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SMAll RuminanTs breeding for Efficiency and Resilience

Periodic Reporting for period 2 - SMARTER (SMAll RuminanTs breeding for Efficiency and Resilience)

Période du rapport: 2020-05-01 au 2021-10-31

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.
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) that have shown a relationship with FE. Among the biomarkers analyzed, blood metabolites and milk fatty acids stand out. We have also identified differentially expressed genes in animals with high and low FE. Furthermore, we have sampled and studied the genetic determinism for traits related to efficiency in commercial populations; first genetic parameters were provided for FE traits in dairy goats and for GHG emissions in sheep.
To characterize resilience, new phenotypes collected included footrot, mastitis, gastro-intestinal parasites, survival and longevity, mothering ability and behavioural reactivity traits. Novel phenotypes such immunity related traits, metabolic stress, tolerance to heat stress, body condition score changes, (BCS), GPS-generated phenotypes, have been explored and we have documented how to record these going forward. We provided many genetic parameters for these traits and delivered the first breeding values for parasite resistance (sheep and goat), footrot & mastitis (meat sheep) and longevity (dairy goats). Moreover, some genetic regions affecting the peri-natal mortality, social behavior, lamb survival, and BCS changes 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 in small ruminants, 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 experimental data was further used to adapt and calibrate resource allocation models, in order to predict response to challenges and various breeding strategies. A software for simulating genomes and phenotypes has been developed.
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 data. The database contains a compendium of genetic and environmental data on 121 sheep and 148 goat populations genotyped for medium to high-density marker panels. Pipeline for data analyses are under construction to interpret the genetic and environmental data into a global demographic and adaptive history of small ruminants.
For the analysis and the selection of resilience and efficiency traits in sheep and goats, methods have been developed or adapted. To detect and analyze 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 developed methods to refine and assess genomic predictions within and across small breeds. We have also devised methods to ensure good selection programs across multiple environments or with various genotyping strategies. Finally, we conceived new methods to assess and handle genetic diversity in small ruminant breeds.
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 collated and compared to find a common panel of informative DNA variants. We have implemented the first across-country genetic evaluations in dairy sheep and goat and in meat sheep, and demonstrated the related technical and economic benefits. Meanwhile, we have started to develop a process flow for routine international genetic evaluations.
We have built methodology and consolidated data (animal and farm level, structured interview, and choice modelling) 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, and feed efficiency, economic weights have been produced for R&E traits including labour, while survey data is flowing in on breeder views, beliefs, preferences, and trait improvement choices.
Intensive dissemination activities towards scientific and non-scientific stakeholders were carried out since the beginning of the project (19 peer-reviewed papers; 59 presentations/posters within conferences/workshops, first batch of practice abstract for end-users)
The measures of predictors of R&E traits will continue in experimental and commercial farms. The genetic analyses will be carried out including more genetic parameters and breeding values and, for some traits, the interaction between genetic and environment and the identification of causal mutations (Quantitative Trait Loci, lethal mutations and selection signatures). The identification of the best genetic predictors for R&E traits to use in selection will be finalized. The trade-off between R&E will be also deciphered using the sheep and goat experimental populations that were created in SMARTER.
For further analysis of R&E traits, some developed methods will be adapted to different traits measured in SMARTER. Moreover, the proposed new genomic selection methods will be evaluated in some breeds to improve mating management, genetic diversity and breeding of selected and under-utilised breeds.
Future genetic diversity analyses are expected to highlight the unique characteristics of hardy and under-utilised breeds and their putative variation involved in adaptation to stressful environmental conditions.
By the end of the project, we expect to improve the efficacy of selection of R&E traits by strengthening international collaboration. In that objective, we will be working on the harmonization of trait definitions and the process flow for routine multi-country genetic evaluations.
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 allow evaluating the relative economic, environmental, and social value of R&E traits.
SMARTER key results and their applications will be discussed with a large representation of stakeholders (farmers, breeders and industrials) during national round tables in 2022.