**-  Beltsville  \ BARC 
-  Animal & Natural Resources 
-  Bovine Functional Genomics 
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**Location: Bovine Functional Genomics**
**2008 Annual Report**
**1a.Objectives (from AD-416)**													The overall objectives of the research project are to apply modern genomic tools to the identification and characterization of genetic pathways, physiological mechanisms, and microbial-host interactions that modulate nutrient uptake, partitioning, and loss in cattle. The specific objectives include development of resources for identification of selectable markers of nutrient efficiency, identification and characterization of genetic pathways and/or genomic regions influencing critical regulatory pathways of nutrient efficiency and transport, and development of intervention strategies to enhance nutrient uptake and partitioning in cattle.						
**1b.Approach  (from AD-416)**													To identify and characterize factors affecting nutrient use efficiency in cattle, resources will be developed including a phenotypic database of dairy efficiency and corresponding DNA and tissue collections, methods for live animal intestinal tissue collection suitable for gene expression studies, and sub-populations of dairy cattle to investigate inflammation and nutrient use interactions. Novel DNA sequencing technology will also be evaluated for its utility in characterizing changes in rumen microbial populations during rumen development. Transcript profiling techniques including microarray and quantitative real-time PCR will be used to establish molecular markers of proliferation, development and differentiation of the bovine gastrointestinal tract, and to identify metabolic and hormone pathways controlling nutrient metabolism in the ruminant gastrointestinal tract. Finally, two dietary strategies that potentially affect the rumen microbial population and production efficiency will be studied for their effects on nutrient use efficiency in cattle.						
**3.Progress Report**													Multiple experiments were conducted during FY 2008 to address the three overall project objectives and FY 2008 National Program 101 Components I.a. Develop Genome-Enabling Tools and Reagents, Ib. Identify Functional Genes and their Interactions, I.d. Develop and Implement Genome-Enabled Genetic Improvement Programs, II.a. Enhance Animal Well-Being and Reduce Stress in Livestock and Poultry Production Systems, and II.c. Improving Efficiency of Nutrient Utilization and Conversion to Animal Products. Details of these experiments are provided below under "Accomplishments." In addition, several studies were initiated examining various aspects of nutrient use efficiency in cattle. One of these studies included an in vitro experiment using specific blood cells (peripheral blood mononuclear cells) isolated from cattle to identify gene networks activated during inflammation. In addition, a study in growing bulls was initiated to test the hypothesis that concentrate- versus forage-based diets increase the supply of alternative substrates for visceral energy metabolism and reduce amino acid use by the rumen and intestinal cells. Third, a study in dairy cows was started in collaboration with the University of Maryland to determine the effects of dietary protein concentration and rumen degradability of protein on nitrogen metabolism. Finally, sample collection was completed for a study in dairy calves to characterize gene pathways involved in rumen development and growth, as well as a survey of expression of genes affecting absorptive capacity of the gut during different stages of growth, pregnancy and lactation of dairy cattle. Knowledge gained from these studies will help to identify factors that modulate nutrient availability, uptake, partitioning, and loss in dairy cattle. A better understanding of these processes will assist in the development of intervention strategies to maximize nutrient utilization, and ultimately reduce impacts of cattle production on the environment.						
**4.Accomplishments**									1.																									Establishing metagenomic sequencing of rumen microbial populations of cattle. To identity microbial species present in the rumen of cattle, multiple samples of rumen contents from pre-weaning and late-weaning dairy calves were collected and metagenomic DNA was successfully extracted. Specific protocols and procedures were optimized in the laboratory for these processes. A pilot study was conducted to develop and optimize protocols for metagenomic sequencing of microbial DNA using a subset of these samples. To date, approximately 1.5 billion base pairs of DNA sequence have been generated and the sequences are being analyzed. This work will improve our understanding of microbial populations in the rumen of cattle, changes in which are thought to have a significant impact on feed efficiency. This project address NP 101 - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources.  Addresses National Program Component I. a) Develop Genome-Enabling Tools and Reagents.													2.																									Identifying diversity and changes in rumen microbe populations in response to diet using a metagenomics approach. A study in dairy calves was completed and samples of rumen contents were collected to identify diversity and changes in the abundance of rumen microbes in response to diet using a metagenomics approach. Primers for real-time qPCR specific for 10 bacterial species involved nitrogen metabolism, including proteolysis and ammonia production and metabolism were designed and validated and will be used to monitor dynamics of these bacteria during rumen development. These data will be compared to the metagenomic sequences obtained using next-generation sequencing technologies. This work will improve understanding of dietary effects on rumen microbial populations and will be used to improve efficiency of nutrient use and conversion to animal products.  This project address NP 101 - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources. Addresses National Program Component II. Enhancing Animal Adaptation, Well-Being and Efficiency in Diverse Production Systems, c) Improving Efficiency of Nutrient Utilization and Conversion to Animal Products.													3.																									Establishing a database to identify markers of feed efficiency in dairy cattle. Information on feed intake and feed efficiency in dairy cattle is extremely limited. Use of a radio-frequency identification-based system to automatically monitor feeding activity and record daily feed intake of individual lactating dairy cows was implemented at the Beltsville Dairy Facility in July 2007. The system continuously monitors intake of approximately 40 cows at a time. To date, approximately 120 cows have been evaluated during the first 90 days of their lactation. DNA samples from these animals were collected and archived for future analysis of genetic markers. Other measures including milk production and composition, body weight and type traits were collected and will be used to assess feed efficiency in these animals. Transfer of data and collection of DNA from a crossbred dairy herd at Virginia Tech, Blacksburg, VA as part of a collaborative study was also completed. These data will be used to develop genetic markers of feed efficiency in dairy cattle.  This project address NP 101 - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources.  Addresses National Program Component I. d) Develop and Implement Genome-Enabled Genetic Improvement Programs.													4.																									Identifying genetic mechanisms associated with improved feed efficiency in cattle. Genetic markers of feed efficiency in cattle are needed to improve selection for this trait. A study was completed in growing steers to identify changes in gene expression associated with increased feed conversion. A microarray approach was used to examine gene expression changes in the liver of growing steers during feed restriction and compensatory weight gain. Gene pathways up regulated during improved feed efficiency included those regulating cellular metabolism, cholesterol biosynthesis, electron transporter activity in the mitochondria, regulation of RNA processing and translation, and lipid metabolism. Mitochondrial complex genes will be targets of additional study because these genes have been associated with increased feed efficiency in poultry and cattle, and with quantitative trait loci for feed efficiency in cattle.  This project address NP 101 - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources. Addresses National Program Component I. b) Identify Functional Genes and their Interactions.													5.																									Establishing methods for culturing primary rumen epithelial cells of cattle. Methods are needed for culturing rumen epithelium for in vitro studies of their function and metabolism. A procedure was developed to successfully isolate and culture primary ruminal epithelial cells from calf rumen. These cells will be used to identify genes mediating proliferation, development and differentiation of the functional rumen and used to establish molecular markers of these processes.  This project address NP 101 - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources. Addresses National Program Component I. b) Identify Functional Genes and their Interactions.													6.																									Characterizing metabolic flux during intestinal development of cattle. Management techniques are needed to improve nutrient uptake and efficient use by cattle. Metabolic flux of specific nutrients was evaluated in two critical intestinal cell types which were isolated from cattle fed diets that alter intestinal development. Partial conversion of glucose to lactate in these cells was shown to play a potential role in preserving 3-carbon units for carbon recycling. Increasing the supply of the amino acid glutamine to these cell types also increased its flux to Krebs cycle intermediates and reduced the use of nutrients from other substrates. This project address NP 101 - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources. Addresses National Program Component II. Enhancing Animal Adaptation, Well-Being and Efficiency in Diverse Production Systems, c) Improving Efficiency of Nutrient Utilization and Conversion to Animal Products.													7.																									Identifying genetic markers for susceptibility to severe inflammation in cattle. Evidence suggests that the outcome of some infections may be associated with plasma levels of the cytokine TNF-a during disease and predicted by variations in the TNF-a gene of humans. A preliminary study was completed to determine whether similar polymorphisms exist in cattle and whether they are associated with response to an immune challenge. Results indicated that variation in the TNF-a gene of cattle may play a role in the intensity of TNF-a response to an immune challenge, as well as susceptibility and recovery from immune stress. These markers may be useful for identifying animals with a greater susceptibility to disease-related stress. This project address NP 101 - Understanding, Improving, and Effectively Using Animal Genetic and Genomic Resources.  Addresses National Program Component II. Enhancing Animal Adaptation, Well-Being and Efficiency in Diverse Production Systems, c) Improving Efficiency of Nutrient Utilization and Conversion to Animal Products.							**5.Significant Activities that Support Special Target Populations**													None						
**6.Technology Transfer****Review Publications***Li, C., Li, R.W. 2008. Butyrate Induced Cell Cycle Arrest in Bovine Cells through Targeting Gene Expression relevance to DNA Replication Apparatus. Gene Regulation and Systems Biology. 2:113-123.**Elsasser, T.H., Caperna, T.J., Li, C.J., Kahl, S., Sartin, J.L. 2008. Critical control points in the impact of the proinflammatory immune response on growth and metabolism. Journal of Animal Science. 86(E. Suppl):E105-E 125.**Farran, T.B., Reinhardt, C.D., Blasi, D.A., Minton, J.E., Elsasser, T.H., Higgins, J.J., Drouillard, J.S. 2008. Source of dietary lipid may modify the immune response in stressed feeder cattle. Journal of Animal Science. 86:1382-1394.**Li, R.W., Li, C. 2008. Effects of butyrate on the expression of insulin-like growth factor binding proteins in bovine kidney epithelial cells. The Open Veterinary Science Journal. 2:1-6.*    Project TeamConnor, Erin Baldwin, Ransom Li, Congjun Li, Robert  
Project Annual Reports FY 2008 Publications  Publications 
Related National Programs Food Animal Production(101) Related Projects  GENOMIC AND METABOLIC BASES UNDERLYING PROTEIN AND FAT ACCRETION IN CATTLE  							Last Modified: 05/14/2009 		ARS Home |USDA.gov |Site Map |Policies and Links FOIA |Accessibility Statement |Privacy Policy |Nondiscrimination Statement |Information Quality |USA.gov |White House

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