Supervisors: Dr Pam Wiener, Professor Sam Martin, Professor Andrea Doeschl-Wilson, Professor Ross Houston, Dr John Benzie
Project Description:
Background:
Nile tilapia (Oreochromis niloticus) is one of the most important farmed food fish in the developing world. Selective breeding of tilapia is a key component of sustainable production, contributing to improvements in fish growth and resilience. However, the consequences of selective breeding on the genetic makeup of the farmed tilapia strains is unknown. This project aims to use modern genomics tools to identify “signatures” (specific regions of the genome) associated with both selective breeding and adaptation to particular farmed environments. Knowledge of these key genomic regions will help inform future tilapia breeding and ultimately contribute to increased tilapia production.
To achieve this aim, whole-genome sequences of farmed tilapia from several tropical countries will be used to identify selection signatures. Comparisons of these signatures between populations will allow separation of the consequences of selection for fast growth from those associated with fish adapting to particular environments. Identification of environment-specific genomic signatures, and subsequently genes and functions associated with these, will reveal functional changes specific to adaptation to the particular environments in which these fish are kept. These genomic regions and functional elements can be utilised for genetic improvement (e.g. via genomic selection, gene editing) to optimise tilapia production. This project involves a collaboration between the Roslin Institute (University of Edinburgh), the University of Aberdeen and WorldFish, an international, non-profit research organization that works to reduce hunger and poverty across the world by improving fisheries and aquaculture. The project will provide an exciting opportunity for a keen student to receive training in cutting-edge genetics and genomics techniques at a world-class research institute while also contributing to improvement of food security in the developing world.
Project outline:
1. To characterise genetic variation in farmed tilapia samples from whole-genome sequence data, thereby providing a valuable dataset for subsequent analyses
2. To identify regions of the tilapia genome showing evidence of past or current selection (“genomic signatures of selection”)
3. To separate genomic signatures of selection into those influenced primarily by selective breeding for fast growth versus those influenced by adaptation to specific environments
4. To characterise the functional elements associated with selection for fast growth or environmental adaptation
Training: The studentship will provide extensive training in transferable skills and techniques in quantitative and population genetics, statistics, bioinformatics and genomic analysis, including analysis of whole genome sequence data. The University of Edinburgh offers a number of valuable taught courses that may benefit the student. The student will also attend a variety of seminars, journal clubs and local meetings and there will be opportunities for attendance at national and international conferences.
References:
Agha, S., W. Mekkawy, N. Ibanez-Escriche, C.E. Lind, J. Kumar, A. Mandal, J.A.H. Benzie, and A. Doeschl-Wilson. Breeding for robustness: investigating the genotype-by-environment interaction and micro-environmental sensitivity of Genetically Improved Farmed Tilapia (Oreochromis niloticus). Animal Genetics (Epub 2018 Jul 30). https://doi.org/10.1111/age.12680.
Robledo, D., C. Palaiokostas, L. Bargelloni, P. Martinez, and R. Houston. 2018. Applications of genotyping by sequencing in aquaculture breeding and genetics. Reviews in Aquaculture 10: 670-682. https://onlinelibrary-wiley-com.ezproxy.is.ed.ac.uk/doi/full/10.1111/raq....
Stainton, J.J., B. Charlesworth, C.S. Haley, A. Kranis, K. Watson and P. Wiener. 2017. Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens. Journal of Animal Breeding and Genetics 134: 87-97. https://doi-org.ezproxy.is.ed.ac.uk/10.1111/jbg.12228
If you wish to apply for this project, please check this link and send your application to this email.
