Location: Animal Genomics and Improvement Laboratory
Project Number: 8042-31310-114-000-D
Project Type: In-House Appropriated
Start Date: Jul 26, 2022
End Date: Jul 25, 2027
Objective:
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.
