Transcriptional consequences of introgression between farmed and wild Atlantic salmon (Salmo salar)

BACKGROUND: The continuing expansion of the global Atlantic salmon (Salmo salar) aquaculture industry has been mirrored by long-term declines in wild salmon stocks. While the extent to which these two observations are related remains to be established, it is clear that studying interactions between wild and farmed salmon will inform management policies directed towards sustainability of salmon aquaculture and the survival and fitness of wild salmon stocks. In particular the consequences of introgression between farmed and wild stocks need to be better documented and understood. This research theme forms part of the AQUATRACE remit to apply cutting-edge genomic methods to the development of high-powered, cost-efficient, forensically validated and transferable DNA-based tools to identify and trace the impact of farmed fish in the wild.

PROJECT: The aim of this 3 year PhD project is to improve general knowledge of the genetic differences between farmed (domesticated) and wild Atlantic salmon by applying transcriptomic technologies (e.g. oligo microarrays, qPCR, RNAseq) to a comparison of wild, farmed and F1 hybrid salmon that have been reared under controlled experimental conditions. The study will concentrate on early stages (egg / fry) but may involve work on later life-history stages according to findings. Studies will examine phenotypic and transcriptomic responses of fish to standardised conditions and to key early life-cycle stressors, in order to characterise differences and similarities between wild and farmed stocks. The study will build upon experience and data derived from a similar existing collaborative project between IOA and the Institute of Marine Research, Bergen (IMR), part of the 'INTERACT' project funded by the Norwegian Research Council. Work will be carried out at both IOA (study centre; molecular and bioinformatic analyses) and IMR (fish rearing / controlled experiments).

The successful applicant will be trained in a range of techniques including; salmon husbandry, experimental design, microarray analysis, sample preparation for high-throughput sequencing and downstream bioinformatics analysis, and quantitative PCR together with more general transferable skills such as scientific writing and conference presentation. He / she will be expected to interact with other participants in the AQUATRACE consortium (22 institutional partners engaged in genetic research on five farmed fish species) during specific research activities and also at annual project meetings. In addition the student will have access to a comprehensive programme of seminars / short courses for postgraduate research students run by Stirling Graduate School.

APPLICANTS: Candidates must hold a First/Upper Second Class BSc or an MSc in a relevant subject. Prior molecular-based laboratory experience is desirable. Candidates must have the aptitude and commitment to be trained and work in both molecular laboratory and field research environments. The applicant will be based at the UoS but will be required to spend up to 2-3 months per year in Norway to undertake experiments at IMR research facilities (under the supervision of Dr Kevin Glover, IMR). Applications are only invited from UK / EU candidates or those with additional independent funding.
Applicants are encouraged to contact Dr. John Taggart ([Email Address Removed] , telephone +44 1786 467927) for further details of the project.

APPLICATION PROCESS: Complete applications, consisting of a covering letter, an up-to-date CV and the name and contact details of two referees (at least one academic referee) should be submitted to Ms Anda Kilpatrick, IOA secretary, [Email Address Removed]. Appropriate candidates will then be selected for interview. Closing date for applications 28th May 2013.