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United States Department of Agriculture

Agricultural Research Service

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

Location: Animal Genomics and Improvement Laboratory

2013 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) as a measurement and selectable trait for feed efficiency in dairy cattle and identify and characterize genetic and physiological factors contributing to its variation. 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. Investigate changes in rumen microbial populations in response to feed additives designed to alter volatile fatty acid production in the rumen using metagenomics approaches, and evaluate impacts on nutrient use efficiency.

Objective 3. Estimate intestinal growth response to post-ruminal delivery of nutrients (e.g., starch and individual amino acids) in 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. Objective 4. Investigate epigenetic regulation of rumen development and intestinal epithelial cell regeneration in dairy cattle, particularly in cows during the dry period, to identify targets for improving net nutrient absorption. Sub-objective 4.A. Characterize histone modification and gene expression in rumen epithelium of dry dairy cows in response to intra-ruminal butyrate infusion. Sub-objective 4.B. Examine the effectiveness of GLP-2 treatment to improve nutrient absorption in the gut of pre-weaned dairy calves.


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:
This year, ten lactating dairy cows were surgically fitted with cannulae of both the rumen and small intestine to conduct experiments to meet research objectives over the 5-year term of the project. The cows were used for three experimental trials addressing 12- and 24-month project milestones described below. This animal resource will be used in the coming year to assess the effects of dietary manipulations on intestinal growth, which can significantly impact feed efficiency of the animal.

Sample collection was completed for a trial of non-lactating dairy cows examining the effects of increasing the concentrate of rumen butyrate (a primary energy source for the cow), on rumen development and growth. Understanding mechanisms controlling this development is important because the rumen environment plays a central role in nutrient absorption and can impact the cow’s capacity to support the high metabolic demands of milk production. This is particularly important during the period of transition from pregnancy to parturition and lactation. Advanced molecular techniques currently are being used to study the interaction between regulatory proteins and DNA, and gene expression within the rumen cells that were exposed to elevated butyrate. This research will provide insight into nutrient-gene interactions and improve our understanding of factors that are critical for efficient nutrient use by the dairy cow for milk production and sustained health.

Two trials were conducted in cows during early lactation to examine the effects of a probiotic (direct-fed microbial known as Propionibacteria strain P169) on the rumen environment. This feed additive is used widely in the cattle industry to improve production performance. Rumen fluid was collected to evaluate probiotic decay and clearance from the rumen using advanced molecular analysis of rumen microbial DNA. Because the probiotic is expected to influence volatile fatty acid production in the rumen, propionate concentration also was evaluated. A second trial was conducted to evaluate the effect of daily feeding of the same probiotic on milk production and feed efficiency during early lactation, and the effects on structure and function of the native rumen microbial community. These studies will provide novel information on the utility of probiotic feeding to alter rumen microbial populations and improve feed efficiency in lactating dairy cows.

A long-term study was initiated to evaluate feed efficiency (known as residual feed intake) in dairy heifers during growth from 10 to 14 months of age using an automated feed intake monitoring system. The same heifers will be evaluated for feed efficiency during lactation as part of an on-going analysis of residual feed intake in the Beltsville Holstein Dairy Herd. The information gathered will be used to determine whether dairy heifers can be selected for high feed efficiency during growth while maintaining high efficiency for milk production. Improving feed efficiency will reduce environmental impacts and feed costs associated with dairy production, which will increase producer profitability and reduce costs for consumers.


4.Accomplishments
1. Identification of a novel therapy for the treatment of calf diarrhea. Diarrhea can cause intestinal damage, reduce nutrient absorption and animal growth rate, and have long-term negative effects on animal production. For instance, the duration of diarrhea during the first few months of life in a heifer calf can have a significant negative effect on her milk production and milk composition as an adult cow. An experimental infection model with coccidia was used to evaluate the use of glucagon-like peptide 2 (GLP-2), a hormone produced by intestinal cells, as a therapy to improve nutrient uptake and reduce intestinal damage caused by diarrhea in neonatal 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 milk production and performance later in life. Development of practical strategies for administering GLP-2 therapy to calves in a production setting are currently being investigated.

2. Brown marmorated stink bug odor compounds do not represent a risk to milk quality. The brown marmorated stink bug (BMSB), Halyomorpha halys, is an emerging invasive species of grave concern to agriculture. It is a polyphagous plant pest with potential negative impacts on the dairy industry due to possible contamination of milk with offensive odors. To assess the risk of BMSB odor to milk quality through involuntary ingestion of bugs present in feed by dairy cows, synthetic secretory compounds (tridecane and E-2-decenal) found in the metathoracic gland of the BMSB were infused into the rumen of cows and subsequently quantified in milk and body fluids of treated cows. The work demonstrated that odor-causing compounds of BMSB are not able to contaminate milk due to bioremediation during the ensiling process of feeds or through metabolism within the cow’s rumen. Therefore, the results indicate that concern over BMSB stink odor compounds contaminating the fluid milk supply, even on highly infested farms, is not warranted.

3. Identification of genetic mechanisms controlling rumen development of calves at weaning. During weaning, the calf’s digestive tract must transition from a pre-ruminant state to one based on the uptake of volatile fatty acids 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. Very little is known about the regulation of this developmental process and how diet during weaning affects development at the molecular level. To identify and characterize genes and gene networks affected by weaning in the calf rumen, global gene expression profiles were determined at different stages of development and under different dietary treatments. Results of these analyses provide molecular markers that can be used by animal scientists to study rumen development, as well as identify putative gene networks regulating differentiation and growth of the rumen tissue. This knowledge will aid in identifying genetic targets and methods for improving rumen development and function, particularly in the growing calf.

4. Application of gene expression profiling to characterize nutrient-gene interactions and regulation. Epigenomics is an emerging area of scientific investigation that is confirming the complex mechanisms regulating how, when, and where gene expression occurs within the animal cell to ensure normal development, health, and homeostasis. Until now, the molecular mechanisms of epigenetic regulation were not well understood. Deep RNA sequencing technology was used to generate novel genetic information related to bovine cell gene transcription induced by the short-chain fatty acid butyrate, an important nutrient for cattle derived from dietary fiber during microbial fermentation in the rumen. This information can be used to gain a deeper understanding of the bovine genome and transcriptome, and epigenetic regulation induced by butyrate in bovine cells. Knowledge gained will be used to optimize rations that improve rumen development and animal health, which impact their overall production efficiency.

5. Novel application of rumen metagenomic DNA sequencing technology to reduce impacts of environmental contaminants. Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a powerful explosive compound that has been used by the U.S. military since WWII to manufacture weaponry. Soil and groundwater contamination by RDX is a serious concern due to its toxicity and potential carcinogenicity. Traditional methods for its cleanup include extensive excavation and subsequent incineration, which are cost prohibitive. The sheep rumen harbors microorganisms that are capable of rapid RDX biodegradation and may provide a practical remediation alternative; however, the microbial taxa performing RDX biodegradation are unknown and metabolic pathways through which RDX is degraded have not been analyzed. In collaboration with scientists at Oregon State University, a holistic analysis of the ovine rumen microbiota was conducted. It was demonstrated that the ovine rumen can significantly reduce and eliminate RDX in a model system within hours. Gene sequence analysis identified known microbial groups capable of RDX degradation in the sheep rumen and several microbial groups of environmental origin that were not previously recognized in the rumen. Our results enable the refinement of a new remediation technology that combines plant intake of explosive compounds from contaminated soils and their biodegradation by ruminal microbes of sheep that graze on these plants.


Review Publications
Connor, E.E., Baldwin, R.L. 6th , Li, C., Li, R.W., Chung, H. 2013. Gene expression in bovine rumen epithelium during weaning indentifies molecular regulators of rumen development and growth. Functional and Integrative Genomics. 13:133-142.

Tao, S., Connor, E.E., Bubolz, J.W., Thompson, I.M., Do Amaral, B.C., Hayen, M.J., Dahl, G.E. 2013. Short Communication: Effect of heat stress during the dry period on gene expression in mammary tissue and peripheral blood mononuclear cells. Journal of Dairy Science. 96(1):378-383.

Connor, E.E., Kahl, S., Elsasser, T.H., Baldwin, R.L., Fayer, R., Santin, M., Sample, G.L., Clover, C.M. 2013. Glucagon-like peptide 2 therapy reduces negative effects of diarrhea on calf gut. Journal of Dairy Science. 96(3):1793-1802.

Wu, S., Li, C., Huang, W., Li, W., Li, R.W. 2012. Alternate splicing regulated by butyrate in the bovine epithelial cell. PLoS One. 7(6):e39182.

Shin, J., Li, R.W., Goa, Y., Bickhart, D.M., Liu, G., Li, W., Wu, S., Li, C. 2013. Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification. PLoS Genetics. DOI:10.4137/GRSB.S11243.

Lacombe, A., Li, R.W., Klimis-Zacasa, D., Kristoa, A.S., Tadepallia, S., Kraussa, E., Young, R., Wu, V.C. 2012. Lowbush blueberries, vaccinium angustifolium, modulate the functional potential of nutrient utilization and DNA maintenance mechanisms in the rat proximal colon microbiota. Functional Foods in Health and Disease. 2(6):228-241.

Li, C., Li, R.W. 2013. Epigenetics and environmental impacts in cattle. Hauppauge, NY: Nova Science Publisher, Inc. 59-82 p.

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.

Li, R.W., Li, C., Wang, T.T. 2012. Transcriptomic alterations in human prostate cancer cell LNCaP tumor xenograft modulated by dietary phenethyl isothiocyanate. Molecular Carcinogenesis. DOI: 10.1002/mc.21873.

Last Modified: 10/24/2014
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