Studying African buffalo evolution to map pathogen resistance genes

Supervisors: Prof Chris HaleyDr Christelle RobertDr Liam MorrisonDr James Prendergast

Project Description:

The African buffalo (Syncerus caffer) is the most closely related African wild bovid to the domestic cow (Bos taurus). Buffalo are infected by all of the most important African cattle pathogens (e.g. trypanosomes, Theileria parva, foot and mouth disease virus, Mycobacteria bovis), but generally do not suffer the serious clinical disease seen in cattle; most likely due to prolonged co-evolution with pathogens selecting for disease control. By contrast, archaeological evidence suggests that cattle were only introduced into Africa within the last 8,000 years and many of the cattle populations used in current agricultural systems have been introduced much more recently. The African buffalo therefore represents a uniquely valuable model in terms of understanding bovine control of infectious disease. Knowledge of how buffalo are able to control infections with these pathogens and the genetic basis of such resistance could be exploitable for devising methods to control the corresponding infections in cattle, either through enhancement of immune responses or by genetic means. The latter is particularly timely with the advent of gene editing technologies, which have opened up new opportunities to modify genes in domestic species based on data from resistant wildlife species. However, there is no reference genome to enable the qualitative analysis of the genetic basis behind important traits, and comparisons with other relevant genomes (e.g. B. taurus and the Asian buffalo Bubalus bubalis).

As a foundation for characterisation of the biological mechanisms underlying African buffalo resistance to cattle pathogens, we have generated a high quality African buffalo reference genome using a combination of Pacbio and Illumina sequencing data.  The aim of this studentship is to use whole genome sequences of 240 buffalo from across Africa to determine the regions of the genome showing evidence of selection, i.e. candidate regions potentially associated with adaptation to the local African environment. Integrating novel African buffalo expression data across a range of tissues and exploiting further genome sequences from across bovids the student will fully characterise the evolution of buffalo genes.

The student will gain training in bioinformatics, population and evolutionary genetics. There will also be opportunities to undertake wet lab work resulting in a cross-disciplinary set of abilities that will provide a highly competitive foundation for a future career in science. This project is in collaboration with colleagues in Africa and there will therefore also be potential to travel during the course of the PhD. 

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