Periodic Reporting for period 3 - SMARTER (SMAll RuminanTs breeding for Efficiency and Resilience) Reporting period: 2021-11-01 to 2022-10-31 Summary of the context and overall objectives of the project To maintain benefits in environments vulnerable to environmental and economic challenges, small ruminants need to be resilient and efficient. SMARTER will use new and collaborative strategies to improve resilience and efficiency (R&E) of the sheep and goat sectors at the animal (A), population/breed (P) and system/farm (S) levels. The overall goal of SMARTER is i) to phenotypically and genetically characterise and understand novel R&E related traits, ii) to improve and develop new genomic prediction techniques, and iii) to establish new breeding and management strategies that include those novel R&E related traits according to their importance and relevance to various systems, breeds and environments. The project will promote optimised resilience of small ruminant farming systems, which are key pillars of socioeconomic sustainability and eco-system services in rural communities throughout Europe and beyond. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far A total of seven experimental populations (9 breeds: 1 goat, 4 dairy sheep and 4 meat sheep breeds) have been established and intensively analysed for proxies for feed efficiency (FE). A list of phenotypic traits (>=30) have shown a relationship with FE. Among the biomarkers analyzed, blood metabolites (such as citrate and amino acids) and milk fatty acid profile stand out as the most promising thus far. Furthermore, a list of candidate phenotypes has been specified as possible proxies including live weight, back fat, muscle depth, milk fat, protein and lactose content, body condition score (BCS), feed intake, and GHG profiles from Pac Chambers. To characterize resilience (R), new phenotypes collected included footrot, mastitis, gastro-intestinal parasites (GIN), survival and longevity, mothering ability and behavioural reactivity traits. Novel phenotypes such immunity related traits, metabolic stress, tolerance to heat stress, BCS changes, GPS-generated phenotypes, have been explored. We provided many genetic parameters for these traits and delivered the first breeding values for GIN (sheep and goat), footrot & mastitis (meat sheep) and longevity (dairy goats). Moreover, some genetic regions affecting the peri-natal mortality, social behaviour, lamb survival, BCS changes and GIN were identified. The genetic link between R&E was studied using existing data, new experimental data and models. Firstly, comprehensive meta-analysis was completed which identified some trade-offs between R&E traits, although evidence was limited. Four sheep and one goat selection experiments were analysed for studying the mechanisms underlying such trade-off between R&E traits. The main findings were: i) little evidence of major trade-offs between selection for R&E and ii) some key resilience mechanisms and phenotypes. The experimental data was further used to adapt and calibrate resource allocation models, in order to predict response to challenges and various breeding strategies. In order to characterize genetic diversity of small ruminants including hardy and underutilized breeds we have created a common repository for existing and newly generated genetic and environmental data for 175 sheep and 167 goat populations. Open-source software for maintaining and using the database for populations genomics analyses has been published on public software repositories. For the analysis and the selection of R&E traits in sheep and goats, methods have been developed or adapted. To detect and analyse environmental stresses and traits associated to resilience we used different approaches (mixture model on variances, resilience in a Norm Reaction model, statistical indicators of deviation to target trajectories). We have also developed methods to i) refine and assess genomic predictions within and across small breeds, ii) ensure good selection programs across multiple environments or with various genotyping strategies, and iii) assess and handle genetic diversity and recessive anomalies. We aim at improving the efficacy of selection of R&E traits by strengthening international collaboration. Thus, we have started harmonizing the trait definitions and completed the prerequisite and tools for an multi country genetic evaluation. Informativeness of individual DNA variants per breed and per country were analysed to find a common panel of informative variants. We have implemented the first across-country genetic evaluations in sheep and goat, and demonstrated the related technical and economic benefits. Meanwhile, a process flow for routine genetic evaluations was developed. A common methodology was built consolidating data (animal and farm level) to support breeding strategies that utilise R&E traits. Early results have been produced on the farm level agro-ecological impacts of breeding for infectious and non-infectious diseases (lameness, gastro-intestinal parasites, mastitis), and feed efficiency, economic weights have been produced for R&E traits including labour, while survey data has been collected and analysed on breeder views, beliefs, preferences, and trait improvement choices. The project is characterized by intensive communication and dissemination activities (33 open access papers, 109 presentations/posters, 105 participation to industry events). Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) The genetic analyses of predictors of R&E traits will continue including more genetic parameters and breeding values and, for some traits, the interaction between genetic and environment and the identification of causal mutations. The trade-off between R&E will be further developed using the sheep and goat experimental populations that were created in SMARTER. For proper analysis of R&E traits, new methods adapted to different traits measured in SMARTER and new genomic selection methods have been proposed, which improve mating management, genetic diversity and breeding of selected and under-utilised breeds. Work is ongoing to characterize the genetic diversity in small ruminants and identify genes involved in their bioclimatic adaptation. A new method dedicated to the historical annotation of these genes is under active development. By the end of the project, we expect major progress in international collaborative selection. In that objective, recommendations on R&E phenotyping on large scale will result in guidelines available for ICAR, and the process flow for routine multi-country genetic evaluations is being elaborated. Finally, new balanced breeding strategies and breeding goals that utilize both R&E related traits and trade-offs will be evaluated using models and simulation studies. Analyses of the interviews and surveys will continue to address the relative economic, environmental, and social value of R&E traits. SMARTER key results and their applications have been discussed in the round table events held in 10 partner countries, allowing the dissemination of the main results to a large portion of the stakeholders. logo-title-4-290x85.jpg
