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Professor Rainer Roehe

Professor of Animal Genetics and Microbiome
Leading Host Genetics and Microbiome Research
Future Farming Systems

Research interests

My overall research interest is to unravel the host animal genomic architecture affecting complex performance traits in livestock. At present my main research interest is to reveal the influence of the gut microbiome on methane emissions, feed conversion efficiency, meat quality, animal health and behavioural traits, and how the host animal shapes the microbiome associated with those traits. In this research, whole-metagenome-sequencing is used to determine microbial community profiles as well as microbial gene abundances in order to understand the complex genetic and functional interactions between host genomics, microbiome and phenotypic traits. The comprehensive insight into these interactions will be used to develop novel cost-effective selection strategies exploiting microbiome information in animal breeding.

Current research interests

  • Understanding the functional genetics and pathways of the rumen microbiome and microbial genes associated with performance traits of animals.
  • Identification of quantitative genetic and genomic links between the host animal and rumen microbial community as well as microbial genes to be exploited for mitigation of methane emissions and improvement of feed conversion efficiency, meat quality, animal health, behavioural and welfare traits in ruminants.
  • Impact of nutrition on reduction in methane emissions and their effects on the composition of the rumen microbial community and on meat quality characteristics in beef.
  • Elucidating the impact of stress on the intestinal microbiota and its use as biomarker for pig wellness and performance.
  • Development of prediction equations for online measurement techniques to assess carcass, meat eating and nutritional quality in beef and sheep using imaging techniques.
  • Genetic improvement of meat quality traits in beef with particular interest in genetic improvement of fatty acids such as omega-3 fatty acids, reported to reduce the risk of cardiovascular diseases.
  • Genetic and genomic background of energy and nitrogen efficiency in pigs to develop strategies for improvement of energy and nitrogen efficiency during growth.
  • Understanding the genetic background and genomic architecture of pig welfare traits such as piglet survival, aggression and related traits such as feed intake behaviour as well as the development of new selection strategies using e.g. canalised selection.
  • Research on the most appropriate statistical methodology to predict the genomic background of complex traits, e.g. the predictability of Bayesian mixture models to estimate the entire genomic background and to identify QTLs of complex traits.

Selected research projects

  • BBSRC: “Understanding the functional and genomic architecture of the rumen microbiome affecting performance traits in bovines”.
  • Scottish Government RESAS WP2.3.1 “Strategies to use rumen microbial information in beef genetic improvement”.
  • BBSRC Newton Fund: “N-CIRCLE: Virtual Joint Centre for Closed-Loop Cycling of Nitrogen in Chinese Agriculture”.
  • Scottish Government HEI funding: “Rumen Microbiome” in collaboration with the Universities of Edinburgh and Aberdeen.
  • Zoetis: “The use of intestinal microbiota as a biomarker for swine wellness and performance”.


  • Course Leader and Lecturer BSc Animal Breeding and Genetics, SRUC.
  • Course Leader and Lecturer MSc Animal Genetic Improvement Module, University of Edinburgh.
  • Lecturer MSc Applied Animal Behaviour and Animal Welfare, University of Edinburgh.

PhD students

  • Joana Lima - “The use of networks of rumen microbial genes associated with performance traits for precision breeding and nutrition in beef cattle”.
  • Tuan Nguyen - “Precision breeding for piglet survival and the use of microbiome information to improve wellness in pigs”.
  • Simon Foister – “Balancing short and long term aggression to maximise welfare and productivity on animal behaviour in pigs”. (Associate Supervisor)
  • Miguel Soley – “The effects of stress on the ruminal microbial environment and its relationship to feed efficiency and methane emissions”. (Associate Supervisor)

Selected publications

See all of Rainer Roehe's publications.

Prof Rainer Roehe

Professor of Animal Genetics and Microbiome

Address: SRUC, Roslin Institute Building, Easter Bush, Midlothian EH25 9RG

Telephone: 0131 651 9367