BBSRC SWBio DTP PhD studentship:The genetic basis of acid tolerance in brown trout (Salmo trutta)

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP). The SWBio DTP is a BBSRC-funded PhD training programme in the biosciences, delivered by a consortium comprising the Universities of Bristol (lead), Bath, Cardiff and Exeter and Rothamsted Research. The SWBio DTP projects are designed to provide outstanding interdisciplinary training in a range of topics in Agriculture & Food Security and world-class Bioscience, underpinned by training in mathematics and complexity science. Each project will be supervised by an interdisciplinary team of academic staff and will follow a structured training 4-year PhD model.

Up to 4 fully-funded studentships at the University of Exeter are being offered to start in September 2017. The studentships will provide funding for a stipend (currently £14,296 per annum for 2016-17), research costs and UK/EU tuition fees at Research Council UK rates for 48 months (4 years) for full-time students, pro-rata for part-time students.

Academic Supervisors:

Main Supervisor: Dr Jamie Stevens, University of Exeter
Co-supervisor: Dr Bruce Stockley, Westcountry Rivers Trust
Co-supervisor: Dr Andrew Griffiths, University of Exeter

Project Description:

Climate change research increasingly focuses on ocean acidification and its negative effects on marine ecosystems. However, many freshwater systems and the animals residing in them are also under threat from rising atmospheric CO2 levels, the acidifying effects of climate change and acid rain. Brown trout (Salmo trutta) have shown themselves able to live in freshwaters with a very broad range of pH (pH 5 – pH 8), and able to survive temporary acidic flushes of down to pH 3, for example in peat moor streams.

This project aims to identify the genetic basis of acid tolerance in brown trout through changes in gene expression (transcriptomics) and population genetic analysis (using single nucleotide polymorphisms – SNPs). We will use two complementary approaches: RADseq and RNAseq to investigate the genetic differences between trout populations inhabiting acid, neutral and alkaline rivers in southern Britain.

Uniquely, collaboration with our CASE partner – The Westcountry Rivers Trust – provides a rare opportunity to research patterns of gene expression in trout inhabiting highly acidic moorland streams of Dartmoor. For the first time, permission has been granted by the Environment Agency to lime (i.e. to artificially reduce the pH) an extremely acid stretch of river on upland Dartmoor. Samples of gill and kidney will be collected from trout at the treatment site, together with those inhabiting acidic waters immediately upstream of the limed site. RNAseq analysis will characterise changes in gene expression related to acidity, identifying genes important to physiological responses in wild populations.

Additionally, we will use RADseq to analysis the genetic profiles of fish from three river types: low pH (Dartmoor streams), neutral rivers (other rivers in Cornwall and Devon) and more alkaline waters (chalk streams in Dorset/Hampshire). We already hold many samples of trout from these regions, including samples from both acid moorland sites and neutral lowland locations. This will allow us to identify SNPs that segregate definitively between ecotypes and to identify regions of the trout genome associated with adaptations to living in a low pH environment.

By combining population genomic and gene expression approaches the study will facilitate understanding of the basis of acid tolerance in salmonids. It also has the potential to reveal the mechanisms of local adaptation in these populations and the genetic architecture underlying such adaptation. This information is invaluable for salmonid conservation and aquaculture in the face of global rises in CO2 levels.


For more information and details on how to apply, go to http://www.exeter.ac.uk/studying/funding/award/?id=2324