Integration of Functional Genomics and Quantitative Genetics to Improve Feed Efficiency in Pigs
Personnel
Dr. Jack Dekkers , Professor of Animal Science, Principal Investigator
Dr. Chris Tuggle , Professor of Animal Science, Co-Principal Investigator.
Dr. Vasant Honavar, Professor of Computer Science and of Bioinformatics and Computational Biology, Co-Principal Investigator
Dr. Dan Nettleton , Associate Professor - Dept. of Statistics, Co-Principal Investigator.
Dr. Lloyd Anderson , Charles F. Curtiss Distinguished Professor in Agriculture; Professor of Animal Science;
Professor of Biomedical Sciences, College of Veterinary Medicine
, Co-Principal Investigator.
Summary
We seek to discover and characterize genetic pathways that control economically important traits related through transcriptional profiling of specific and relevant tissues during the growth period. Profiling studies will be based on several complementary animal level contrasts and their interactions, including: quantitative differences in and neuro-endocrine treatments that perturb feed intake physiology. This project investigates differential expression of genes in several key tissues with the following specific objectives:
- Identify genes and pathways that are differentially expressed between pigs that differ in residual feed intake and that respond to a restriction in feed intake.
- Identify genes and pathways that respond to intra-cerebroventricular injection of agonists and antagonists of Melanocortin 4 (MC4) in pigs with alternate genotypes at the MC4 Receptor gene.
- Identify genes and pathways that are differentially expressed between pigs that differ in residual feed intake and MC4R genotype.
- Integrate expression profile results from Objectives 1, 2, and 3 and with data from other species to identify genes and pathways that control feed intake and feed efficiency.
We seek to answer questions regarding individual genes as well as those involving sets of genes, including:
- Which genes or sets of genes are expressed in specific tissues at the growth stage collected?
- Which genes or sets of genes have significantly different expression in these tissues as a result of specific treatments/factors?
- How does their difference in response relate to the biological function of that gene and to the biological nature of the treatment/factor imposed?
- Which genes or sets of genes that are differentially expressed subject to feed intake restriction or with different MC4R genotype have a different response in high versus low RFI animals and how does this relate to their biological function?
- Which genes or sets of genes have a different response to neuro-endocrine treatment with MC4 agonists or antagonists, how does this depend on genotype at MC4R, and how does this relate to their biological function and to MC4 pathways?
- How do expression profiles identified here correspond to expression profile results in human and in model species such as the mouse and the rat?
- Which genes identified above are predicted to map near QTL for growth, composition, and feed intake in the pig or other species?
In order to be able to identify patterns of responses of individual or clusters of genes and relate them to their biological function, as a means to identify underlying genetic pathways we will integrate the results of our experiments with complementary set of treatments and contrasts by leveraging the knowledge on the molecular genetics of feed intake from other studies in other species.
Funding
This research is being funded by a grant from the United States Department of Agriculture
