Location: Animal Genomics and Improvement Laboratory
2024 Annual Report
Objectives
Objective 1: Develop genomic resources and molecular tools to determine limitations to nutrient use efficiency in dairy cattle.
Sub-objective 1.A: Using phenotypically well-defined lines of Holstein dairy cattle selected and monitored for feed efficiency, investigate the biological and genetic bases of nutrient use efficiency and support genomic selection studies by identifying highly affected pathways against a backdrop of known RFI phenotype and methane emissions.
Sub-objective 1.B: Continue to refine and validate a short-term isolated duodenal model for assessing intestinal epithelial tissue transcriptomic changes in ruminant gastrointestinal tissues in vivo in response to changes in luminal nutrient flow.
Objective 2: Develop and apply novel nutritional strategies for calf rearing and weaning to reduce feed and nutritional costs to dairy cattle production through further refining the global landscape of genomic and epigenomic regulatory elements, exploring the regulatory dynamics of chromatin states in rumen development during weaning and for complex traits.
Sub-objective 2.A: Characterize molecular phenotypes of the calf rumen transcriptome through strand-specific RNA sequencing (ssRNA-seq) and single-cell RNA sequencing during development.
Sub-objective 2.B: Functionally annotate the calf rumen epigenome and identify transcriptional cis-regulatory modules during development, including histone modification, chromatin accessibility, and architecture using Chromatin Immunoprecipitation-sequencing (ChIP-Seq) technologies.
Objective 3: Using in vitro and in vivo gastrointestinal tissue responses (ruminal, duodenal, and colon) in lactating and non-lactating cows, investigate perturbations in luminal factors (changes in nutrient flow) at single-cell resolution.
Sub-objective 3.A: Assess short-term (days) responses of metabolism- and transport-related genes and proteins of the intestinal epithelia in response to direct delivery of individual substrates or nutritional components (e.g., nutrients, metabolites, humoral factors).
Sub-objective 3.B: Evaluate the impact of nutrient use efficiency, as defined by dairy efficiency as determined RFIlac, on total tissue, animal protein, and lipid carcass composition.
Approach
To improve feed efficiency and reduce methane emissions of dairy cattle through genetic selection and management understanding the basis for dairy cows which are divergent in feed efficiency is necessary. A database of the genetic and production information, including enteric methane emissions, has been compiled for more than 15 years and will continue to facilitate extensive analysis. Additionally, these highly phenotyed animals will be used to assess changes in tissues known to affect efficient use of nutrients. Methods to temporarily isolate regions of small intestine of live, adult cows will be established to study direct nutrient effects on gut function and gene expression. Moreover, epigenetic factors controlling rumen development during weaning will be investigated using state-of-the-art molecular technologies. Finally, changes in gastrointestinal cells of dairy cows related to gut growth and function during critical stages of production will be characterized by examining gene expression in gut tissues of cows under different dietary and production conditions over time.
Progress Report
Progress was made on all three Objectives of project 8042-31310-114-000D (Improving Dairy Cow Feed Efficiency and Environmental Sustainability Using Genomics and Novel Technologies to Identify Physiological Contributions and Adaptations). This represents the second year of this project. Under Objective 1, an additional 35 Holstein dairy heifers from the Beltsville, Maryland herd were evaluated for feed efficiency during a 91-day growth trial using an estimate called residual feed intake (RFI). Daily enteric methane and carbon dioxide production also were measured for each heifer using an automated monitoring system called GreenFeed to determine relationships between the feed efficiency of dairy cattle and their contribution to greenhouse gas emissions. Blood plasma was collected monthly from heifers during the growth trial for analysis of indicators of inflammation, metabolism, and stress. Genomic DNA was isolated from each heifer for high- density single-nucleotide polymorphism genotyping using the Illumina BovineHD Genotyping BeadChip with over 777,000 markers. The collected data were added to a database with information from over 400 growing heifers from the same herd to investigate the biological and genetic bases of nutrient use efficiency and to support genomic selection studies.
Holstein dairy cows from the Beltsville, Maryland herd also were evaluated for feed efficiency during the first 100 days of lactation using RFI estimates and associated production measures. Those data were added to a database with information from over 1500 lactating cows from the same herd and are being used to investigate the genetic basis of feed efficiency in dairy cattle. All data were shared with international partners as part of a multimillion-dollar grant led by investigators at the University of Guelph in Guelph, Canada, to improve genetic selection for feed-efficient dairy cattle. Finally, enteric methane emissions of 250 dairy cows from 100 to 150 days of lactation have been evaluated as well as their residual feed intake to gain a better understanding of the relationship between feed efficiency during lactation as part of a $2 million Foundation for Food and Agriculture grant with Michigan State University and greenhouse gas emissions of dairy cows as part of a $2 million Greener Cattle initiative with University of Wisconsin. Thirty Holstein dairy cows phenotypically described for RFI lac have been euthanized for the collection of over 40 distinct tissues in support of a comprehensive data set to provide a resource for the development of the FarmGTex atlas for basic functional knowledge of genome function to decipher the genotype-to-phenotype (G2P) link in farmed animals. Systematic characterization of molecular states of cells in livestock tissues is essential for understanding cellular and genetic mechanisms underlying economically and ecologically important physiological traits. As a part of a coordinated international action to accelerate genome to phenome, a comprehensive Cattle Cell Atlas (CattleCA) by generating and analyzing single-cell/nucleus RNA sequencing (sc/snRNA-seq) data has been built. Stereo-single cell RNA sequencing, the newest state-of-the-art technology, is also applied in this project. A comprehensive cattle cell atlas is an invaluable resource for cattle genetics and genomics, developing cell-based food systems, and evolutionary cell biology.
Accomplishments
1. Understanding the genetic basis for differences in feed efficiency. Feed costs still represent greater than 60% of the cost of dairy production. Thus, the genetic basis of feed efficiency (FE) is of great interest to both the animal research and producer communities, specifically to enable the development of management and selection tools to improve FE in herds. The development of strategies for enhanced genomic selection and informed management approaches requires tool development. ARS scientists at Beltsville, Maryland, explored modifications (methylations) on the chromosomes (epigenetics) that affect the expression of genes that are differentially expressed in high and low-efficiency cows using a methylation array assay developed for mammals and determined 37,554 specifical methylation sites associated with FE by assaying 48 Holstein cows with extreme residual feed intake (RFI; a measure of feed efficiency). Further, 421 sites were related to 287 genes associated with RFI, including several genes that had previously been associated with feeding or digestion functions. Finally, extensive changes in the expression and co-expression of these genes indicate a complex regulation of FE in cattle. These results provide insight into the epigenetic basis of RFI and putative gene targets for improved FE selection in dairy cattle.
2. Regulatory elements controlling tissue-specific gene expression in livestock tissues. Systematic characterization of molecular states of cells in livestock tissues is essential for understanding cellular and genetic mechanisms behind physiological phenotypes of economic and ecological importance, contributing to the development of sustainable and precision agriculture-food systems. As part of the Farm Animal Genotype-Tissue Expression project (FarmGTEx; a comprehensive gene expression map across tissues, physiological status, sex, etc.) in collaboration with global partners, ARS Scientists at Beltsville, Maryland, built a comprehensive reference map of 1,793,854 cells by sequencing the messenger RNA (representative of a snapshot of gene expression) from 131 distinct cell types from 59 cattle tissues in both sexes across development stages. Within and across-tissue analyses highlighted the cellular diversity regarding gene expression, transcription factor regulation, and cell-to-cell communications. Integrative analysis with genetic variants of various monogenic (single gene) and complex (multiple genes and networks) traits revealed novel underlying cellular and molecular mechanisms, such as in sperm cell regeneration, genes responsible for sperm motilities and excitatory neurons, and genes affecting milk fat yield. Comparative analysis demonstrated gene expression and regulation similarity between cattle and humans at single-cell resolution, enabling the detection of relevant cell types for complex human traits and diseases. This cattle cell atlas is an invaluable resource for genetics and genomics, cell-based food system development, evolutionary cell biology, and human biomedicine.
Review Publications
Wang, X., Gao, Y., Li, C., Fang, L., Liu, G., Zhao, X., Zhang, Y., Cai, G., Xue, G., Liu, Y., Wang, L., Zhang, F., Wang, K., Zhang, M., Li, R., Gao, Y., Li, J. 2023. The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle. BMC Genomic Data. 24:39. https://doi.org/10.1186/s12863-023-01139-0.
Ding, Y., Wang, P., Zhang, Y., Yang, C., Zhou, X., Wang, X., Li, C., Su, Z., Ming, W., Zeng, L., Shi, Y., Li, C., Kang, X. 2023. Sodium butyrate induces mitophagy and apoptosis of bovine skeletal muscle satellite cells through the mammalian target of rapamycin signaling pathway. International Journal of Molecular Sciences. 24:13474. https://doi.org/10.3390/ijms241713474.
Cavani, L., Parker Gaddis, K.L., Baldwin, R.L., Santos, J.E., Koltes, J.E., Tempelman, R.J., Vandehaar, M.J., White, H.M., Penagaricano, F., Weigel, K.A. 2024. Consistency of dry matter intake in Holstein cows: Heritability estimates and associations with feed efficiency. Journal of Dairy Science. 107(2):1054–1067. https://doi.org/10.3168/jds.2023-23774.
Kang, X., Li, C., Liu, S., Baldwin, R.L., Liu, G., Li, C.-J. 2023. Genome-wide acetylation modification of H3K27ac in bovine rumen cell following butyrate exposure. Biomolecules. 13(7):1137. https://doi.org/10.3390/biom13071137.
Houlahan, K., Schenkel, F., Miglior, F., Jamrozik, J., Lassen, J., Gonzalez-Recio, O., Charfeddine, N., Segelke, D., Butty, A., Stratz, P., Vanderhaar, M., Weigel, K., White, H., Koltes, J., Santos, J., Baldwin, R.L., Baes, C. 2024. Estimation of genetic parameters for feed efficiency traits using random regression models in dairy cattle. Journal of Dairy Science. 107(3):1523–1534. https://doi.org/10.3168/jds.2022-23124.
Van Staaveren, N., De Oliveira, H.R., Houlahan, K., Chud, T.C., Oliveira, Jr, G.A., Hailemariam, D., Kistemaker, G., Miglior, F., Plastow, G., Schenkel, F.S., Cerri, R., Sirard, M., Stothard, P., Pryce, J., Butty, A., Stratz, P., Abdalla, E.A., Segelke, D., Stamer, E., Thaller, G., Lassen, J., Manzanilla-Pech, C., Stephansen, R.B., Charfeddine, N., Garcia-Rodriguez, A., Gonzalez-Recio, O., Lopez-Paredes, J., Baldwin, R.L., Burchard, J., Parker Gaddis, K.L., Koltes, J.E., Penagaricano, F., Santos, J.E., Tempelman, R.J., Vandehaar, M.J., Weigel, K.A., White, H.M., Baes, C. 2024. The Resilient Dairy Genome Project - A general overview of methods and objectives related to feed efficiency and methane emissions . Journal of Dairy Science. 107(3):1510–1522. https://doi.org/10.3168/jds.2022-22951.