Genome, epigenome and environmental interactions in RAS reared Atlantic salmon

水产养殖每年为英国经济贡献超过18亿英镑，支持着8800多人的生计，其中许多人生活在偏远社区。养殖的苏格兰鲑鱼是英国最有价值的养殖食品出口产品。工业和政府有强烈的增长愿望（从2016年的162,817吨到2030年的bb300,000吨，苏格兰海洋科学和水产养殖增长到2030年，苏格兰食品和饮料），以满足不断增长的市场需求。然而，由于疾病爆发和损失造成的紧急收成，农业部门正面临相当大的压力。通过采用新的养殖技术（包括封闭再循环水产养殖系统- ras）和控制鱼类生理（向海水转移的时间和早熟）的养殖制度，鲑鱼产业得以在全球迅速扩张。苏格兰的大多数鲑鱼生产商要么已经建成，要么正在建设这种大型RAS生产装置。这些系统明显优于陆基水流和淡水湖泊系统，包括减少用水量、改善废物和排放管理、控制疾病和操纵淡水环境条件，从而实现全年生产和市场供应。在可控条件下（恒定的高温和连续的光周期）在RAS中生产的鲑鱼幼崽和幼崽可以达到更大的尺寸，并且可以比以往更早地转移到海水中。然而，我们对这些新的养殖系统对鲑鱼生理的影响的了解非常有限，RAS养殖的幼鱼在SW转移后的表现似乎不如湖泊养殖的鱼。重要的是，RAS系统性能的遗传基础知之甚少，这些信息对支持未来的选择性育种计划至关重要。该项目的目的是首先研究整个RAS生产周期中大西洋鲑鱼关键性能性状（生长、渗透适应、免疫和健康状况、收获质量）的遗传基础。该项目旨在确定RAS中产生的这些性状的遗传参数，并与环境生产系统进行比较。为此，该项目将利用目前BBSRC/NERC资助的ROBUSTSMOLT项目（BB/S004432/1和BB/S00436X/1分别授予UoS和UoE）已经计划在2021-2022年进行的全面实验，比较RAS与湖产幼鱼的性能。博士项目将利用高通量基因分型技术（SNP-chip）对来自RAS和湖泊的鱼类进行表型分析，以获得商业上相关的性状，并对其进行基因分型。此外，该项目还旨在研究早期环境条件的表观遗传效应，通过全基因组DNA甲基化分析和组蛋白修饰DNA靶点的全基因组谱分析，利用斯特林大学现有的实验性RAS设施。环境驱动的基因组表观遗传调控也可以解释鱼类在RAS中表达的表型差异。最后，该项目将利用一系列分子生物标志物来表征RAS对鱼类渗透调节功能的影响，以改进对熏蒸特性的评估，熏蒸特性在SW转移后的性能中起着关键作用。未来的学生将成为UoS水产养殖研究所和UoE罗斯林研究所多学科小组的一员，并将获得大西洋鲑鱼生理学，分子生物学，遗传学和表观基因组调控方面的专业知识。该学生将参与通过环境实验运行大型基因型，在整个生产周期中采样以评估大西洋鲑鱼的一系列商业和科学相关性状，设计和运行性状相关生物标志物的qPCR，分析高通量基因型分析和下一代表观遗传效应测序。这个学生将接受培训

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