Skip to main content
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

2016 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 therapeutic peptide to improve nutrient absorption in the gut of pre-weaned dairy calves will be assessed.

3. Progress Report:
Relative to Objective 1, evaluation of Holstein dairy heifers from the Beltsville Agricultural Research Center (BARC) herd for feed intake and growth rate continued in order to assess individual heifer net feed efficiency during growth from 10 to 14 months of age. Genomic DNA was isolated from each heifer and analyzed for high-density single nucleotide polymorphism (SNP) genotyping. ARS initiated evaluation of growing heifers for net feed efficiency during their first lactation to determine whether feed conversion efficiency during growth can be used as a proxy for net feed efficiency during lactation. Measurements of feed efficiency during lactation and collection of high-density SNP genotypes also continued on all lactating cows in the BARC herd to expand our existing database for identifying genetic markers/genomic regions associated with improved feed conversion efficiency. Analysis of structural variations in the bovine genome called copy number variations, or CNV, using high-density SNP genotyping of our lactating dairy cows was initiated to determine whether there are CNV associated with feed efficiency traits and the gene pathways involved. Our database, currently consisting of more than 900 lactations (over 550 individuals), is being shared with national and international collaborators to produce genomic predictions for feed efficiency and methane emissions in dairy cattle to apply in future breeding programs, as well as to develop novel phenotypes associated with dairy cow feeding behavior. Two manuscripts were published and 3 manuscripts were submitted for publication based on these data. Relative to Objective 2, the effect of probiotic feeding on the structure and function of the native rumen microbiome in dairy cows was examined using metagenomics and bioinformatics tools. The probiotic strain P169 was present in the rumen at a very low abundance prior to probiotic feeding. After a single oral daily dose of 1.0 x1011 colony-forming units (CFU) of P169 feeding for 2 weeks, the probiotic strain P169 remained low but could be reliably detected using either real-time PCR or high-throughput sequencing. The microbiome data were analyzed using 3 different clustering algorithms, CD-HIT, CROP, and CLC. While the disruption of the native rumen microbiome by the probiotic feeding was minimal, we did detect a novel bacterial species belonging to the family Lachnospiraceae that was significantly increased by the P169 feeding. As common residents of the gut microbial ecosystem of humans and farm animals, certain members of Lachnospiraceae have been implicated in human disease progression. For example, some species belonging to this family possess key enzymes in butyrate biosynthesis pathways and have abilities to produce butyrate, subsequently impacting intestinal health and disease. Thus probiotic strain P169 feeding of dairy cows has potential to modulate the rumen microbiome, possibly leading to the improvement of their gut health and energy metabolism. Also relative to Objective 2, data collection was initiated on carbon dioxide and methane emissions from eructations of individual 10-month-old dairy heifers during 2-week sampling periods using an automated radio-frequency identification-based system called GreenFeed. The data are being used to evaluate the relationship between feed conversion efficiency and methane emissions in growing dairy cattle. The data also are being shared with research partners in Canada, Australia, and the United Kingdom to establish a reference population for genomic analysis and selection for reduced methane emissions. Relative to Objective 3 (Subobjective 3.A.), studies were completed using doubly cannulated dairy cows (ruminal and duodenal) to evaluate site-specific impacts of direct nutrient infusion on intestinal gene expression during non-lactating (dry) and lactating physiological states. Biopsies from ruminal and duodenal epithelial tissues were collected during continuous infusion with either the single volatile fatty acid butyrate, or more complex partially hydrolyzed starch in order to evaluate changes in expression of selected genes associated with intestinal nutrient transport and growth. The work is novel in that multiple sampling of intestinal tissues from a single animal over time has not been reported previously in cattle. Prior research required terminal studies and interpretations of results were difficult due to collection of tissues from different animals over time. Moreover, this research provides the necessary groundwork for the future assessment of other factors for their impacts on intestinal health in mature cattle. Relative to Objective 3 (Subobjective 3.B.), comprehensive sample collection of critical tissues from 16 lactating dairy cows divergently selected on the basis of feed efficiency (measured as residual feed intake during the first and second lactations) and tissue analyses were completed. Initial results suggest that changes in visceral organ mass are contributing to differences in lactating dairy cow feed conversion efficiency due to the high metabolic activity of these tissues. Greater gastro-intestinal and visceral adiposity was observed in less efficient cows.

4. Accomplishments
1. Identified and characterized the biological functions of a unique set of genes induced by butyrate in cattle cells. Butyrate is a nutrient that can alter expression of individual genes through its actions as an inhibitor of enzymes that alter DNA structure and regulate cell division, called DNA histone deacetylases. ARS scientists at Beltsville, Maryland identified a unique group of genes activated by butyrate in cultured cells of cattle using global gene expression profiling, and their functions were characterized to gain insight into the basic molecular mechanisms of how butyrate alters the cellular machinery that controls gene expression. Their analysis indicated that genes activated by butyrate treatment have major functions related to cell structure, cell division, and programmed cell death. The information is useful to cell biologists and those studying the regulation of gene expression and cell division.

2. Identified beneficial effects of vitamin E feeding on dairy cow health. Vitamin E has been shown to be beneficial for reducing damage to the body caused by inflammation. ARS scientists at Beltsville, Maryland fed Vitamin E containing a mixture of 3 forms of tocopherol (alpha, beta, and gamma) in soybean meal to lactating dairy cows. The 3 forms were found to differ in how they were deposited among critical body tissues that support lactation, including the liver, muscle, and mammary gland. Studies of cultured cells showed differences among the 3 forms in their ability to protect cells from disease-induced stress. In particular, the gamma and delta forms when fed to dairy cows as a total mixture of vitamin E for as little as 4 to 5 days reduced organ and cell damage from bacterial disease. The work provides practical means to improve dairy cow health through dietary interventions.

3. Determined that artificial sweetener feeding to dairy calves may reduce gut damage from coccidiosis. Over 50% of early-life calf mortality is due to diarrhea (scours). Cryptosporidium parvum is a coccidian parasite which is among the primary causative factors of this disease, contributing to calf morbidity, impaired nutrient absorption, and poor production performance. ARS scientists at Beltsville, Maryland evaluated whether feeding of an artificial sweetener, which is known to stimulate release of a protective gut hormone called GLP-2, could reduce intestinal damage from a low-grade exposure to the parasite C. parvum compared to calves treated directly with GLP-2 or a control. It was shown that the GLP-2 and artificial sweetener treatments provided minor benefits including reduced diarrhea and fecal shedding of parasite eggs, and improved intestinal health and markers of inflammation. The work provides novel means to reduce the negative effects of diarrhea and its impacts on animal productivity, and to promote gut health in calves.

5. Significant Activities that Support Special Target Populations:

Review Publications
Manzanilla-Pech, C., Veerkamp, R., Tempelman, R., Van Pelt, M., Weigel, K., Vandehaar, M., Lawlor, T., Spurlock, D., Armentano, L., Connor, E.E., Staples, C., Hanigan, M., De Haas, Y. 2016. Genetic parameters between feed-intake-related traits and conformation in 2 separate dairy populations—the Netherlands and United States. Journal of Dairy Science. 99(1):443-457.

Lu, Y., Vandehaar, M.J., Spurlock, D.M., Weigel, K.A., Armentano, L.E., Staples, C.R., Connor, E.E., Wang, Z., Bello, N.M., Tempelman, R.J. 2015. An alternative approach to modeling genetic merit of feed efficiency in dairy cattle. Journal of Dairy Science. 98:6535-6551.

Li, R.W., Li, W., Baldwin, R.L., Yu, P., Urban Jr, J.F. 2016. The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome. Scientific Reports. 6:20606.

Li, C., Li, R.W., Baldwin, R.L., Blomberg, L., Wu, S., Li, W. 2016. Transcriptomic sequencing reveals a set of unique genes activated by butyrate-induced histone modification. Scientific Reports. 10:1-8.

Qian, X., Li, X., O Ilori, T., Klein, J.D., Hughey, R.P., Li, C., Abdel, A.A., Song, X., Chen, G. 2015. RNA-Seq analysis of glycosylation related gene expression in STZ-induced diabetic rat kidney. Frontiers in Physiology. doi: 10.3389/fphys.2015.00274.

Benjamin, A.L., Korkmaz, F.T., Elsasser, T.H., Kerr, D.E. 2016. Neonatal lipopolysaccharide challenge does not diminish the innate immune response to a subsequent lipopolysaccharide challenge in holstein bull calves. Journal of Dairy Science. 99(7):5750-5763.

Garcia, M., Elsasser, T.H., Juengst, L., Qu, Y., Bequette, B., Moyes, K.M. 2016. Short communication: amino acid supplementation and stage of lactation alter apparent utilization of nutrients by blood neutrophils from lactating dairy cows in vitro. Journal of Dairy Science. 99(5):3777-3783.

Garcia, M., Elsasser, T.H., Juengst, J., Qu, Y., Zhu, X., Moyes, K.M. 2015. Glucose supplementation has minimal effects on blood neutrophil functionand gene expression in vitro. Journal of Dairy Science. 98(9):6139-6150.