Project Number: 3040-31000-100-00-D
Project Type: In-House Appropriated
Start Date: Jan 18, 2018
End Date: Jan 17, 2023
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.
Challenges to sustainability of beef and lamb production include aspects of animal health and wellbeing, societal expectations of reduced antibiotic use and/or development of alternatives, and pressure to reduce environmental impact of production. Advances in genomic and related technologies have opened new avenues to better understand the relationships between variants of animal genomes, production traits, and the microbes that are associated with animal production. The technologies support and depend on development of research populations with pertinent phenotypes that broadly sample industry genetics, continuing improvement in annotation of animal genomes, identification and characterization of microbial species relevant to animal production, and continued assessment of the interaction of genome variation and production phenotypes. This project plan will merge previous genetics and genomics projects into a broader systems approach, that will encompass (1) genome annotation and identification of functional variation among genomes, (2) development of phenotyped populations in which the effects of variation can be estimated, (3) characterization of the overall microbial diversity associated with the animals and dependencies of this diversity on animal genome variation, and (4) molecular-level characterization of microbial or parasitic organisms that impact on animal health, productivity, and reproduction. The systems approach will be combined with population management strategies, application of advancements in statistical methodology, and partnering with commercial producers. This combination will enable broader understanding of the components contributing to production efficiency, environmental impact, and animal welfare, while developing specific technologies for release to beef cattle producers and improved strains for the sheep industry.