BBSRC EASTBIO DTP - Genetic history and adaptation of African cattle: Identifying the genetic variants associated with bovine tropical adaptations

Identifying the genetic variants associated with bovine tropical adaptations is crucial to developing more productive cattle breeds that can tolerate the environmental challenges of sub-Saharan Africa. Despite their lower productivity in comparison to European breeds, native African breeds display markedly better survival rates as a result of thousands of years of both natural and human-imposed selection. The aim of this project is to analyse and compare the genomes of indigenous crossbred cattle from across different agro-ecological zones of East Africa to identify African-specific adaptive mutations.

The history of cattle in Africa is complex, involving a series of migrations of both taurine (Bos taurus taurus) and indicine (Bos taurus indicus) animals, and possibly independent domestication event(s). As a result, modern African cattle are genetic mosaics, with varying levels of European taurine, African taurine and Asian indicine origins. Dissecting the genome structure of these populations is expected to reveal the genetic basis of adaptation to biotic and abiotic environmental factors. The working premise is that when Asian zebu cattle arrived in Africa (the major wave starting around 700 A.D.), they were not as adapted to the local environment as the “native” taurine breeds, leading to selective crossbreeding with the local taurines. The goal of this study will be to use whole-genome sequence data from East African “zebu” cattle, which are mainly taurine-indicine hybrids, and a variety of statistical tools to identify genomic regions that have been under climate- and/or human-imposed selection. These will include admixture-based tools aimed at identification of genomic regions with African taurine or indicine origins, similar to approaches used to identify the genetic contributions to modern human genomes.

The student will first undertake bioinformatics analyses of the raw sequence data: sequences for each individual will be mapped to the cattle reference genome and genetic variants will be identified. The subsequent population genetic analysis will include a range of techniques aimed to address several goals: to identify genomic regions with taurine and indicine origins; to identify genomic regions showing evidence of selection; to map genomic regions associated with adaptation phenotypes; to characterise the stability of genetic hybrids; and to perform a functional analysis of genomic regions associated with adaptation.

The studentship will provide training in transferable skills and techniques in quantitative and population genetics, statistics, bioinformatics and genomic analysis. Depending on the student’s background, it may be appropriate to attend MSc courses at the University of Edinburgh. The student will also be expected to regularly attend seminars, journal clubs and local meetings. There will be opportunities for attendance at national and international conferences.