Infection and selection in indigenous East African cattle

Interested individuals should email [Email Address Removed] directly. Send a two page Curriculum Vitae including contact details for two academic referees; a one page statement of research interests and grades/transcript of marks.

The Infectious Diseases of East African Livestock (IDEAL) project is producing unique data on the life histories and infectious disease burdens of a cohort of 500 indigenous cattle in Western Kenya. It is a collaborative project between the University of Edinburgh, the International Livestock Research Institute (ILRI) and other national and international partners. The overall aim is to generate a better understanding of the genetic and phenotypic factors that allow these animals to tolerate a massive infectious disease pressure in an environment where there is minimal use of vaccination or other preventive measures. This knowledge will ultimately inform breed improvement programmes (which have been repeatedly attempted in the study area) aiming to increase food security by increasing productivity, especially milk yields.
The project will integrate genetic analyses based on high-density (>400,000) SNP profiles for every cow in the study and epidemiological analyses based on histories of infection with over 30 different pathogen species. Whole genome sequences are available for a small subset of animals. There is epidemiological evidence that infectious diseases (including East Coast fever, trypanosomiasis and heartwater) exert strong selection pressure on the study population. We now wish to identify signatures of selection in the SNP data. Selection is likely to have occurred over two timescales: 1) in the last 10-20 years when there has been significant cross-breeding between European taurines and the indigenous population; and 2) over the past 1000+ years since Asian zebu cattle were interbred with African taurines. Appropriate analyses are expected to include admixture mapping, candidate gene studies, localisation of QTL, and genome scans for signatures of hitchhiking events. Particular attention will be paid to identifying pathways containing an excess of genes in genome regions under selection. Previous work suggests several candidate pathways, including MAPK signalling and cholesterol metabolism. The cholesterol pathway plays an important intrinsic role in host defence against infection via a pathway molecularly coupled to innate immunity. These studies underscore key host protection pathways in infection that can help inform planned genetic investigations.
The successful applicant will have a biological sciences degree, either a 1st or 2i, and possibly an MSc in population genetics or biological computation. An interest in and some experience of statistical analysis of biological and/or genetic data is important. Training will be provided in the state-of-the-art methodologies in statistical genomics and pathway analysis, involving analysis of SNP data and interrogation of genome sequences, backed up by access to our taught MSc in Quantitative Genetics & Genomic Analysis. Access to, and training in the use, of high performance computing facilities (including the part BBSRC-funded HECToR machine) will be provided. The student will spend time working in 2 very active research group studying epidemiology and genetics and pathway biology of infection – these will provide a very supportive intellectual environment. Some field work in Kenya may also be required. This will be arranged through ILRI, which has structures in place to support visiting research students.