A breeding programme simulation software for aquaculture

   College of Medicine and Veterinary Medicine

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

About the Project

This project will be an exciting collaboration between the Global Academy of Agriculture and Food Systems, The Roslin Institute, 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.

Agriculture (1)

Funding Notes

This 3.5 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.
Application form can be downloaded via
https://www.ed.ac.uk/sites/default/files/atoms/files/rdsvs_gaffs_roslin_foundation_studentship_application_form_2024-25.doc. Applications should be emailed to [Email Address Removed].
If you are applying for more than one studentship please submit a separate application with a closing date of noon on 8th January 2024 at https://www.ed.ac.uk/roslin/work-study/opportunities/studentships


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?

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