Edinburgh Research Explorer

Prof Chris Haley, BSc, PhD, FRSE

Programme Leader/ Professorial Fellow

Profile photo

Willingness to take Ph.D. students: Yes

Exploring the Genetics of Complex Traits in Humans, Livestock and other species

Education / Academic qualification

Bachelor of Science, University of Birmingham
Doctor of Philosophy (PhD), University of Birmingham
Selection in drosophila melanogaster


I  hold joint appointments as a Group Leader in the MRC Human Genetics Unit in the MRC Institute of Genetics and Molecular Medicine and as a Principal Investigator in the Roslin Institute, both these organisations being part of the University of Edinburgh. I have published over 200 refereed journal articles and my ISI Web of Science h index is 41. My research interests lie in developing an understanding of the control complex traits, where inter-individual variation within and between populations is controlled by variation at a number of genes (often referred to as quantitative trait loci or QTL), by environmental factors and by the complex interactions of these components. Most variation between individuals within and between populations is in the form of complex traits. Consequently variation in complex traits is responsible for most inter-individual variation in susceptibility to disease (both infectious and metabolic) in humans, livestock and other species and underlies responses to selection, both artificial selection in livestock and natural selection in all species. We can only be really effective in understanding and treating many diseases, in predicting individual’s risk of developing particular conditions and in dissecting the causes and consequences of natural selection if we understand the genetic control of variation in complex traits.

My research focuses both on developing approaches to dissect complex traits and in applications of these approaches to specific biological models. My group has developed the most widely used approaches for linkage mapping of QTLs livestock. These have been made available to the community the through the software QTL Express (http://QTL.cap.ed.ac.uk) and latterly through GridQTL (http://gridQTL.org.uk ). We have further developed and applied methods for the analysis of the high density of markers that are available in human populations and which are becoming available in various livestock breeds and developed, disseminated and applied analysis methods for detection of gene interactions (epistasis). I have has led and collaborated in a large number of projects focusing on the dissection of complex traits in a range of species. These have included the first genome-wide scan of QTLs in livestock and many subsequent studies as well as studies in humans, fish, model vertebrates and plant species. Current research includes focus on the use of genomic information to predict individual’s complex trait phenotypes and health outcomes, the development and application of statistical approaches to capture rare variants, epistatic variation and other genetic variation that escapes standard genome-wide association analysis and understanding and utilizing the genomic causes of complex trait variation.

Current Research Interests

Understanding complex trait variation in humans and other species.

Research Interests

My research group is interested in understanding the control of complex trait variation in humans and other species. But what does this mean exactly? Well if we look within populations of humans or other species we see that individuals differ from one another in almost all characteristics or traits. For example height and weight, personality traits and even susceptibility to colds and flu or arthritis all differ between people. For such traits variation is controlled by a number of different genes and environmental events or lifestyle choices as well as interactions between these varius factors. Thus there is no simple cause of variation between individuals and such traits are termed complex. Our research uses computational and statistical analysis of data where traits have been measured on large samples of humans or other species and data on genetic, environmental and other potentially causative factors have also been measured. We use these analyses to estimate the extent of genetic and environmental influences on variation and ultimately we hope to identify the most important environmental influences and genes with the bigest impact. This information can ultimately be used build models that can help identify individuals susceptible to disease or contribute to the design of treatments and drugs that may ameliorate disease.


I have been teaching on MSc courses at the University of Edinburgh for more than 25 years. I was involved in the reorganisation of the MSc in Animal Breeding which became the MSc in “Quantitative Genetics and Genome Analysis” in 2000. This reorganisation expanded teaching of quantitative genetics from animal breeding to unite the areas of quantitative genetics applied to human, livestock and natural populations. Since the launch of the new MSc I have sat on the examination board of the MSc as representative of the Roslin Institute since then. With Sara Knott I co-organise the “Linkage and Genome Analysis” section of the course and teach over a period of three weeks on this course. I also supervise summer MSc research projects.

I have both organised and taught on international post-graduate courses on livestock genomics and run international courses on QTL analysis.

My research in a nutshell

I am interested in understanding why individuals vary one from the other. Most characteristics, whether it is in a population of humans or of farm animals, vary from individual to individual. Some are taller, some shorter; some are quick growing and some slow growing; some are more susceptible to disease and some more resistant. Variation in such characteristics is usually controlled by many different genes combined with environmental factors such as diet and upbringing. However, for most characteristics we know very little about the genes that are involved or how they act to influence an individual’s growth, strength and health. Therefore, my research involves analysing variation of characteristics in large populations of animals or humans and attempting to identify the genes that may contribute to this variation. An improved knowledge of how genes act to control variation between individuals could be valuable in a number of ways. For example an understanding of the biology would help in the design of drugs to combat disease in humans and livestock and knowledge of the genes involved could help select cows that have naturally more efficient milk production.

Highlighted research outputs

  1. Detecting epistasis in human complex traits

    Research output: Contribution to journalArticle

  2. An Evolutionary Perspective on Epistasis and the Missing Heritability

    Research output: Contribution to journalArticle

  3. The genomic signature of trait-associated variants

    Research output: Contribution to journalArticle

  4. The heritability of human disease: estimation, uses and abuses

    Research output: Contribution to journalArticle

  5. A cornucopia of maize genes

    Research output: Contribution to journalArticle

  6. Towards in vitro genetics

    Research output: Contribution to journalArticle

  7. Methodological aspects of the genetic dissection of gene expression

    Research output: Contribution to journalArticle

  8. Genetical genomics in humans and model organisms

    Research output: Contribution to journalArticle

  9. Epistasis: too often neglected in complex trait studies?

    Research output: Contribution to journalArticle

  10. Multitrait least squares for quantitative trait loci detection

    Research output: Contribution to journalArticle

  11. Detecting QTLs for uni- and bipolar disorder using a variance component method

    Research output: Contribution to journalArticle

  12. DNA microsatellite analysis of Dolly

    Research output: Contribution to journalArticle

  13. Confidence intervals in QTL mapping by bootstrapping

    Research output: Contribution to journalArticle

  14. Genetic mapping of quantitative trait loci for growth and fatness in pigs

    Research output: Contribution to journalArticle

View all (330) »

Research activities & awards

  1. PLoS Genetics

    Activity: Editorial work or peer review of publicationsEditorial activity

  2. Scientific Review Committee

    Activity: External academic engagementMembership of peer review panel or committee

  3. Hosting Yoshinobu Uemoto

    Activity: External academic engagementHosting an academic visitor

View all (3) »

ID: 393785