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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Research Project #423564

Research Project: Understanding Genetic and Physiological Factors Affecting Nutrient Use Efficiency of Dairy Cattle

Location: Animal Genomics and Improvement Laboratory

2014 Annual Report


1a. Objectives (from AD-416):
The overall goal of this research is to identify and elucidate genetic and physiological factors that influence the efficiency of nutrient use in dairy cattle in order to reduce feed costs and nutrient losses associated with milk production. These goals will be attained through a multidisciplinary approach that employs genomics, nutrition, physiology, and molecular and cell biology. Objective 1. Evaluate residual feed intake (RFI), or other measures of nutrient use efficiency, as a measurement and selectable trait for feed efficiency in dairy heifers and lactating dairy cattle and identify and characterize genetic and physiological factors contributing to its variation. Determine the relationship between measures of nutrient use efficiency in dairy heifers and subsequent nutrient use efficiency as lactating cows; including the evaluation of selection for improved nutrient use efficiency during heifer development on reproduction, lactation performance, stayability, health and milk traits in the lactating cow for potential development of estimated breeding values. Sub-objective 1.A. Expand our existing dairy efficiency database for characterizing RFI and factors contributing to its variation. Sub-objective 1.B. Characterize the relationship between RFI during growth in dairy heifers and subsequent RFI during lactation. Sub-objective 1.C. Examine genetic variation in high- and low-RFI dairy cattle to identify putative physiological pathways contributing to its variation among cows. Objective 2. Determine the relationships between ruminal microbial communities, animal genotype, and/or methane production with feed/nutrient use efficiency and/or lactation performance in response to varying nutritional regimens in beef or dairy cattle. Objective 3. Estimate intestinal growth response to post-ruminal delivery of nutrients; and effects of diet composition, intake level, passage rate, and related factors in individual dairy cows to determine regulation and impacts on overall animal energetic efficiency. Sub-objective 3.A. Evaluate the intestinal and ruminal epithelial tissue responses to short-term (14-d) luminal infusions of partially hydrolyzed starch introduced ruminally or post ruminally. Sub-objective 3.B. Assess differences in the relative contribution of visceral organs to total body composition in cows exhibiting divergent efficiencies for milk production as determined by RFI.


1b. Approach (from AD-416):
To identify and characterize factors affecting nutrient use efficiency in dairy cattle, an existing dairy efficiency database will be expanded for characterizing RFI and factors contributing to its variation. In addition, the relationship between RFI during growth in dairy heifers and subsequent RFI during lactation will be characterized, and genetic variation including genome-wide single nucleotide polymorphisms and gene copy number variations in high- and low-RFI dairy cattle will be examined. The contributing role of visceral organs and total body composition to differences among cows in efficiency (RFI) for milk production also will be examined in a slaughter study. Changes in rumen microbial populations in response to feed additives designed to alter volatile fatty acid production in the rumen will be characterized using metagenomics approaches, and impacts on nutrient use efficiency will be examined. Using transcriptomics, the impact of site of nutrient delivery on intestinal and ruminal epithelial tissue growth and metabolism will be evaluated, as well as histone modification and gene expression in rumen epithelium of dry dairy cows in response to elevated rumen butyrate concentrations. Finally, the effectiveness of a therapteutic peptide to improve nutrient absorption in the gut of pre-weaned dairy calves will be assessed.


3. Progress Report:
Relative to Objective 1, Holstein dairy heifers (n = 49) from the Beltsville Agricultural Research Center (BARC) dairy herd were evaluated for growth rate and feed intake to estimate their net feed efficiency (measured as residual feed intake or RFI) during growth from 10 to 14 months of age. Genomic DNA was isolated from all heifers for use in high-density genotyping using single nucleotide polymorphisms to examine relationships between feed efficiency and genotype. Heifers from last year’s trial also began calving in February and are being evaluated for feed efficiency (RFI) during the first 100 days of lactation. Comparisons will be made between RFI measured during growth and RFI during lactation to determine whether feed efficiency measured during growth can be used as a proxy for feed efficiency measured during milk production. Measurements of RFI during lactation also continued on all lactating cows in the BARC dairy herd to expand our existing dairy efficiency database for characterizing RFI and factors contributing to its variation. The database is being shared with national and international Collaborators to further characterize feed efficiency traits in lactating dairy cows and to develop genetic markers for selection for improved feed efficiency in dairy cattle. Relative to Objective 2, a study was conducted wherein volatile fatty acids were measured, including butyrate and propionate, from rumen samples taken during two probiotic feeding trials in dairy cows. A total of 70 rumen microbiome samples from these trials were sequenced. Over 200,000 paired-end raw sequence reads of the 16S rRNA gene were generated per sample. Approximately 96% of these raw reads passed various quality control parameters using the FastQC algorithm. The resultant quality reads from the pair-end sequences were merged to form contiguous sequences, which are being analyzed to understand the changes in the structure of the rumen microbiome induced by probiotic feeding using the RDP Classifier and two operational taxonomic unit-calling algorithms named CD-HIT-OTU and CROP. In addition, long (500 to 600 base pair) shotgun sequences with more than 50X genome coverage of a probiotic strain (P. freudenreichii strain P169) were generated. The probiotic dynamics (decay, clearance, and fate) in the bovine rumen are being verified using real-time PCR. This work will assist in understanding the impact of probiotics on the native gut microbiota of dairy cows and will facilitate the development of optimal strategies for the administration and delivery of probiotics to enhance nutrient use efficiency in lactating dairy cows. Relative to Objective 3, a total of 12 dairy cows to date that were divergently selected for feed efficiency based on RFI estimated in the first and second lactations were slaughtered for total body composition analysis. It is anticipated that the analysis of a total of 16 cows (8 high efficiency, 8 low efficiency) will be completed by late October 2014. Initial results suggest that cows with low feed efficiency exhibit greater liver, rumen, and small intestine weights, and have longer small intestines, which may contribute to greater maintenance requirements and poorer metabolic efficiency among these cows. Additionally, cows evaluated for RFI during the first 100 days of lactation under Objective 1 of the project are being evaluated for immune cell function using two separate in vitro assays. Results will be used to determine whether differences in RFI among cows can be attributed to differences in their ability to illicit an immune response to an infection. Also relative to Objective 3, a total of 10 fistulated Holstein cows were used in an experiment to assess the changes in rumen epithelial cell gene expression that occur during the normal management cycle in lactating dairy cows to gain a better understanding of molecular mechanisms involved in rumen tissue growth during early lactation. Rumen tissues from eight cows to date have been biopsied at -14, 0, 14, 28 and 45 days relative to calving. Corresponding samples of rumen fluid were collected for analysis of rumen microbial population fluctuations and rumen conditions (such as pH and volatile fatty acid concentrations) that occur during this stage of lactation. This work is complementary to an upcoming experiment that will evaluate how specific changes in nutrient delivery to the rumen affect gene expression changes in rumen tissue. Because growth of visceral organs can increase maintenance energy requirements associated with milk production and, therefore, impacts cow feed efficiency, this research will help to determine the extent to which physiological state or nutrient delivery is responsible for changes in visceral organ mass during lactation.


4. Accomplishments
1. Creation of the first chromatin epigenomic landscape map for a livestock species. Epigenomics is the study of the complex mechanisms regulating how, when, and where genes are expressed in cells to ensure their normal development, function, and homeostasis. Butyrate is an important nutrient that induces changes in growth, proliferation, and energy metabolism of cattle cells, and serves as an excellent model of epigenetic regulation. An epigenomic landscape map was created using chromatin immunoprecipitation and next-generation sequencing technologies (ChIP-seq), which is the first and most extensive epigenomic study in cattle cells. It offers a new framework and resource for testing the role of epigenomes in cell function and the regulation of gene transcription in mammalian cells.

2. Identification of tumor protein p53 (TP53) as a key regulator of butyrate-induced epigenomic regulation in cattle cells. Butyrate is a nutrient known to affect cell proliferation, differentiation, and motility. It also inhibits activities of specific cellular factors (histone deacetylases) to arrest cell division and induce programmed cell death. A study of the transcriptome of cattle cells responding to butyrate treatment was conducted using next-generation sequencing and bioinformatic data mining technologies, which identified TP53 as one of the most active regulators of the gene transcription changes induced. Nine additional transcription factors were identified that are involved in TP53 signaling pathways. These findings provide basic knowledge of the molecular mechanisms underlying epigenomic regulation in animal cells.


Review Publications
Yong-Zhen, H., Li, M., Wang, J., Womack, J.E., Sun, J., Li, C., Lan, X., Lei, C., Zhang, C., Chen, H. 2013. A 5'-regulatory region and two coding region polymorphisms modulate promoter activity and gene expression of the growth suppressor gene ZBED6 in cattle. PLoS One. 8(11):e79744.doi:10.1371/journal.pone.007974, 2013.

Zhang, L., Yang, M., Li, C., Xu, Y., Jia, S., Sun, J., Lan, X., Lei, C., Chen, H. 2013. Identification and genetic effect of a variable duplication in the promoter region of the cattle ADIPOQ gene. Animal Genetics. 45:171-179. DOI.10.1111/age.12112.

Li, C., Li, R.W., Baldwin, R.L., Elsasser, T.H. 2014. Butyrate: A dietary inhibitor of histone deacetylases and an epigenetic regulator. Butyrate: Food Sources, Functions and Health Benefits. New York, NY:Nova Science Publishers. p.233-258.

Young-Zhen, H., Liangzhi, Z., Xin-Sheng, L., Yu-Jia, S., Li, C., Xian-Yong, L., Chu-Zhao, L., Chun-Lei, Z., Xin, Z., Hong, C. 2014. Transcription factor ZBED6 mediates IGF2 gene expression by regulating promoter activity and DNA methylation in myoblasts. Scientific Reports. 4:4570. DOI:10.1038/srep04570.

Baldwin, R.L., Zhang, A., Fultz, S., Abubeker, S.U., Harris, C., Connor, E.E., Van Hekken, D.L. 2014. Hot Topic: Brown marmorated stink bug odor compounds do not transfer into milk by feeding bug-contaminated corn silage to lactating dairy cattle. Journal of Dairy Science. 97:1877-1884.

Connor, E.E., Baldwin, R.L., Walker, M.P., Ellis, S., Li, C., Kahl, S., Chung, H., Li, R.W. 2014. Transcriptional regulators transforming growth factor-beta 1 and estrogen-related receptor-alpha identified as putative mediators of calf rumen epithelial tissue development and function during weaning. Journal of Dairy Science. 97:4193-4207.

Li, C., Li, R.W. 2014. Bioinformatic dissecting of TP53 regulation pathway underlying butyrate-induced histone modification in epigenetic regulation. Genetics and Epigenetics. Doi: 10.4137/GEG.S14176.