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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

2015 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. Data collection of carbon dioxide and methane emissions in eructations measured from individual heifers during the growth trials also began using an automated radio-frequency identification-based system called GreenFeed to begin evaluation of the relationship between feed conversion efficiency and methane emissions. The same heifers also are being evaluated 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. Our database, currently consisting of more than 825 lactations (> 525 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. Relative to Objective 2, the temporal variation in the rumen microbial composition of dairy cows at mid-lactation was monitored using deep next-generation sequencing and bioinformatic tools. Greater than 80 rumen microbiome samples have been analyzed to date. Approximately 95% of raw sequence reads passed various quality control parameters. Greater than 217,081 quality pair-end sequences were merged to form contiguous sequences (contigs). These consensus contigs were analyzed using taxonomy-dependent and -independent clustering algorithms, such as CD-HIT-OTU, to understand the temporal changes in the structure of the rumen microbiome during lactation. Decay, clearance, and fate of certain rumen microbes in the bovine rumen were monitored using real-time quantitative PCR. Relative to Objective 3, comprehensive sample collection of critical tissues from 16 lactating dairy cows divergently selected on the basis of feed efficiency (residual feed intake during the first and second lactations) was completed. Tissue analyses are ongoing with RNA and DNA composition completed. Nitrogen analysis is expected to be completed in the first quarter of 2016. Initial analysis appears to confirm the concept that changes in visceral mass are contributing to differences in lactating dairy cow feed conversion efficiency due to the high metabolic activity of visceral tissues. Additional lactating cows (n = 48) divergent for feed efficiency also were evaluated for immune function using two in vitro assays to determine whether differences in immune function contribute to variation in feed efficiency. Results indicated no significant relationship between feed efficiency and the ability of immune cells to elicit a response to an immune challenge. Also relative to Objective 3, bioinformatics assessment was performed on mammary tissue biopsy samples collected from cows exposed to endophyte-infected fescue during the dry period. This treatment effectively eliminated circulating prolactin and inhibited the characteristic prolactin surge observed at parturition. Of interest, once the cows were removed from treatment, we observed a net increase of 8 to 10% in milk production during the subsequent lactation. The mechanism of increase appears to be due to a lactogenic versus a proliferative response in the mammary gland. Research is ongoing using RNA sequencing technology to understand the mammary specific gene expression changes that occurred in response to this dietary treatment. This knowledge may be applied on-farm to more effectively use endophyte-infected fescue fields to maintain dry cows, rear calves, and increase milk production.


4. Accomplishments
1. Demonstrated that elevated rumen butyrate does not improve nitrogen retention by growing ruminants. It is believed that butyrate produced in the rumen may enhance urea recycling by increasing urea uptake in the rumen. The direct effect of elevated ruminal butyrate on urea nitrogen recycling, overall nitrogen use, and rumen tissue protein turnover rate were evaluated by ARS scientists in Beltsville, Maryland, in a growing sheep model to provide direct evidence for a role of butyrate in regulation of urea nitrogen uptake by the rumen. In these experiments, butyrate failed to directly improve overall nitrogen retention, but butyrate may play a role in the redistribution of urea nitrogen fluxes in the overall scheme of nitrogen metabolism. Although no direct effects of butyrate on nitrogen retention were demonstrated, butyrate-enhancing diets may provide indirect effects on the intestine that benefit ruminant health and productivity at weaning. The research is important for the formulation of ruminant diets and benefits ruminant nutritionists and procedures.

2. Defined the core rumen microbiome of cattle, sheep, and goats using deep 16S ribosomal RNA sequencing. Substantial variation exists in the microbial composition and functionality among individual rumen samples within a species and among ruminant species. It is probable that a set of core microbial taxa or species are shared by the rumen microbiome of all ruminant species within the large context of temporal and spatial variations, contributing to basic rumen function. ARS scientists in Beltsville, Maryland compared microbial community compositions of the rumen of cattle, sheep, and goats in order to define the core rumen microbiome using deep 16S ribosomal RNA sequencing. The results showed that collectively 22 phyla and 94 families are detected in the rumen microbiome of cattle, goats, and sheep. The core rumen microbiome consists of 8 phyla and 15 families; however, the relative abundance of the 15 families varies significantly among the three species, despite their high prevalence. For example, the abundance of the family Prevotellaceae, the most abundant family in the rumen of all three species, comprises 24% of the goat rumen microbiome, 51% in cattle, and 35% in the sheep rumen, while the abundance of Ruminococcaceae is significantly higher in the sheep rumen (20%) than in the rumen of cattle (8%) and goats (4%). On the other hand, the abundance of Lachnospiracea is relatively stable in the rumen of all three species. Our findings provide a mechanistic insight into rumen function in physiology and nutrition of ruminants.


Review Publications
Li, R.W. 2015. Rumen Metagenomics. Book Chapter. New Delhi, India: Springer India. 379 p. doi: 10.1007/978-81-322-2401-3.

Leski, T.A., Li, R.W., Hervey, J.W., Lebedev, N., Hamdan, L.J., Wang, Z., Deschamps, J.R., Kusterbeck, A.W., Vora, G.J. 2014. Integrated metagenomic and metaproteomic analyses of marine biofilm communities. BIOFOULING. 30:10, 1211-1223. DOI:10.1080/08927014.2014.977267.

Li, R.W., Giarrizzo, G., Wu, S., Li, W., Duringer, J.M., Craig, M.A. 2014. Metagenomic insights into RDX-degrading potential of the ovine rumen microbiome. PLoS One. 9(11):e110505. DOI:10.1371/journal.pone.0110505.

Wang, Z., Leary, D.H., Malanoski, A., Li, R.W., Hervey, W.J., Eddie, B., Vora, G.J., Tender, L.M., Lin, B.C., Strycharz-Glaven, S.M. 2014. A previously uncharacterized, nonphotosynthetic member of the chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode. Applied and Environmental Microbiology. 81:699–712. DOI:10.1128/AEM.02947-14.

Zhang, L., Jia, S., Yang, M., Xu, Y., Li, C., Sun, J., Huang, Y., Lan, X., Lei, C., Zhou, Y., Zhang, C., Zhao, X., Chen, H. 2014. Detection of copy number variations and their effects in Chinese bulls, BMC Genomics 2014, 15:480.

Shin, J., Xu, L., Li, R.W., Gao, Y., Bickhart, D.M., Liu, G., Baldwin, R.L., Li, C. 2014. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Animal Genetics. 45:40–50. DOI:10.1111.age.12147.

Huang, Y., Sun, J., Zhang, L., Li, C., Womark, J.E., Li, Z., Lan, X., Lei, C., Zhao, X., Chen, H. 2014. Genome-wide DNA methylation profiles and their replationship with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos Taurine). Scientific Reports. 4:6546. DOI: 10.1038/srep06546.

Walker, M.P., Clover, C.M., Elsasser, T.H., Connor, E.E. 2015. Tight junction gene expression in gastrointestinal tract of dairy calves with coccidiosis and treated with glucagon-like peptide-2. Journal of Dairy Science. 98(5):3432-3437.

Connor, E.E., Clover, C.M., Walker, M.P., Elsasser, T.H., Kahl, S. 2015. Comparative physiology of glucagon-like peptide-2 – Implications and applications for production and health of ruminants. Journal of Animal Science. 93:492-501.

Templeman, R.J., Spurlock, D.M., Coffey, M., Veerkamp, R.F., Armentano, L.E., Weigel, K.A., De Haas, Y., Staples, C.R., Connor, E.E., Hanigan, M.D., Lu, Y.F., Vandeharr, M.J. 2015. Heterogeneity in genetic variation and energy sink relationships for residual feed intake across research stations and countries. Journal of Dairy Science. 98(3):2013-2026.

Zhao, C., Zan, L., Wang, Y., Updike, M., Liu, G., Bequette, B.J., Baldwin, R.L., Song, J. 2013. Functional proteomic and interactome analysis of proteins associated with beef tenderness in angus cattle. Livestock Science. 161:201-209.

Baldwin, R.L., Mcleod, K.R. 2014. Role and function of short chain fatty acids in rumen epithelial metabolism, development and importance of the rumen epithelium in understanding control of transcriptome. In: Congjun, Li, Editor. Butyrate: Food Sources, Functions and Health Benefits. New York, NY: Nova Science Publishers. p. 119-218.

Agarwal, U., Hu, Q., Baldwin, R.L., Bequette, B. 2015. Role of rumen butyrate in regulation of nitrogen utilization and urea nitrogen kinetics in growing sheep. Journal of Animal Science. 93:2382-2390. DOI: 10.2527/jas.2014-8738.

Connor, E.E. 2014. Improving feed efficiency in dairy production systems – challenges and possibilities. Animal-The International Journal of Animal Biosciences. 9(3):395-408.

Sun, J., Sonstegard, T.S., Li, C., Yongzheng, H., Li, Z., Wang, J., Zhang, C., Lei, C., Zhao, X., Chen, H. 2015. Altered microRNA expression in bovine skeletal muscle with age. Scientific Reports. 46(3):227-238. DOI: 10.1111/age.12272.

Yakirevich, A., Pachepsky, Y.A., Guber, A., Kuznetsov, M. 2014. MaSTiS, microorganism and solute transport in streams, model documentation and user manual. Software and User Manual Public Release. p.1-23.