Supervisor(s): Prof Claire Wathes and Dr Zhangrui Cheng

Department: Pathobiology and Population Science

Background

Recent advances in genomic selection (GS) have paved the way for potentially rapid advances in animal breeding. However, to date, the ‘black box’ nature of GS has added little to our understanding of the molecular nature of the traits that compose our selection indices. All of the important genetic traits governing cow performance are strongly influenced by the animal’s health and by environmental factors such as nutrition and management systems. We now need to develop a better understanding of the biological pathways which regulate the cow’s performance within the herd and influence the extent to which she can operate to her maximum genetic ability. The Encyclopaedia of DNA Elements (ENCODE) project showed that the expression of each coding gene within the human genome is controlled by multiple regulatory sites located both near and distant from it, and that gene regulation is much more complex than was previously recognised. The Holstein cow is the dominant dairy breed worldwide and offers an ideal animal model in which to determine the genetic components responsible for biological trait variation.

Hypothesis

Variations in metabolite concentrations in blood and milk are correlated with gene expression in circulating white blood cells and liver in early lactation and can predict cow performance in the subsequent lactation.

Aim

To use bioinformatics analysis of existing data to explore the relationships between gene expression, health and metabolic status in early lactation with subsequent fertility.

Objectives

  1. Undertake basic training in bioinformatics and use of relevant websites, e.g. http://bovinegenome.org and http://www.pantherdb.org/ to develop expertise in data mining
  2. Write a literature review on chosen aspect
  3. Organize RNAseq and health/metabolite data into an appropriate database for analysis and run initial exploratory tests e.g. using correlation analysis
  4. Obtain lists of differentially expressed genes and run pathway analyses
  5. Develop new ideas on the regulatory links between metabolic and immune function in dairy cows
  6. Determine relationships between metabolic and immune function with subsequent fertility
  7. Write MRes Dissertation

This is a full-time (12 month) project commencing in October 2018. Part-time applicants will also be considered at 50%.

Project costs are covered but the successful applicant must cover course fees and their living expenses.

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