Objective 1: Improve genomic tools for beef cattle and sheep. Sub-objective 1A: Complete improved reference assemblies for beef cattle and sheep using genome-wide and locus-targeted approaches, in addition to comparative approaches, to improve accuracy and contiguity. Sub-objective 1B: Improve annotation of the reference assemblies by conducting specific assays as outlined in the FAANG consortium guidelines, enhanced with parent-of-origin allele expression pattern data. Sub-objective 1C: Develop comprehensive databases of existing variation with predicted impact of those variations on gene expression and protein sequence. Objective 2: Develop systems to improve performance through combined genetic and genomic approaches. Sub-objective 2A: Improve breeding and management decisions by characterizing current genetic and phenotypic variation within and between predominant beef breeds and crosses. Sub-objective 2B: Identification of genomic variation associated with industry-relevant phenotypes in beef cattle. Sub-objective 2C: Development of low-input production lines of sheep, including genetic and genomic resource development to support characterization of these lines. Objective 3: Identify and characterize microbes, microbial populations, and parasites associated with normal and diseased populations. Sub-objective 3A: Profile microbial populations in the respiratory tract (RT) of cattle throughout the production life-cycle in the context of BRDC. Sub-objective 3B: Characterize genomic variation among sheep parasites, for correlation with anthelmintic resistance and animal genotype. Objective 4: Combine products from Objectives 1, 2, and 3 to synthesize a broader knowledge base. Sub-objective 4A: Synthesize genome annotation from Objective 1 and genetics by selection and assessment of impact of predicted non-functional alleles. Sub-objective 4B: Synthesize parasite and metagenomics from Objective 3 with genetics and genomics from Objective 2. Sub-objective 4C: Synthesize variant genotypes and annotation from Objective 1, animal phenotypes from Objective 2, and microbial profiles from Objective 3, by partitioning microbial variation into host genetic and enviromental influences on phenotypic expression.