Towards the causal factors underlying the genetic resistance of Atlantic salmon to infectious disease

由于传染病的爆发，通过水产养殖实现鱼类的可持续生产面临着严重和持续的威胁。与英国特别相关的是传染性胰腺坏死（IPN）和胰腺疾病（PD）等病毒性疾病对大西洋鲑鱼的影响。对于这两种疾病，我们看到鱼类之间在抗性方面存在明显的遗传差异，可以利用这种差异来减少疾病的发病率及其对生产的影响。本研究的总体目标是使用新方法来了解宿主遗传抗性，重点关注对IPN抗性的主要位点的范例。众所周知，IPN在鲑鱼生命周期的两个不同窗口期产生影响；首先是在孵化后不久的淡水中，其次是在转移到海水后不久。我们之前的研究已经证明，对IPN的遗传抗性跨越两个易感性窗口是在基因组的单个区域（QTL）的控制下。通过对不同基因型患病鱼的基因表达研究，我们也开始揭示这种QTL效应背后的重要基因和途径。“下一代”测序技术的快速发展为定位和理解该QTL背后的因果因素提供了新的机会。通过这样做，这项研究将大大促进我们对鲑鱼基因组的理解，并导致对疾病抗性的基本理解取得进展，提供了宿主基因组中假设的单一突变与显著改变疾病后果的例子。为了实现这些目标，拟议的研究将集中于创造所需的资源，以(i)鉴定IPN QTL效应的潜在基因，（ii）确定影响PD抗性的基因组区域，以及（iii）进一步了解鲑鱼基因组及其遗传。首先，将高通量DNA测序技术应用于已知QTL基因型的鱼类，以促进标记的产生，并将QTL定位到更小的基因组区域。其次，鲑鱼的基因表达谱将通过应用于基因抗性和易感鱼类的尖端测序技术进行表征。研究不同基因型鱼类之间的基因、途径和网络差异，将有助于了解QTL的作用方式。第三，这些结果将通过将相关标记和序列映射到鲑鱼基因组序列上进行整合。这将导致假定的功能性抗病基因和遗传变异，将对其因果关系进行测试。所产生的资源还将用于绘制鲑鱼对PD抗性的QTL，研究鲑鱼选择的遗传特征，以及在鲑鱼基因组中观察到的剩余四倍体的各个方面。这项研究的结果将包括对抗病基因座急剧改变感染结果的机制的知识进展，对宿主和病原体基因组的相互作用及其进化军备竞赛具有影响。鲑鱼序列数据的大规模生成将导致对即将到来的鲑鱼基因组序列中基因的改进注释。此外，阐明鲑鱼对病毒病具有抵抗力的基因将有助于开发提高抵抗力的基因测试，并有机会开发新的疫苗和诊断方法，这些疫苗和诊断方法可用于鲑鱼水产养殖业，以降低与疾病有关的死亡率。与鲑鱼养殖公司Landcatch Natural Selection Ltd的合作确保了开发成果的明确路线。

The sustainable production of fish through aquaculture faces a serious and persistent threat due to infectious disease outbreaks. Of particular relevance to the UK is the impact on Atlantic salmon of viral disease such as Infectious Pancreatic Necrosis (IPN) and Pancreas Disease (PD). For both these diseases, we see clear genetic differences between fish in their resistance, which can be exploited to reduce the incidence of disease, and its impact on production. The overall aim of this research is to use novel approaches to gain an understanding of host genetic resistance, focusing on the exemplar of a major locus underlying resistance to IPN. IPN is known to impact at two distinct windows of the salmon lifecycle; firstly in freshwater shortly after hatching, and secondly shortly after transfer to seawater. Our previous research has demonstrated that the genetic resistance to IPN across both windows of susceptibility is under the control of a single region of the genome (QTL). We have also begun to unravel the important genes and pathways underlying this QTL effect, through gene expression studies of disease-challenged fish of different genotypes. The rapid development of 'next-generation' sequencing technology offers novel opportunities to move towards locating and understanding the causal factors underlying this QTL. In doing so, the research will significantly advance our understanding of the salmon genome, and lead to advances in the fundamental understanding of disease resistance, providing an example of a hypothesised single mutation in the host genome with dramatically altered disease consequences. To achieve these goals, the proposed research will focus on creating the resources required to (i) identify the genes underlying the IPN QTL effects, (ii) determine the regions of the genome that affect resistance to PD, and (iii) to gain further understanding of the salmon genome and its inheritance. Firstly, a novel application of high-throughput DNA sequencing will be applied to fish of known QTL genotype to facilitate marker generation, and mapping of the QTL to a smaller region of the genome. Secondly, the gene expression profile of salmon will be characterised through cutting-edge sequencing techniques applied to genetically resistant and susceptible fish. Investigation of the genes, pathways and networks differing between the fish of alternative genotypes will yield information on the mode of action of the QTL . Thirdly, these results will be integrated through mapping relevant markers and sequences onto the salmon genome sequence. This will lead to putative functional disease resistance genes and genetic variation, which will be tested for causality. The resources generated will also be applied to map QTL underlying the resistance of salmon to PD, to investigate genetic signatures of selection in salmon, and aspects of the residual tetraploidy observed in the salmon genome. The outcomes of the research will include advances in knowledge of the mechanisms through which disease resistance loci drastically alter the outcome of infection, with implications for the interaction of host and pathogen genomes and their evolutionary arms race. The large-scale generation of salmon sequence data will lead to an improved annotation of the genes in the forthcoming salmon genome sequence. Furthermore, elucidation of the genes underlying salmon resistance to viral disease will lead to the development of genetic tests for improved resistance, and opportunities for novel vaccines and diagnostics, which can be applied in the salmon aquaculture industry to reduce disease-related mortality. The collaboration with salmon breeding company Landcatch Natural Selection Ltd ensures a clear route for the exploitation of the results.