Location: Genetics and Animal Breeding
Project Number: 3040-31000-104-000-D
Project Type: In-House Appropriated
Start Date: Jul 26, 2022
End Date: Jul 25, 2027
Objective 1. Improve genomic resource and annotation tools for beef cattle and sheep. Sub-objective 1A: Create pangenome resources for cattle. Improve accuracy of imputed cattle genotypes by using pangenome resources. Sub-objective 1B: Improve annotation of assemblies through FAANG cooperation. Objective 2. Develop systems to improve performance through combined genetic and genomic characterization, heterosis, selection and analytical approaches. Sub-objective 2A: Characterize genetic, genomic and phenotypic variance among and within diverse and influential beef cattle populations toward improved sustainable breeding and management decisions. Sub-objective 2B: Estimate correlated responses to reducing an index of natural loss-of-function (LOF) alleles on reproduction, health, longevity, and traditional beef production traits. Sub-objective 2C: Examine whether sequence changes that affect protein structure or expression (functional and structural variants) also effect traits important to beef cattle production efficiency and sustainability. Sub-objective 2D: Develop strategies to incorporate commercial data into national genetic evaluations. Sub-objective 2E: Investigate interactions of beef breeds with management systems in diverse environments. Sub-objective 2F: Develop improved statistical methods for quantitative genetic and genomic analysis of beef cattle data. Objective 3. New methods for metagenome assembly, analysis, and characterization. New methods for characterizing genome function of microbes, protists and parasites. Sub-objective 3A: Develop methods for combined metagenomic assembly of complete microbial, protist, and parasite genomes from relevant microbiomes related to animals (rumen, gut, feces, environment). Sub-objective 3B: Develop methods and computational models to characterize genome function of microbes, protists and parasites affecting animal health of sheep and cattle. Sub-objective 3C: Profile bacterial populations (16S rRNA gene) in the respiratory tract of weaned beef calves after initiation of an inflammatory response. Sub-objective 3D: Profile bacterial populations (16S rRNA gene) in the digestive tract (rumen) of cattle from source populations from USMARC and Colorado.
Challenges to sustainability of beef production include aspects of animal health and wellbeing, societal expectations of reduced antibiotic use and/or development of alternatives, and pressure to reduce the 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, health, and well-being. These technologies support and depend on 1) continued improvement in annotation of cattle and sheep genomes, 2) development of research populations with pertinent phenotypes that broadly represent industry genetics, 3) identification of genomic variants segregating in beef cattle populations and assessment of the interaction of variation with production phenotypes as influenced by environment and management, and 4) characterization of microbes and microbiomes relevant to beef production. The proposed Project Plan will modernize and improve the relevance of phenotyped populations in which the effects of variation can be estimated, enhance genome annotation to sharpen the focus for evaluation of effects of variation on phenotype, and extensively characterize the content and impact of microbiomes and key microbes on target traits. Population-independent and population-specific management strategies will be assessed in cooperation with the ARS Beef Grand Challenge and related programs, using advancements in statistical methodology and partnering with commercial producers and other ARS locations. This combination will enable broader understanding of the components contributing to production efficiency, environmental impact, and animal welfare, while developing specific technologies and estimates of across-breed expected progeny difference (EPD) and heterosis effects for release to beef cattle producers.