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Novel epigenetic markers of embryo quality to improve fish domestication.

University of Exeter - College of Life and Environmental Sciences

Qualification Type: PhD
Location: Exeter
Funding for: UK Students, EU Students
Funding amount: BBSRC SWBio DTP funded CASE studentship available for September 2022 entry. The studentship will provide funding of fees and a stipend which is currently £15,609 per annum for 2022-23, on a full time basis.
Hours: Full Time
Placed On: 22nd October 2021
Closes: 6th December 2021
Reference: 4275

Aquaculture production is increasing as food security becomes one of the main concerns for a growing population which increasingly requires more fish in their diet. 

Successful aquaculture relies in domestication, which in fish is very recent compared to birds and mammals. Fish depend upon their environment to trigger the different steps of their reproductive cycle, particularly oogenesis, affecting both oocyte quality and embryo developmental success. Global epigenetic changes occurring during embryogenesis are also influenced by the rearing environment, and the farm environment is known to cause large phenotypic and epigenetic changes. 

Epigenetic modifications can regulate gene expression without altering the DNA sequence. In mammals there is a reprogramming of DNA methylation during embryogenesis, but in some fishes it seems to be different, although it has only been studied in a few species to date. While in zebrafish DNA methylation does not undergo extensive erasure in embryos immediately after fertilisation, in medaka reprogramming seems to be similar to mammals, and our work suggests that in Atlantic salmon a small proportion of epigenetic changes caused by the rearing environment can be transmitted to the offspring.  

These data suggest that it might be possible to manipulate the rearing environment to control fish development and potentially embryo quality through epigenetic modifications, an option still underexplored in aquaculture. Moreover, if the epigenetic changes are passed to the next generation, epigenetic programming could establish an “environmental memory” during development to enhance adaptation to the farm environment and improve domestication. The main aim of this project is to identify epigenetic markers related to embryo quality and development which could be used to develop fish strains better adapted to live in captivity. 

For this, the student will develop a multidisciplinary project which will combine an experimental approach with methods on embryology and molecular biology (gene expression and epigenomics) using zebrafish and tilapia to assess the role of temperature changes development in determining embryo quality and its molecular basis. Specific training will be provided in fish husbandry and experimental design as well methods in embryology, DNA/RNA extraction, Next Generation Sequencing and Bioinformatics. 

Eligibility 

To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria. 

Please refer to the regulations or Annex 1 of the Research Council Training Grant Guide to confirm that you meet the residence criteria for a fully-funded studentship.  Any further queries in relation to residency must be directed to the institution. 

* An enhanced stipend is available for students with a recognised veterinary degree qualification (£24,090 per annum for 2022-2023). There may also be enhanced stipends associated with projects that have a CASE partner (highlighted as *CASE in the project lists). 

Applicants should have obtained, or be about to obtain, a 1st or 2:1 UK Honours degree, or equivalent qualifications gained outside the UK, in an appropriate area of science or technology.  Applicants with a Lower Second Class degree will be considered if they also have Masters degree or significant relevant non-academic experience. 

In addition, a minimum of a grade B in A-level Maths or equivalent qualification or experience is required. 

Equivalent qualifications/experience 

  • Physics A-level (grade B and above)
  • Undertaking units as part of your degree that have a significant mathematical component*

* eg maths, statistics, bioinformatics. 

Applicants must highlight their Maths background within their application and upload any supporting evidence. 

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