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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic and Metagenomic Approaches to Enhance Efficient and Sustainable Production of Beef Cattle

Location: Genetics, Breeding, & Animal Health

2013 Annual Report


1a.Objectives (from AD-416):
Objective 1: Improve the draft bovine genome sequence and enhance annotation of genes (both protein-coding and noncoding), gene functions, and gene-gene interactions (functional networks). Objective 2: Identify inter-individual genome sequence variation in beef cattle, and explore the effect of this variation on a wide range of production traits. Objective 3: Develop information about variation in metagenomes associated with beef cattle production, including microenvironments within the animals or their production settings, and interactions of metagenomes with host genotypes from birth through reproductive or harvest endpoints.


1b.Approach (from AD-416):
Current challenges to the beef industry include pressure to reduce use of antibiotics, create healthier products, and a need to accommodate dietary changes imposed as corn is diverted to use as a fuel. The Project is designed to interact with and complement approved Projects in (1) the Nutrition Research Unit on feed efficiency and impacts of using distiller’s grain as a feedstuff, (2) the Animal Health Research and Meat Safety and Quality Research Units on reducing antibiotic use, and creating a healthier product, and (3) the Reproduction Research Unit to explore lifetime productivity of cows. This Project Plan is the primary vehicle for including genomics tools and approaches in these collaborating Projects, and the goals are to use genomics and related technologies to begin to address the current industry challenges. Our hypothesis is that substantial genetic variation exists among beef cattle that could be used to meet these challenges through selection. We expect that some desirable genetic effects may be exerted through interactions with the microbiome, and propose that enhanced knowledge of the bovine genome and microbial communities associated with the animals and their production environment can be utilized to target improvements in production, health, food safety, and product quality traits. The goals of the Project are to use molecular genetics and genomics techniques to identify inter-individual genome variation associated with the health, lifetime reproductive efficiency, feed efficiency, and food safety phenotypes recorded on the large research herd maintained in cooperation with the other approved Project Plan in the Genetics and Breeding Unit at USMARC. The Project will also develop knowledge of the microbial communities associated with beef production, and examine putative interactions between the bovine genome and microbiome variation. Since the current draft cattle genome assembly is inadequate to support our approaches, we will participate in international efforts to improve it. The Project will provide the industry with technology to support prediction of genetic merit for measures of animal health, fertility, and efficiency that are difficult to record outside a research setting. It will also provide basic knowledge to address the role(s) of microbial populations in beef production, while continuing commitment to support basic research and tools for investigation of genome biology of ruminants, historically a key role of USMARC in cattle genomics. We will expand this role to microbiomes associated with beef cattle production.


3.Progress Report:
The primary effort of the bovine genomics project was collection of sequence/genotype data from the USMARC, Clay Center, Nebraska mapping populations, and of appropriate samples to conduct studies on respiratory disease and female fertility. Whole genome shotgun sequencing for 270 animals of the USMARC populations, as well as gene-targeted “exome” sequencing to higher coverage for over 100 animals, was used to predict function of variants observed in 234 of these bulls. Additionally, tens of thousands of new markers, or validation of public markers in our herds, emerged from this analysis, setting us up very well to make progress in identifying markers associated with traits in the following years. We genotyped over 7,000 animals in the Germplasm Evaluation (GPE) pedigree with DNA chips of varying densities, including animals from resource populations related to respiratory disease, female reproduction, and feed intake/efficiency. We collected over 12,000 lung samples from abattoir to support a case/control study designed to identify genomic regions of cattle harboring variation affecting the occurrence of respiratory disease. This was complemented by collection of thousands of fluid or solid samples to characterize the respiratory and gastrointestinal tract microbiomes of cattle. We identified genomic regions harboring variation affecting reproductive success. Commercialization of the Mass Genotyping by Sequencing Technology (MGST) by our CRADA partner (58-3K95-1-1519) is going well. They have added several large customers and have expanded the applications in the past year.

Significant advances have been made in developing protocols and pipelines to produce finished bacterial genome sequences of bovine pathogens and other bacteria important to food safety, and to survey bacterial populations in ecological niches of importance to cattle production. Collaboration with researchers at the U.S. Meat Animal Research Center, Clay Center, Nebraska and the National Biodefense and Countermeasures Center in Maryland to produce the first report of a complete, closed circular genome sequence of a bacterium (Bibersteinia trehalosi, a respiratory pathogen of cattle) available, which was also the first time that a finished genome had been produced entirely by assembly of shotgun sequence data with no manual finishing steps required. We have since generated complete genome sequences for dozens of additional bacterial isolates, including both human and bovine pathogens found in the beef cattle production environment.

We have independently developed methods to collect full-length 16S rRNA sequence from environmental microbial DNA samples, the first time that high-throughput next-generation sequencing has produced the high resolution, full-length sequence (which provides greater ability to identify particular species present in an environment, for example nasal cavity). We have produced preliminary protocols and data for examining the complete bacterial genome complement in the respiratory and recto-anal mucosal environments, which required substantial refinement of known techniques to adapt for those microbiomes.


4.Accomplishments
1. Finding markers to predict reproduction efficiency by using a Genome Wide Association Study (GWAS) approach. Reproductive efficiency is arguably the most economically important trait in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed to breeding. Identification of variation in the genome with predictive merit for reproductive success would facilitate accurate prediction of daughter pregnancy rate in sires enabling effective selection of bulls producing daughters with improved fertility. Scientists at Clay Center, Nebraska applied a Genome Wide Association Study (GWAS) approach, using a procedure based on genotyping multi-animal pools of DNA to increase the number of animals that could be genotyped with available resources. The study identified regions of the genome associated with reproductive efficiency, which are being targeted for further analysis to develop robust marker systems, and demonstrated that DNA pooling can be used to substantially reduce the cost of GWAS studies in cattle. A specific deletion of DNA along chromosome 5 in Bos indicus crossbred cattle was identified that appears to be strongly correlated with reproductive failure, providing a potentially useful marker for breeders in southern states that make use of these types of cattle.

2. Development of new technology to monitor disease status and vaccine success. The primary health issue in beef cattle production is Bovine Respiratory Disease (BRD), costing the industry hundreds of millions of dollars per year in total for losses and treatment. It is the primary reason for the health-related use of antibiotics in the industry that has come under increased scrutiny as antibiotic-resistant bacteria become a more common problem in human disease. Despite decades of research into BRD, the incidence and impact have not been significantly reduced, suggesting that new approaches to the problem are required. Scientists at Clay Center, Nebraska developed an approach to apply the latest DNA sequencing technology, called circular consensus sequencing, to obtain profiles of the antibody repertoires that cattle produce as they mature and encounter pathogens that can cause respiratory disease. The researchers believe that molecular-level characterization of the immune response will help to guide development of more useful vaccines, and can potentially be used as high-resolution phenotype to identify animals better able to resist BRD. Presentation of this data at various meetings and conferences has led to development of several new collaborations, and garnered extramural support from two funded grants.


Review Publications
Melters, D.P., Bradnam, K.R., Young, H.P., Telis, N., May, M.R., Ruby, J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J.L., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan, S.W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. 14(1):R10. doi:10.1186/gb-2013-14-1-r10.

Larsen, P.A., Smith, T.P. 2012. Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire. BioMed Central (BMC) Immunology. 13:52 doi:10.1186/1471-2172-13-52.

Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., King, D.A., Shackelford, S.D., Wheeler, T.L., Freetly, H.C. 2012. Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits. Animal Genetics. 43:599-603.

Last Modified: 8/29/2014
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