H2020 SMARTER Project: Genetic improvement of small ruminants to achieve efficiency and resilience

Seven experimental populations (9 breeds: 1 goat, 4 dairy sheep, and 4 meat sheep) were established and extensively analyzed for feed efficiency (FE). A list of phenotypic traits (>=30) showed a relationship with FE. Among the biomarkers analyzed, blood metabolites and milk fatty acid profile stood out as the most promising. In addition, a list of candidate phenotypes was specified as potential indicators, including live weight, backfat, muscle depth, milk fat, protein and lactose content, body condition score (BCS), feed intake, feeding behavior, rumen lipidome and rumen microbiota, and Pac Chambers GEI. For these FE traits, SMARTER provided heritability, correlation with production and GEI traits, and some genomic results. To characterize resilience (R), novel phenotypes were collected, including foot rot, mastitis, gastrointestinal (GI) parasites, survival and longevity, maternal ability, and behavioral reactivity traits. Novel phenotypes, such as immunity-related traits, rumen temperature, metabolic stress, heat stress tolerance, changes in BC, and GPS-generated phenotypes, were explored.

We provided many genetic parameters for these traits and delivered the first breeding values for GIN (sheep and goats), footrot and mastitis (sheep), and longevity (goat). Genomic studies were conducted for 11 of these traits across seven breeds, leading to a better understanding of the genes and mechanisms controlling resilience. The genetic link between R&E was studied using existing data, new data, and experimental and genomic models. First, a comprehensive meta-analysis was completed, which identified some trade-offs between R&E traits. Genomic studies were used to identify and characterize pleiotropic loci associated with both R&E traits. Four selection experiments in sheep and one in goats were analyzed to study the mechanisms underlying such trade-offs between R&E traits. The main findings were: little evidence of major trade-offs between selection for R&E and some key resilience mechanisms and phenotypes, and new methods and indicators for analyzing resilience trajectories in the face of challenges. The experimental data were also used to adapt and calibrate resource allocation models to predict responses to challenges and various breeding strategies.

The model provided the first real-world empirical evidence that immunity has an energetic cost. To characterize the genetic diversity of small ruminants, including resistant and underutilized breeds, SMARTER created a common repository for existing and newly generated genetic and environmental data for 285 sheep and 166 goat populations (17,000 animals). Using standard population analysis methods, as well as a novel statistical method dedicated to historical gene annotation, SMARTER characterized the genetic relationships among small ruminant populations and identified genomic regions involved in their bioclimatic adaptation. Methods were developed or adapted for the analysis and selection of R&E traits in sheep and goats. To detect and analyze environmental stress and resilience-associated traits, SMARTER employed different approaches (mixture model on variances, resilience in a normal reaction model, statistical indicators of deviation from target trajectories). Methods were also developed to refine and evaluate genomic predictions within and between small breeds, ensure good selection programs in multiple environments or with diverse genotyping strategies, and assess and manage genetic diversity and recessive anomalies.

With the goal of improving the efficiency of R&E trait selection by strengthening international collaboration, SMARTER created the conditions and tools necessary for international genetic evaluation. The first transnational genetic evaluations in small ruminants were implemented, demonstrating technical and economic benefits. Meanwhile, SMARTER developed a process flow for routine genetic evaluations and assessed national interest in such evaluations.

Recommendations on phenotyping 31 large-scale R&E traits were developed, resulting in guidelines for ICAR. An informative panel of genotypes in sheep populations was developed and is available on the SMARTER website. Research findings on the agroecological impacts of breeding at the farm and population levels demonstrated that: there are significant opportunities to generate value through genetic improvement of R&E traits; farmers clearly see the need for animal resilience and efficiency in robust, future farming systems; and there is scope to set breeding objectives that achieve the desired balance of selection between production and R&E traits. An informative panel of genotypes in sheep populations was developed and is available on the SMARTER website. Research findings on the agroecological impacts of breeding at the farm and population levels demonstrated that: there are significant opportunities to generate value through genetic improvement of R&E traits; ii) Farmers clearly see the need for animal resilience and efficiency in robust and future-proof farming systems; and there is scope to set breeding objectives that achieve the desired balance of selection between production and R&E traits.

An informative panel of genotypes for sheep populations was developed and is available on the SMARTER website. Research results on the agroecological impacts of breeding at the farm and population levels demonstrated that: there are significant opportunities to generate value through genetic improvement of R&E traits; farmers clearly see the need for animal resilience and efficiency in robust, future farming systems; and there is scope to establish breeding objectives that achieve the desired balance of selection between production and R&E traits.