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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Research Project #424177

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

Location: Genetics and Animal Breeding

2014 Annual Report

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 sheep, and explore the effect of this variation on a wide range of production traits. Objective 3: Assess variation in metagenomes associated with microenvironments within animals or their production settings, to identify potential novel strategies and techniques that manipulate microbial populations for improved production methods less reliant on antimicrobial use, while improving growth and production efficiencies in cattle and sheep.

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.

Progress Report
The bovine genomics project has entered an exciting phase of discovery, using whole-genome sequence and genotype data from the U.S. Meat Animal Research Center, Clay Center, Nebraska, mapping populations to identify chromosomal regions, genes, and in some cases specific DNA differences appearing to affect respiratory disease occurrence and female fertility. This year we added high-coverage whole genome sequencing of nearly a hundred animals that supports whole-genome genotyping, and lower coverage sequence for nearly a hundred others, as well as gene-targeted “exome” sequencing to higher coverage for yet another hundred animals. This additional genome sequence permitted refinement of the process to identify pertinent variation in the bovine genome affecting the animal's ability to resist respiratory disease or to have high reproductive success, traits of high value in modern beef production systems. One finding from these studies is that immunity-related genes tend to have a higher level of variation affecting protein sequence than other types of genes. We participated in international collaborations to use gene expression profiles to identify networks of genes associated with puberty and postpartum anoestrus, and used these networks to refine genetic marker tests to optimize these traits in beef cattle herds. In particular, a set of 141 markers were developed that explained one third of the additive genomic variation contributing to success of rebreeding (defined as successful pregnancy after first calf). A surprising amount of sequence variation predicted to prevent function of genes was observed, yet these loss-of-function mutations did not appear to explain any of the variation in carcass traits like muscle size, meat tenderness, etc. Rather, variation in these traits tended to be associated with variation in gene regulatory regions. All of these efforts are underpinned by mapping sequence reads to the bovine genome assembly that we helped to create, but which still has significant deficiencies that interfere with progress towards identification of variation affecting production traits. So we expanded our efforts to improve the Hereford breed Bos taurus genome assembly, participating in international efforts to improve the reference, as well as create completely new, independent reference assembly for a tropically adapted Bos indicus breed called Nelore. We tested novel approaches based on emerging sequencing technology to improve assemblies, which indicate as much as 30-fold improvement in the length of continuous sequence is achievable. Since many conclusions can be drawn from comparative genomic studies among related species, we participated in international consortiums to create goat, water buffalo, and bison genome assemblies. All three of these efforts were successful, especially the goat genome that was performed using Single Molecule Real Time (SMRT) sequencing technology in use at USMARC and provides a model for improving the bovine genome. Commercialization of the "MGST" genotyping technology by our CRADA partner is going well. They have added a number of customers and recently signed an agreement to provide genotyping services to one of the primary providers of bovine DNA testing. Our CRADA partner was recently awarded a Phase II Small Business Innovation Research grant to develop and commercialize a larger panel of markers to support imputation in cattle. This larger panel of markers will substantially expand the market for MGST products and will also provide a useful tool for this Project. We have begun applying protocols and pipelines we developed last year to characterize the bacterial composition in target environments in the rumen, rectum, and nasopharyngeal areas of cattle for feed efficiency, food safety, and respiratory disease studies, respectively. Initial results show a dramatic change in the composition of the microbiome in the airways of cattle when they are trucked from the sale barn to the feedlot and begin their days on feed, information that will help to guide management practices. In addition, thousands of additional samples to support this effort were collected.

1. Prediction of genetic merit from 50,000 genomic markers is breed-specific. Genomic prediction has the potential to accelerate genetic improvement by increasing the accuracy of prediction of young breeding cattle, but it requires large training data sets. Because many breeds contribute to U.S. beef production, it would be useful to be able to share training data between breeds. ARS researchers at Clay Center, NE, and university collaborators determined that training data from other breeds contributes relatively little in addition to within-breed training with current analysis models and only 50,000 markers. Results suggest that further research to increase the number of genomic markers, improve methods of choosing markers, and improve analytical approaches, is needed.

2. Markers to improve accuracy of genetic evaluation with respect to respiratory disease. Bovine respiratory disease (BRD) is the primary health issue in beef cattle production, costing the industry hundreds of millions of dollars per year in total for losses and treatment, and 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. Scientists at Clay Center, Nebraska, identified 84 markers associated with the observation of lung lesions at slaughter (an indication of BRD). These markers were found near genes with functions related to immunity and tissue regeneration, among others. These markers can now be used to test the hypothesis that breeding or selective management can reduce the incidence of BRD and the need for antibiotic use in beef cattle.

Review Publications
Lindholm-Perry, A.K., Kuehn, L.A., Oliver, W.T., Kern, R.J., Cushman, R.A., Miles, J.R., McNeel, A.K., Freetly, H.C. 2014. DNA polymorphisms and transcript abundance of PRKAG2 and phosphorylated AMP-activated protein kinase in the rumen are associated with gain and feed intake in beef steers. Animal Genetics. 45(4):461-472.
Lindholm-Perry, A.K., Kuehn, L.A., Oliver, W.T., Sexten, A.K., Miles, J.R., Rempel, L.A., Cushman, R.A., Freetly, H.C. 2013. Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain. PLoS One. 8(11):e80882.
Kim, M.S., Kim, J., Kuehn, L.A., Bono, J.L., Berry, E.D., Kalchayanand, N., Freetly, H.C., Benson, A.K., Wells, J. 2014. Investigation of bacterial diversity in the feces of cattle fed different diets. Journal of Animal Science. 92:683-694.
McClure, M.C., Sonstegard, T.S., Wiggans, G.R., Van Eenennaam, A., Weber, K., Penedo, M., Berry, D.P., Flynn, J., Garcia, J., Santana Do Carmo, A., Regitano, L., Albuquerque, M., Silva, M.V., Machado, M.A., Coffey, M., Moore, K., Boscher, M., Genestout, L., Mazza, R., Taylor, J.F., Schnabel, R., Simpson, B., Marques, E., Mc Ewan, J., Cromie, A., Lehmann Coutinho, L., Kuehn, L.A., Keele, J.W., Piper, E., Cook, J., Williams, R., Hap Map Consortium, B., Van Tassell, C.P. 2013. Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds. Frontiers in Genetics. 4:176. DOI.10.3389/fgene.2013.00176.
Melters, D.P., Bradnan, K., Young, H., Telis, N., May, M., Ruby, G.J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan-Simon, W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. doi:10.1186/gb-2013-14-1-r10.
Rohrer, G.A., Rempel, L.A., Miles, J.R., Keele, J.W., Wiedmann, R.T., Vallet, J.L. 2014. Identifying genetic loci controlling neonatal passive transfer of immunity using a hybrid genotyping strategy. Animal Genetics. 45(3):340-349.
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Smith, T.P.L., Pollak, E.J., Cole, J.B., Keele, J.W. 2014. Genomewide association study of reproductive efficiency in female cattle. Journal of Animal Science. 92(5):1945-1957.