Roslin Foundation Studentship - A breeding programme simulation software for the aquaculture sector at University of Edinburgh on FindAPhD.com

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Dr G Gorjanc, Dr Alastair Hamilton, Dr Smaragda Tsairidou No more applications being accepted Competition Funded PhD Project (Students Worldwide)

Edinburgh United Kingdom Genetics Genomics

College of Medicine and Veterinary Medicine, University of Edinburgh

About the Project

This project will be an exciting collaboration between The Roslin Institute, the Global Academy of Agriculture and Food Systems, and Hendrix Genetics, a world-leading multi-species breeding company with extensive experience in aquaculture, animal breeding technologies, and genetics. The aim of the project is to develop a computational platform for modelling aquaculture breeding programmes by expanding the AlphaSimR simulation software (Gaynor et al. 2020).

AlphaSimR is being implemented primarily for professional purposes, to model animal and plant breeding programmes. The research community and industry have also recognised the importance of AlphaSimR for training, and we have recently released an online course for specialised training in AlphaSimR. As the aquaculture sector is fast growing in the UK and globally, advanced data tools tailored for this sector are needed to help optimise commercial breeding programmes and predict outcomes in-silico before they are deployed in practice.

In this PhD, the student will build strong skills in computer programming, modelling and data analysis, and develop a deep understanding of the principles of quantitative genetics, breeding programme design, and genomic selection. The student will develop a novel simulation framework for aquaculture and test it for shrimp breeding, a rapidly growing sector, using real data from Hendrix Genetics. Throughout the project, the student will be guided by Supervisors with extensive experience in quantitative genetics, breeding, and data analysis, and will be supported to obtain additional training to further enhance their skills. In addition, the proposed project will allow the student to acquire experience in a commercial environment via placements at Hendrix Genetics Headquarters (Netherlands) and their hatchery (Scotland). The successful applicant will be expected to spend most time in Edinburgh, attend regular in-person and online meetings with the supervisory team and the industrial partner, attend and contribute to seminars and relevant conferences, and publish in academic journals.

Funding Notes

This 4 year studentship opportunity is open to UK and international students and provides funding to cover enhanced stipend, tuition fees and enhanced consumable and travel costs. Applications including a statement of interest and full CV with names and addresses (including email addresses) of two academic referees, should be emailed to [Email Address Removed].
When applying for the studentship please state clearly the project title/s and the supervisor/s in your covering letter.

References

Gaynor, R.C., Gorjanc, G., Hickey, J.M. (2021), AlphaSimR: an R package for breeding program simulations, G3 Genes|Genomes|Genetics, 11(2), jkaa01. https://doi.org/10.1093/g3journal/jkaa017
–> AlphaSimR reference paper
Gaynor, R.C., Gorjanc, G., Bentley, A.R., Ober, E.S., Howell, P., Jackson, R., Mackay, I.J. and Hickey, J.M. (2017), A Two-Part Strategy for Using Genomic Selection to Develop Inbred Lines. Crop Science, 57: 2372-2386. https://doi.org/10.2135/cropsci2016.09.0742
–> Publication that has used AlphaSimR and led to a paradigm-shift in large plant breeding programmes, such as Bayer CropSciences (ex Monsanto), as manifested by significant internal reorganisations
Tsairidou, S., Hamilton, A., Robledo, D., Bron, J.E., Houston, R.D. (2020), Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon. G3, 10(2):581-590. https://doi.org/10.1534/g3.119.400800
–> Our past experience with low-cost genotyping and genomic selection using imputed genotypes in aquaculture

Where will I study?

University of Edinburgh

One of the world''s top universities, consistently ranked in the world top 50 and placed 20th in the QS World University Rankings 2020. We provide a stimulating working, learning and teaching environment with access to excellent facilities and attract the world''s best, from Nobel Prize winning laureates to future explorers, pioneers and inventors.