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Deciphering the genetics of adaptation to the environment in wild and domesticated bovidsat the University of Edinburgh

Details

Date & time	Nov 22 '21
Location	The University of Edinburgh, United Kingdom
Creator	LouiseLHarris
Category	call
Registration	Link

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Basic

Description

Deciphering the genetics of adaptation to the environment in wild and domesticated bovidsat the University of Edinburgh

Population genetics and bioinformatics techniques will be used to characterize the genetic structure of African cattle and buffalo populations and to identify common genomic signatures of environmental adaptation.

Apply by Thursday January 06 2022 at 12.0

Project background

A better understanding of animal adaptation to the natural environment can inform both conservation of wild species and management of domesticated breeds without excessive reliance on external inputs. In particular, as climate change continues to impact global conditions, it will become increasingly important to promote those genotypes that can tolerate new environmental challenges.

Despite their lower productivity in comparison to European breeds, native African cattle (Bos taurus) display better survival rates as a result of thousands of years of both natural and human-imposed selection and admixture with Asian breeds. The closely related wild species, African buffalo (Syncerus caffer), inhabits many of the same ecological regions as cattle and thus has been subjected to many of the same selection pressures. Because buffalo (unlike cattle) have only been under natural selection, shared selection signatures between the two species are likely to be associated with environmental factors rather than human-imposed pressures. In this project, the student will analyse whole-genome sequence data from hundreds of cattle and buffalo sampled across Africa, using a variety of statistical tools to identify the most important environmental selection pressures on the two species and the genes and gene networks that have been under common selection.

Research questions

Is there evidence of genetic differentiation between African buffalo populations from different geographic locations or environmental conditions?

What environmental factors impose the strongest signals of selection on the genomes of African cattle and buffalo populations?

Which genes and gene networks show evidence of environmental selection in cattle and African buffalo? Are these associated with genetic admixture from different origins?

Is there evidence for shared environmental adaptation across bovids and more generally, across ruminants?

Methodology

The student will have access to unique cattle and buffalo whole genome sequencing datasets spanning hundreds of animals for both species, and they will first conduct bioinformatics analyses of these data to identify genetic variants segregating in different breeds and sub-species.

Subsequent population genetic analyses will address several goals: evaluate structure of cattle and buffalo genomes and test for evidence of admixture; map genomic regions associated with environmental adaptation phenotypes; perform a functional analysis of genomic regions associated with adaptation; and compare the genomic basis of environmental adaptation across species.

Year 1:

Training and familiarisation with software in population genetics, statistical analysis and bioinformatics techniques.

Preparation of literature review on genetics and ecology of African bovids. Identification of genetic variants in African buffalo data from raw sequence data. Assessment of genetic structure for cattle and African buffalo.

Year 2:

Identification of key environmental factors influencing cattle and African buffalo populations. Identification of regions of the genome showing evidence of adaptation to these factors.

Year 3:

Functional characterisation and comparison between the genes and processes underlying environmental adaptation in the two bovid species and other ruminants.

Training

A comprehensive training programme will be provided comprising both specialist scientific training and generic transferable and professional skills. Specialised skills include techniques in quantitative and population genetics, statistics, bioinformatics and genomics.

Requirements

The ideal student will have strong quantitative and computational skills and interests in genetics. Applicants should have at least a 2.1 degree. An MSc or equivalent experience in bioinformatics, computational biology, genetics or a related field will be an advantage.

References

Wiener, P., et al. 2021. Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations. Genome Biology and Evolution 13(3). https://academic.oup.com/gbe/article/13/3/evab014/6121100

Friedrich & Wiener. 2020. Selection signatures for high-altitude adaptation in ruminants. Animal Genetics, 51(2), 157-165. https://onlinelibrary-wiley-com.ezproxy.is.ed.ac.uk/doi/full/10.1111/age.12900

Meadows & Lindblad-Toh, 2017. Dissecting evolution and disease using comparative vertebrate genomics. Nature Reviews Genetics, 18(10), 624-636. https://www-nature-com.ezproxy.is.ed.ac.uk/articles/nrg.2017.51