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EASTBIO Genomics and evolution of recombination rates in the Soay sheep of St Kilda


   School of Biological Sciences

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  Dr S Johnston, Dr G Gorjanc, Prof P Keightley  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

When animals and plants produce eggs or sperm, chromosome pairs will recombine (or ‘cross-over’) to create new combinations of alleles. The generation of new genetic variation can help populations to respond to selection faster. However, recombination can also

break up good allele combinations and causes harmful mutations. These costs and benefits of recombination can vary within and between populations. If there is genetic variation underlying recombination rate itself, then it can respond to selection and evolve over time. However, we know little about if, how and why recombination rates are evolving. 

This project will address this question by identifying the genetic causes of recombination rate variation and the effects that this has an individual reproductive success. The student will use a large genomic dataset from one of the most intensively studied wild mammals in the world, the Soay sheep of St Kilda (https://twitter.com/SoaySheep).

 Key research objectives:

 1. What are the genomic variants driving variation in individual recombination rates?

2. How are recombination hotspots localised in a system with multiple copies of PRDM9, a mammalian hotspot gene?

3. Are high recombination rates associated with high mutation rates?

4. Are recombination rate and hotspot loci under selection?

 Analyses: The student will gain experience in working with whole genome sequence data; phasing the genome to identify chromosome crossovers; conducting gene-mapping, genome-wide association studies and genomic prediction to find the genetic basis of recombination; and/or other analyses that suit their interests.

 Research Training: The project will be mostly computational and will suit students who are willing to learn and further develop their bioinformatic skills. The first year includes a course on population genetics, quantitative genetics and statistics which will provide a foundation for the analytical work. Further training will be provided by EASTBIO workshops/symposia and Edinburgh Genomics. The student will also be able to take advantage of local, national and international collaborative links of the supervisors in both evolutionary genetics and animal breeding communities.

 Fieldwork: The student will be encouraged to contribute to fieldwork on St Kilda, a dual UNESCO World Heritage Site, to collect samples and learn about the ecology of the system.

https://sejohnston.com

[Email Address Removed]

http://www.homepages.ed.ac.uk/pkeightl/

The School of Biological Sciences is committed to Equality & Diversity: https://www.ed.ac.uk/biology/equality-and-diversity

The “Institution Website” button will take you to our online Application Checklist. From here you can formally apply online. This checklist also provides a link to EASTBIO - how to apply web page. You must follow the Application Checklist and EASTBIO guidance carefully, in particular ensuring you complete all the EASTBIO requirements, and use /upload relevant EASTBIO forms to your online application.


Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership http://www.eastscotbiodtp.ac.uk/how-apply-0
This opportunity is open to UK and International students and provides funding to cover stipend at UKRI standard rate (£17,668 annually in 2022) and UK level tuition fees. The fee difference will be covered by the University of Edinburgh for successful international applicants, however any Visa or Health Insurance costs are not covered. UKRI eligibility guidance: Terms and Conditions: https://www.ukri.org/wp-content/uploads/2020/10/UKRI-291020-guidance-to-training-grant-terms-and-conditions.pdf International/EU: https://www.ukri.org/wp-content/uploads/2021/03/UKRI-170321-InternationalEligibilityImplementationGuidance.pdf

References

Johnston SE et al. (2016) Conserved genetic architecture underlying individual recombination rate variation in a wild population of Soay sheep. Genetics, 203, 583–598.
Stapely J et al. (2017) Variation in recombination frequency and distribution across Eukaryotes: patterns and processes. Philosophical Transactions of the Royal Society B, 372, 20160455.

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