Genome, epigenome and environmental interactions in RAS reared Atlantic salmon

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Aquaculture contributes more than £1.8bn to the UK economy every year and supports over 8,800 livelihoods - many in remote communities. Farmed Scottish salmon is the most valuable farmed food export in the UK. Industry and Government have strong aspirations for growth (from 162,817t in 2016 to >300,000t by 2030, Marine Scotland Science and Aquaculture growth to 2030, Scotland Food and Drink) to meet increasing market demands. However, considerable pressures are being experienced by the farming sector because of emergency harvests due to disease outbreaks and losses. The rapid global expansion of the salmon industry has been made possible through the adoption of new farming technologies (including contained recirculation aquaculture systems-RAS) and husbandry regimes to manipulate the fish's physiology (time to seawater transfer and early maturation). Most salmon producers in Scotland have either already built or are in the process of building such large RAS production units. These systems have clear advantages over land-based flow through and freshwater loch systems including a reduction in water usage, improved management of wastes and discharges, the control of disease and the manipulation of environmental conditions in freshwater (FW) allowing year-round production and market supply. Salmon parr and smolts produced in RAS under manipulated regimes (constant high temperature and continuous photoperiod) reach larger sizes and can be transferred to seawater (SW) earlier than ever before. However, our knowledge of the impacts these new rearing systems have on salmon physiology is very limited and RAS produced smolts do not appear to perform as well as loch produced fish following SW transfer. Importantly, the genetic basis of performance in RAS systems is poorly understood, and such information is critical to support future selective breeding programmesThis project aims are firstly to study the genetic basis of key performance traits (growth, osmotic adaptation, immunity & health status, harvest quality) throughout the RAS-based production cycle in Atlantic salmon. The project intends to identify genetic parameters for these traits produced in RAS, and to compare to ambient production systems. To do so, the project will take advantage of a full scale experiment already planned in 2021-2022 as part of current BBSRC/NERC funded ROBUSTSMOLT project (BB/S004432/1 and BB/S00436X/1 awarded to UoS and UoE, respectively) comparing performances of RAS vs. loch produced smolts. The PhD project will phenotype fish from RAS and loch for commercially relevant traits and genotype them using high-throughput genotyping technologies (SNP-chip). In addition, the project also aims to study the epigenetic effects of early environmental conditions through genome wide analyses of DNA methylation and genome-wide profiling of DNA targets for histone modification using available experimental RAS facilities at the University of Stirling. Environmentally driven epigenetic regulations of the genome may also explain differences in fish phenotypes expressed in RAS. Finally, the project will characterise the effects of RAS on fish osmoregulatory function using a range of molecular biomarkers to improve the assessment of the smoltification trait which plays a critical role in post SW transfer performances.The prospective student will be part of a multidisciplinary group at the Institute of Aquaculture in UoS and at The Roslin Institute in UoE and will acquire expertise in Atlantic salmon physiology, molecular biology, genetics and epigenomic regulations. The student will be involved in running a large genotype by environment experiment, sampling throughout the production cycle to assess a range of commercially and scientifically relevant traits in Atlantic salmon, designing and running qPCR for trait related biomarkers, analysing high-throughput genotyping analyses and next generation sequencing for epigenetic effects. The student will received traini