on marine ingredients, the research will be conducted by a consortium gathering French experts in fish genetics, nutrition, physiology and behavior, pathology, immunology, microbiology, and representatives of the French aquaculture industry.
We will investigate (i) rainbow trout isogenic lines that we previously identified as highly divergent for responses to plant-based diets and (ii) a population of rainbow trout which we selected for its aptitude (survival and growth) to cope with plant-based diets. We will compare the responses of the different groups when fed a plant-based diet free of marine ingredients versus a diet containing FM and FO to decipher the adaptive mechanisms implemented at short and long terms by the contrasting genotypes. The characterization of isogenic lines, used here as a model of strong genetic divergence in adaptive capacity, will both use "sans a priori approach" and focus on specific targets known to be affected by plant ingredients: feed intake, gut and associated microbiota, liver metabolism, nutrient utilization and growth. The comparison of the selected (3rd generation) and control populations will target the selection criteria (survival, growth), the major nutritional bottlenecks and the responses to challenging situations and to several pathogens, in order to assess the fish robustness as a major determinant of fish production efficiency. Also, the soundest biomarkers (functional phenotypes, gene expression…) of adaptation found in the isogenic lines will be tested in the selected and control populations. Signatures of selection will be searched in the genome of the selected line, and combined with results from transcript analysis in the isogenic lines to mine candidate genes. The most consistent signatures will be then tested in a commercial population, in the individuals showing the largest difference when fed a diet devoid of FM and FO from the first feeding.
Finally, all data will be gathered into an integrative map chart of the functional alterations and adaptive mechanisms induced by diet according to genetic groups, from which relevant biomarkers of the adaptive capacity of fish fed plant-based diets will be identified. This knowledge and the new tools generated will allow enhancing the genetic selection for better adaptation of domestic fish populations to the major diet shifts in feed composition and to improve formulation of aquafeeds, and will be disseminated for application in aquaculture industry through SySAAF.