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United States Department of Agriculture

Agricultural Research Service

2012 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:
Progress was made on all objectives over the life of the project. Products of the research included animal and genomic resources for identifying genes and physiological processes controlling feed efficiency, methods to assess changes in rumen microbial populations, and basic scientific information on biochemical pathways affecting nutrient metabolism, and nutritional epigenetics. Results will be useful for improving animal management and selection to promote nutrient uptake and greater feed efficiency in dairy cattle. Progress continued on resource development for assessing feed efficiency (as residual feed intake) in dairy cows during early lactation. We continue to evaluate relationships between feed efficiency and traits such as feeding behavior, body condition, and somatic cell count, as well as optimal test duration to assess feed efficiency. We are expanding our capability to measure feed intake in growing heifers to assess relationships between efficiency for growth and subsequent efficiency for milk production. This work will address objectives for renewal of the current project plan. A study was completed to evaluate use of a gut hormone called GLP-2 to improve nutrient absorption and reduce intestinal cell damage in calves with scours using a parasite infection model. The hormone has been used successfully to improve gut function and nutrient uptake in humans with Crohn’s disease. Preliminary results indicated that GLP-2 may improve nutrient absorption and increase proliferation of cells lining certain regions of the gut, but did not appear to improve absorptive capacity of the gut based on histological assessment of gut morphology. Genes and pathways affected by weaning were characterized in the calf rumen using a whole-genome bovine microarray. Results will provide molecular markers of rumen development during weaning, as well as identify potential gene networks regulating differentiation and growth of the rumen epithelium to aid in developing methods to improve rumen development and function in the growing calf. Bioinformatic tools for metagenomic data analysis were used to evaluate our ability to change the rumen microbial population of dairy cows in response to a dietary treatment (butyrate infusion). Results showed strong resiliency of the rumen microbial ecosystem in that stimulated butyrate-producing bacterial populations were detected only during infusion, but returned to pre-disturbed status when infusion was discontinued. The work supports objectives for renewal of the current project plan to alter rumen microbial populations through feed additives. As a follow-up to a request of the ONP, impacts of the Brown Marmorated Stink Bug (BMSB) on silage quality were evaluated at local farms with high and low BMSB presence in collaboration with University and ARS scientists. There was concern about carryover of malodorous compounds from BMBS to silage, causing feed aversion among cows. Results indicated no contamination by the odor-associated compound of BMBS in either field or mini-silo silage experiments following fermentation. Thus, it appears that the BMSB is not a major concern for dairy production.

1. Identified the regulatory effects of butyrate on gene expression of bovine cells. Butyrate is a major dietary energy source for cattle. Additionally, butyrate is known to have anti-cancer and anti-inflammatory properties in mammalian cells. To characterize the regulatory effects of butyrate on gene expression in bovine cells, studies of butyrate treatment were conducted in both live cows and in vitro. Butyrate was administered into the rumen (the first compartment of the stomach) of cows and cells lining the rumen were isolated by biopsy for gene expression profiling. From this study, over 200,000 potential mRNA splicing junctions and over 2,800 exon skipping events were detected, which could influence gene expression and function. For instance, 7 genes were found to have exon skipping events and exhibited changes in expression level in response to butyrate treatment. In addition, over 200 genes having multiple isoforms were shown to be differentially regulated by butyrate. Similar work was also done in the Madin-Darby bovine kidney cell line to examine the effects of butyrate treatment on gene expression through acetylation of histone proteins on DNA. The results provide insight into specific molecular mechanisms by which butyrate controls gene transcription and function. This information is useful for understanding the effects of butyrate on cell growth and physiology at the DNA level, including its anti-cancer and anti-inflammatory properties, and will guide future efforts to exploit the beneficial effects of butyrate on animal well-being and human health.

2. Developed and validated bioinformatic pipelines and toolkits for metagenomic data analysis and interpretation. Tools are needed to understand the functions and metabolic potentials of microbial ecosystems in the rumen of cattle from metagenomic data. Using “next-generation” DNA sequencing technologies and newly developed bioinformatic pipelines, the diversity and population dynamics of microbes in the rumen of newborn calves during development and during dietary manipulation in mature dairy cows and beef steers were systematically surveyed. Collectively, 21 phyla, 31 classes, 93 families, 219 genera, and at least 1,079 operational taxonomic units in the rumen of these animals were identified. It was determined that the core rumen microbiome, regardless of the rumen developmental status or breed, consists of 8 phyla, 11 classes, 15 families, and 17 genera. The bacterial communities in the rumen of pre-ruminant dairy calves, dairy cows, and beef steers also were clearly distinguishable. For instance, greater abundance of Fibrobacteraceae and Ruminococaceae in the rumen of beef steers were demonstrated, which may be associated with differences in their diet from newborn calves and dairy cows, and likely reflect the need for enhanced fiber-digesting capacity in beef cattle. Results of this work are important for analysis of metagenomic data and understanding changes in rumen microbial populations of cattle during rumen development and in response to dietary changes. A better understanding of the rumen microbiome will assist in optimizing cattle diets to promote feed efficiency.

3. Exploited an established dairy cattle feed efficiency database to examine mechanisms contributing to differences in feed efficiency among lactating dairy cattle. During the 5-year life of the current project, a database was established containing over 450 lactations of Holstein dairy cows for milk production, feed intake, feeding behavior, and other production measures, along with corresponding DNA samples from over 300 cows to date. Using this resource, relationships between a measure of feed efficiency called residual feed intake and structural variation in the genome (gene copy number variation) of these animals were examined. The results suggested that more efficient cows may have a reduction in their immune function relative to less efficient cows, whereas less efficient cows may have a greater capacity for organ and bone development. This work is important for identifying potential mechanisms contributing to differences in feed efficiency among dairy cattle and enable animal selection or management practices that optimize both production efficiency and animal health.

4. Demonstrated that alteration of form and site of nutrient delivery to cattle affects gene expression in muscle. Nutritional management to enhance the rate of gain and carcass quality of cattle impacts animal nutrient use efficiency and may reduce nutrient losses to the environment. A study was completed in beef steers that examined tissue growth and development at the gene transcript level. Beef steers were infused at two separate locations within the digestive tract (into the rumen or post-ruminally into the glandular stomach) with specific nutrients known to result in different protein accretion rates in growing cattle. Samples of multiple tissues were collected for analysis of gene expression using “next-generation” DNA sequencing technologies. In particular, it was found that specific nutrients can cause functional changes in gene expression of economically important tissues (muscle and intramuscular fat), including those involved in fat metabolism. Results of this basic research provide an understanding of how specific dietary components influence muscle and fat development and will be used to optimize cattle diets to promote feed efficiency.

Review Publications
Sitao, W., Li, R.W., Li, W., Li, C. 2012. Transcriptome characterization by deep-RNA-sequencing underlies the mechanisms of butyrate-induced epigenomic regulation in bovine cells. PLoS One. DOI:10.1371/journal.pone.0036940.

Heon Shin, J., Li, R.W., Gao, Y., Baldwin, R.L., Li, C. 2012. Genome-wide ChIP-seq mapping and analysis of butyrate-induced H3K9 and H3K27 acetylation and epigenomic landscape alteration in bovine cells. Functional and Integrative Genomics. 12(1):119-130.

Li, C., Li, R.W., Elsasser, T.H. 2012. Nutrients and Epigenetics in Bovine Cells. In: Hasan Khatib, Editors. Nutrients and Epigenetics in Bovine Cells. In: Hasan Khatib, Editor. Livestock Epigenetics. New York, NY. Nova Science Publishers. p. 161-177.

Li, R.W., Wu, S., Li, W., Baldwin, R.L., Li, C. 2012. Perturbation dynamics of the rumen microbiota in response to exogenous butyrate. Public Library of Science Biology. 7(1):e29392. DOI:10.1371/journal.pone.0029392.

Baldwin, R.L., Wu, S., Li, W., Li, C., Bequette, B.J., Li, R.W. 2012. Quantification of transcriptome responses of the rumen epithelium to butyrate infusion. Gene Regulation and Systems Biology. 6:67–80.

Connor, E.E., Hutchison, J.L., Olson, K.M., Norman, H.D. 2011. Opportunities for improving milk production efficiency in dairy cattle. Journal of Animal Science. 90:1687–1694.

Li, R.W., Connor, E.E., Li, C., Baldwin, R.L., Sparks, M. 2011. Characterization of the rumen microbiota in pre-ruminant calves using metagenomic tools. Environmental Microbiology. 14(1):129-139.

Connor, E.E., Hutchison, J.L., Norman, H.D. 2012. Estimating feed efficiency of lactating dairy cattle using residual feed intake. In: Hill, R.A., editors. Feed Efficiency in the Beef Industry. Wiley-Blackwell, NJ. Chapter 11.

Baldwin, R.L., Li, R.W., Li, C., Song, J., Bequette, B.J. 2012. Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers. Physiological Genomics. 44:543-550. DOI:10.1152/physiolgenomics.

Li, C., Li, R.W., Elsasser, T.H., Kahl, S. 2011. Alpha-Tocopherol alters transcription activities that modulate tumor necrosis factor alpha (TNF-a)-induced inflammatory response in bovine cells. Gene Regulation and Systems Biology. 6:1-14.

Zhao, Tian, Yu, Luo, Hu, Bequette, Baldwin, R.L., Liu, G., Zan, Updike, Song 2012. Muscle Transcriptomic Analyses in Angus Cattle with Divergent Tenderness. Molecular Biology Reports. 39(4):4185-93.

Wu, S., Baldwin, R.L., Li, W., Li, C., Connor, E.E., Li, R.W. 2012. The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA genes. Metagenomics. 1:11. DOI:10.4303/mg/235571.

Last Modified: 4/19/2014
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