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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

2017 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:
This is the final report for the Project 8042-31320-077-00D which will end July 25, 2017. New NP101 PrePlan entitled “Improving Feed Efficiency and Environmental Sustainability of Dairy Cattle through Genomics and Novel Technologies” is currently being reviewed. Substantial accomplishments related to each objective were made over the 5 years of the project. Relative to Objective 1, a dairy cow feed efficiency phenotype and genotype database was created to support genomic selection studies. Specifically, high-density genotypes and multiple production measurements needed to estimate feed efficiency were collected from cows during growth and lactation in the ARS Beltsville, Maryland, Holstein dairy herd beginning in 2008. The database contains feed efficiency estimates measured during the first 100 days of lactation on over 995 lactations (>615 individual cows), phenotypes on 108 cows collected during a full 305-day lactation, feed efficiency data measured during growth of >195 dairy heifers (from 10 to 14 months of age), and enteric methane emissions of >70 growing dairy heifers. High-density genotypes (consisting of over 770,000 SNP markers) are available on 96% of the cows in the database, as well as daily feeding behaviors such as time spent feeding per day, number of meals per day, and feeding rate. This database has been used by numerous collaborators and in 2 multi-million dollar grant projects with domestic and international partners to characterize the genetics of feed efficiency traits in dairy cattle (e.g., heritability and repeatability), study physiological and genetic factors contributing to variation in feed efficiency, and develop novel statistical methods to model genetic merit of feed efficiency in dairy cattle. Results of this work will assist in the creation of tools to select for more feed efficiency and lower methane emitting dairy cattle through genomics. Relative to Objective 2, a novel therapy was developed to improve gut health in newborn dairy calves because diarrhea can cause intestinal damage, reduce nutrient uptake and animal growth rate, and have long-term negative effects on animal production, such as reduced future milk production and lower milk quality. An experimental parasite infection model was used to evaluate a naturally occurring gut hormone, called glucagon-like peptide 2 (or GLP-2), as a therapy to improve nutrient uptake and reduce intestinal damage caused by diarrhea in newborn Holstein calves. The results suggested that pharmacological use of GLP-2 in dairy calves can reduce intestinal damage associated with diarrhea, which could improve their subsequent milk production and performance later in life. Practical strategies for stimulating natural GLP-2 secretion in calves to gain beneficial gut health effects also were investigated. These studies showed that feeding of milk replacer supplemented with an artificial sweetener could help protect the gut from coccidiosis, likely by activating intestinal sweet taste receptors and stimulating intestinal GLP-2 release. Also relative to Objective 2, genetic regulators of rumen development of calves at weaning were identified. During weaning, the calf’s digestive tract must transition from a pre-ruminant state to one based on the uptake of volatile fatty acids (e.g., butyrate) produced during fermentation by the newly established rumen microbes. Proper development and function of the rumen is critical for efficient nutrient uptake and use by the animal. During this transitional period, the rumen undergoes a substantial increase in size, nearly doubling its capacity. Thus development of the rumen significantly impacts the net efficiency of feed conversion in growing cattle. Global gene expression profiles were determined at different stages of development and under different dietary treatments to identify and characterize genes and gene networks affected by weaning in the calf rumen. A total of 971 genes that respond to weaning were identified in the calf rumen. The primary functions of these genes were related to free-radical scavenging and molecular transport. The top molecular networks identified were those participating in fat metabolism, cell morphology and cell death, cellular growth and cell division, molecular transport, and the cell cycle. The work further identified two key regulators of gene expression (transforming growth factor-ß1 and estrogen-related receptor-a) affecting development of cells that line the rumen and energy metabolism. Results of these analyses provide molecular markers that can be used by animal scientists to study rumen development, as well as identify possible gene networks regulating differentiation and growth of the rumen tissue. This knowledge will aid in creating new ways to improve rumen development and function, particularly in the growing calf. Finally related to Objective 2, interactions between dietary nutrients and the genome were characterized and the first chromatin epigenomic landscape map was created for a livestock species. Epigenomics is an area of scientific investigation that determines how, when, and where gene expression occurs within the animal cell to ensure normal development, health, and stability. Deep RNA sequencing technology was used to generate novel genetic information related to gene transcription in cow cells induced by the short-chain fatty acid butyrate, an important nutrient for cattle derived from dietary fiber during microbial fermentation in the rumen. Tumor protein p53 (TP53) was identified as one of the most active regulators of the gene transcription changes induced by butyrate. Nine additional transcription factors were identified that are involved in TP53 signaling pathways. This information can be used to gain a deeper understanding of the bovine genome and transcriptome, and epigenetic regulation induced by butyrate in cells of cattle. Knowledge gained will be used to optimize animal diets that enhance rumen development and animal health, ultimately improving overall production efficiency. 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. Relative to Objective 3, critical factors affecting nitrogen use in the rumen and whole-body nutrient efficiency of dairy cattle were determined. Nitrogen (N) is a critical nutrient to support milk production. The mechanisms regulating movements of N into and out of the rumen are complex and multiple factors determine the net capture of recycled urea-N. Butyrate is a short-chain fatty acid produced in the rumen as an end product of feed degradation and has many apparent beneficial impacts on N and whole-body nutrient use. For example, butyrate affects gene transcription, cellular function, and rumen development, and therefore, may be important in regulating nutrient use efficiency in mature cattle. The effects of increasing ruminal butyrate on urea-N recycling, overall N use, and rumen tissue protein turnover rate were studied using a direct rumen infusion model in sheep. Results showed that butyrate alters urea-N flux in the rumen by substantially increasing the rate of protein synthesis occurring in epithelial cells of the rumen. To understand the regulatory mechanisms in lactating and dry dairy cows, a direct ruminal-infusion approach was combined with serial rumen epithelial tissue biopsy. Two critical transcription factors regulating gene networks (CREBBBP and TTF2) affecting major macro-molecular components like claudins, tight-junction proteins, and adhesion molecules were identified, as well as transporters and enzymes known to affect short-chain fatty acid metabolism. These findings provide animal scientists with molecular markers and targets to control differentiation and growth of the rumen tissue to improve rumen function and whole-cow nutrient use efficiency.


4. Accomplishments
1. Identified candidate genes controlling feed efficiency of dairy cattle. Improving feed conversion to milk and meat is important for economic and environmental sustainability of the dairy industry. Feeding costs represent up to 60 percent of total production costs for Dairy farmers while inefficient digestion results in losses of nutrients to the environment; further, feed conversion efficiency is controlled, in part, by genetics but the underlying genes affecting the trait remain unclear. In a collaborative project led by Iowa State University, researchers from ARS, Beltsville, Maryland, universities in the U.S., Canada, the Netherlands, and United Kingdom examined relationships between genetic markers across the cattle genome and dairy production traits of feed conversion efficiency, body weight, feed intake, and milk production. Most notably, a candidate gene controlling feed efficiency was identified, named ADRB3, which functions in body fat mobilization and the production of body heat. A second candidate gene regulating feed efficiency and feed intake was identified, named leptin, which functions in regulation of appetite and body fat reserves. Results of this work provide insights into factors controlling economically important traits of dairy cattle and provide potential targets for genetic improvement in our dairy cattle populations.

2. Identified potential mechanisms affecting differences in feed intake and feed efficiency of dairy cows using novel genetic markers. Improving feed conversion to milk and meat is important for economic and environmental sustainability of the dairy industry and several types of genetic markers may be used to discover regions of the genome that control production traits, such as feed efficiency, of interest. One type of marker is based on large repeated regions of the genome called copy number variants, or CNV. These regions can vary from one cow to another and may contribute to differences in their production performance, such as milk yield, feed intake, or feed efficiency. ARS researchers from Beltsville, Maryland, identified CNV markers across the cattle genome and studied their association with 10 economically important production traits of dairy cows. Regions of the genome that harbor multiple proteins affecting perceptions of odor (olfactory receptors) and appetite were identified that may impact feed intake and feed efficiency of dairy cows. These results suggest that olfactory receptors may play a role in appetite regulation of dairy cows and provide potential novel targets for manipulating feed intake-related traits of livestock.

3. Identified a set of genes in the rumen epithelium of dairy cattle that are consistently expressed and can serve as a reference or basis to study other genes in molecular biology studies. Investigations into the molecular and genetic aspects of feed efficiency are needed to develop management strategies and selective tools for enhancing nutrient use efficiency by dairy cattle. The rumen is a forestomach in the digestive tract of the dairy cow and other ruminants like sheep and goats. The rumen plays a vital and unique role in cattle health and productivity. ARS researchers from Beltsville, Maryland, identified six genes that are present at constant levels in the rumen of dairy cows across an array of physiological and nutritional states. This enables their use as excellent reference genes or internal controls to enable comparative study of gene expression throughout the production cycle of dairy cows. These results provide necessary molecular biology tools for future research efforts seeking to understand the complex control of rumen development and differentiation in response to management and nutritional changes.


Review Publications
Li, C. 2016. Flow cytometry analysis of cell cycle and specific cell synchronization with butyrate. Methods in Molecular Biology. 1524:149-159.

Lu, Y., Vandehaar, M.J., Spurlock, D.M., Weigel, K.A., Armentano, L.E., Staples, C.R., Connor, E.E., Wang, Z., Coffey, M., Veerkamp, R.F., De Haas, Y., Tempelman, R.J. 2017. Modeling genetic and non-genetic variation of feed efficiency and its partial relationships between component traits as a function of management and environmental factors. Journal of Dairy Science. 100(1):412-427.

Yao, C., De Los Campos, G., Vandehaar, M.J., Spurlock, D.M., Armentano, L.E., Coffey, M., De Haas, Y., Veerkamp, R.F., Staples, C.R., Connor, E.E., Wang, Z., Hanigan, M.D., Tempelman, R.J., Weigel, K. 2017. Use of genotype x environment interaction model to accommodate genetic heterogeneity for residual feed intake, dry matter intake, net energy in milk, and metabolic body weight in dairy cattle. Journal of Dairy Science. 100(3):2007-2016.

Die, J.V., Baldwin, R.L., Rowland, L.J., Li, R.W., Oh, S., Li, C., Connor, E.E., Ranilla, M. 2017. Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium. PLoS One. 12(2):e0172674.

Connor, E.E., Clover, C.M., Wall, E.H., Baldwin, R.L., Santin, M., Elsasser, T.H., Bravo, D. 2016. Glucagon-like peptide 2 and its beneficial effects on gut function and health in production animals. Domestic Animal Endocrinology. 56:S56-S65.

Connor, E.E., Wall, E.H., Bravo, D.M., Clover, C.M., Elsasser, T.H., Baldwin, R.L., Santin, M., Kahl, S., Vinyard, B.T., Walker, M.P. 2017. Reducing gut effects from Cryptosporidium parvum infection in dairy calves through prophylactic glucagon-like peptide 2 therapy or feeding of an artificial sweetener. Journal of Dairy Science. 100(4):3004-3018.