IMPROVING ROBUSTNESS AND CLIMATIC RESILIENCE IN US SHEEP POPULATIONS THROUGH GENOMICS

The overarching goal of this project will be to develop the background knowledge and tools needed for the successful implementation of genomic selection for robustness and climatic resilience in all major US sheep breed-types (hair, semi-prolific, fine-wool, terminal-sire). This will entail investigating the genetic structure of these sheep populations and the development of novel indicator traits by identifying those that can be pragmatically measured in industry flocks. The genomic mechanisms contributing to their underlying phenotypic variation will also be comprehensively investigated. These goals will be achieved by establishing a database that integrates existing and new genotypic information with large-scale phenotypic records on a representative breed from each of these breed-types (i.e., Katahdin, Polypay, Rambouillet, Suffolk). All the methods and tools developed as part of this project will be readily translatable and applicable to all other routinely-evaluated traits in the US sheep breeding programs.Goal one. The first goal will be to generate genomic datasets and to estimate genomic diversity metrics essential for the successful implementation of genomic selection in US sheep. Using genotypes that already exist or that will be generated as part of the project, the levels of linkage disequilibrium and consistency of gametic phase across breeds (for evaluating potential across-breed genomic predictions) will be estimated. In addition, genomic-based effective population size, genomic inbreeding based on multiple metrics [e.g., Runs of Homozygosity], and genomic connectedness across flocks will be obtained. As the final objective, utilizing the complete pedigree data on the four breeds engaged in the project available through the National Sheep Improvement Program (NSIP), pedigree analyses will be performed with pedigree and genomic relationships compared to assess current levels of pedigree-based inbreeding coefficients as well as pedigree completeness and errors.Goal two. The second goal will be to build reference populations for key robustness and climatic resilience traits in the four breeds, and to understand their underlying genomic background. The initial objective will be to combine existing genotypes and phenotypes, with additional data to be collected on these breeds at USDA ARS centers and in industry flocks, to build reference populations in all four breeds. Through the integration of these datasets, the subsequent object will be to comprehensively evaluate indicator traits of robustness and climatic resilience, including lamb survival, ewe longevity, gastrointestinal parasitism, and udder health. Climatic resilence will be characterized by changes in body weights and condition scores across seasons, resilience to environmental challenges, and hair shedding in the Katahdin breed. To understand the genomic background of these traits, genomic-based genetic parameters (e.g., heritabilities, genetic correlations) will be estimated among all novel traits collected as part of this project and those routinely measured. As the final objective, to unravel candidate genes and metabolic pathways associated with these traits, genome-wide association studies and functional genomic analyses of important genomic regions associated with all the traits evaluated will be conducted.Goal three. The third goal will be to evaluate genotyping strategies and methods for optimizing genomic prediction of breeding values in the main US sheep breed-types. As the first objective, prediction methods and corresponding genomic evaluation tools will be comprehensively evaluated and validated. As the subsequent objective, genotyping strategies to enable wide adoption of genomic selection across all four breed-types will be assessed. The evaluations of alternative strategies for choosing the animals to be genotyped and for implementation of genomic selection will be done based on both real and simulated datasets.