Project : USDA ARS

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Research Project: Genomes to Phenomes in Beef Cattle Research

Location: Genetics and Animal Breeding

2025 Annual Report

Objectives
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 functions 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.

Approach
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.

Progress Report
The Project Plan achieved all major goals set for the 5-year cycle, with the exception of Milestone 3B that encountered a critical vacancy which is being addressed by a revision to the milestone that has been submitted. Objective 1 was on track to exceed original goals expanding to >110 haplotypes of different breeds available for the pangenome. Assembly of over 10 different cattle breed pangenomes were completed. A beef breed pangenome was also assembled using publicly available long-read assemblies available from National Center for Biotechnology Infomation (NCBI) and different approaches to mapping short reads and calling variant genotypes from short reads mapped to the beef breed pangenome are currently being evaluated. Phase 1” pangenome graphs were completed with the goal of testing available algorithms for preparing, indexing and utilizing for population read mapping. The PanGenome Graph Builder algorithm appeared to provide the best characteristics and the “Phase 2” pangenome with maximum number of breeds has been prepared for testing and application. This comprehensive pangenome will improve identification of genetic variants by identification of novel variation and elimination of false markers generated by data of individuals that improperly maps to the incomplete current reference genome. Pangenome activities will support continued research of Objective 2; the Germplasm Evaluation Program (GPE) project continues from the previous project plan cycle with its evaluation of 18 different cattle breeds. The GPE project continued to strengthen genetic connections to cattle at other locations this year. Angus and Brahman semen was again provided to Texas A&M AgriLife at McGregor and semen from multiple breeds was provided to Texas A&M AgriLife at Beeville. Both locations, as well as the ARS location in El Reno, Oklahoma, are continuing to add progeny and replacement heifers to compare with those born at Clay Center, Nebraska. These other locations will facilitate estimation of Genotype by Management by Environmental (GEM) interactions and allow direct comparisons involving purebred Brahman, which cannot be fairly evaluated at Clay Center, Nebraska, due to their lack of cold tolerance. Objective 2 also included release of across-breed expected progeny difference (EPD) adjustment factors in Spring 2025. Currently, the GPE project has approximately 2,980 breeding females, which is an increase of over 200 females from 2024. This expansion was due to keeping 750-800 breeding heifers in each of the last two years, and this strategy will continue until we reach a target herd size of 3,600-4,000 breeding females. Cow numbers have decreased in recent years due to drought, sending breeding females to cooperators in El Reno, Oklahoma and Beeville, Texas, and due to an unexpected loss of breeding heifers in 2023. We sampled over 40 industry bulls in 2025 with a focus on increasing the diversity of our sample in several breeds. We will continue sampling other bulls in 2026 in cooperation with breed associations to target impactful sires in most of the GPE breeds. Work has continued on metagenomic data from rumen samples conducted during the project (see Objective 3). Efforts have continued in using DNA pooling as a strategy for incorporating commercial beef cattle data into national genetic evaluations and using these evaluations to inform management of commercial animals by identifying genetic connections between commercial and seedstock animals. Linkage disequilibrium (LD) or correlations between single nucleotide polymorphisms (SNP) was evaluated using data from commercial animals. Correlations between SNP may allow more accurate connections between purebred bulls and commercial animals. Individual genotypes in livestock species have also been used to identify shared segments that are identical by descent between commercial and seedstock sectors of the industry that can be used to genetically evaluate seedstock animals for survival in the commercial environment from birth through finishing. These genotyping strategies have continued the effort to provide industry with more cost-effective tools for employing genomics to improve production and sustainability. The SFA (Selection for Functional Alleles) population is in the third year of utilizing Red Angus bulls in the MARC I composite to generate a higher quality, more marketable composite by improving marbling EPD through imputation of functional alleles associated with this (and other) trait(s). The Red Angus bulls were split into heifer and cow mating groups using their calving ease and birth weight EPD. Analysis of SFA cow weight and cumulative productivity is nearing completion. The analyses are considering genomic additive and dominance effects as well as various measures of genomic inbreeding and heterosis. Low-coverage sequence on GPE and SFA calves was imputed to whole-genome genotypes and used to determine the most likely sires for both sets of calves, resulting in updated pedigrees for GPE and SFA cattle. An analysis of SFA cow weight and cumulative productivity was conducted and this will allow for evaluating associations of genotypes with production traits. While the current focus has been on genomic inbreeding effects on production, additive and dominance effects of individual variants can be determined from the same analyses. Objective 3 provided new methods and data to incorporate knowledge about the microbial communities of beef cattle and assess their impact on a variety of production traits, animal health, and food safety. It was shown that the genetic structure of Mannheimia haemolytica, a major bacterial cause of respiratory disease in cattle, can change significantly. This leads to diverse forms with altered activity and potential resistance to treatments and is crucial for developing effective strategies to combat bovine respiratory disease, potentially reducing antibiotic use, and improving animal health. The first year was completed for evaluation of the bacterial profiles of the upper nasal cavity of feedlot cattle administered lipopolysaccharide to reproduce an immune response similar to bovine respiratory disease. Nasal swabs have been collected for sequencing bacterial profiles. These data will add to the current databases for metagenomic data and improve our knowledge of the bacterial pathogens associated with respiratory disease. Employment of recent advances in long read metagenome assembly was implemented to improve resolution of microbial genomes and distinguish between closely related strains to increase the number of high-quality metagenome-assembled genomes (MAGs) from about 1,200 distinct genomes to >2,200. The high-quality MAGs from this effort were used to estimate bacterial genome abundance and metabolic potential (MP) of microbiomes of rumen from >700 animals that were part of a feed efficiency study. Novel information about the level of animal-to-animal and diet-to-diet variation in microbiome composition and MP was developed and will provide the basis for developing associations of MP with phenotype in the final stage of this project. Evaluation of the rumen microbial community as part of the Beef Grand Challenge continued with characterization of samples from Clay Center, Nebraska; Miles City, Montana; and El Reno, Oklahoma, in preparation for analysis to identify environment-specific and general contributions of microbial diversity to beef cattle production.

Accomplishments
1. Estimation of breed-specific heterosis for growth and carcass traits for 18 U.S. beef breeds. Heterosis, or hybrid vigor, is traditionally defined as the advantage of crossbred progeny relative to the average performance of their purebred parents. This advantage is due to increased heterozygosity which increases phenotypic expression in traits affected by dominance. Heterosis effects may vary depending on the breed of animals in the original cross; however, breed-specific estimates are difficult to obtain because of the resources required to estimate the effects. The Germplasm Evaluation Program at Clay Center, Nebraska, is designed to evaluate crosses of 18 diverse and prominent U.S. beef cattle breeds. ARS scientists at Clay Center, Nebraska, estimated specific heterosis of breed types (British, Brahman, Continental) as well as the average heterotic advantage of each of these 18 breeds for growth and carcass quality. Results suggest exceptional hybrid vigor in Brahman crosses, as well as specific advantages for several other breeds. Average increases in productivity due to heterosis ranged from 1.3% for fat thickness to a 9% increase in carcass weight. This increase in carcass weight alone would result in increased profitability for producers creating crossbred animals. These results will enable breeders to take advantage of diverse breeds in crossbreeding programs to improve offspring performance.

2. Genotype host using metagenome samples. ARS scientists at Clay Center, Nebraska, and collaborators demonstrated that the microbiome of a living bovine host may contain enough of the host’s DNA for genotyping. DNA extracted from eye swabs taken to examine microbes associated with pinkeye in calves was sequenced and mapped to the bovine genome. This step is needed to separate host DNA from microbial DNA in each sample. Rather than discarding the host sequence as is typical for microbiological studies, the host sequence was further processed through a genotype imputation pipeline designed for low-coverage sequence. After removing low-confidence genotype calls, 98% of the imputed genotypes agreed with genotypes obtained from the powerful GGP-100K single nucleotide polymorphism (SNP) array, which is the current standard for beef cattle genome mapping. These results indicate that various samples obtained to screen for pathogens or metagenomic analysis may also be useful to genotype animals and to ensure proper identity of the animal samples. Similarly, non-bovine sequence in samples obtained for genotyping might be used to screen for pathogenic organisms. Both options will decrease input cost when beef animals are sampled for microbial sequencing.

3. Phase variation in Mannheimia haemolytica challenges the static genome paradigm. Bovine Respiratory Disease (BRD) is the costliest illness affecting U.S. feed yard cattle, driving significant antibiotic use. A primary cause is the bacterium Mannheimia haemolytica. ARS scientists at Clay Center, Nebraska, determined that this pathogen is not a static target. In the low-oxygen conditions of an infected lung, it actively shuffles large segments of its genetic code in a process called phase variation. This was not observed under normal oxygen conditions. This genetic instability allows the bacterium to generate variants that may be better equipped to survive, creating “persister” cells that can evade antibiotic treatments and lead to persistent infections as has been shown in other species. If this phenomenon is found to be widespread, it could explain why BRD often poses challenges in treatment and why some treatments may not succeed. Our findings fundamentally challenge the current "static genome" approach to developing vaccines and treatments. To effectively combat BRD, reduce economic losses, and promote antimicrobial stewardship, we must develop new strategies that account for this pathogen’s dynamic, adaptive nature. Continued research in this area is critical to creating next-generation tools that can outsmart this adaptable threat to our nation's cattle industry.

4. Microbial compositions of the respiratory tract of neonatal dairy calves in a longitudinal probiotic trial. Probiotics are a promising intervention to improve animal health by influencing the bacterial populations of the gut. However, research is needed to determine if, and how, oral probiotics impact bacterial populations of the respiratory tract. ARS scientists in Clay Center, Nebraska, and collaborators characterized the bacterial populations present in the nostril, tonsil, and lung of calves fed probiotics for 52 days. Variation in bacterial population diversity within tissue samples were observed and indicated distinct bacterial compositions among sampling sites. Differentially abundant bacteria in the probiotic treated calves were identified and were unique to their sampling site. These findings characterize the dynamic nature of bacterial diversity and provide insight for the impact of oral probiotics on the gut as well as other systems including respiratory tract microbiome.

U.S. DEPARTMENT OF AGRICULTURE

Genetics and Animal Breeding: Clay Center, NE