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

由于传染病爆发，水产养殖的可持续鱼类生产面临严重和持续的威胁。与英国特别相关的是病毒性疾病对大西洋鲑鱼的影响，如传染性胰腺坏死（IPN）和胰腺疾病（PD）。对于这两种疾病，我们看到鱼类之间在抵抗力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生率及其对生产的影响。本研究的总体目标是使用新的方法来了解宿主的遗传抗性，重点是对IPN抗性的主要位点的范例。已知IPN影响鲑鱼生命周期的两个不同窗口;首先是在孵化后不久的淡水中，其次是转移到海水后不久。我们以前的研究已经证明，在两个敏感窗口中对IPN的遗传抗性是在基因组的单个区域（QTL）的控制下。通过对不同基因型的疾病挑战鱼的基因表达研究，我们也开始解开这种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的因果因素提供了新的机会。在这样做的过程中，这项研究将大大推进我们对鲑鱼基因组的理解，并导致对抗病性的基本理解的进步，提供了宿主基因组中假设的单一突变的一个例子，大大改变了疾病的后果。为了实现这些目标，拟议的研究将集中在创造所需的资源，以（i）确定IPN QTL效应的基因基础，（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，高通量DNA测序的新应用将应用于已知QTL基因型的鱼，以促进标记产生，并将QTL定位到基因组的较小区域。其次，鲑鱼的基因表达谱将通过应用于遗传抗性和易感鱼类的尖端测序技术来表征。对不同基因型的鱼之间不同的基因、途径和网络的调查将产生关于QTL作用模式的信息。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来整合。这将导致推定的功能性抗病基因和遗传变异，这将被测试的因果关系。所产生的资源也将被应用于映射QTL的鲑鱼抗PD，研究鲑鱼选择的遗传特征，以及鲑鱼基因组中观察到的残留四倍体的方面。该研究的成果将包括对抗病基因座大幅改变感染结果的机制的了解，以及对宿主和病原体基因组相互作用及其进化军备竞赛的影响。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的基因的改进注释。此外，阐明鲑鱼对病毒性疾病的抵抗力的基因将导致开发用于提高抵抗力的基因测试，以及开发新疫苗和诊断方法的机会，这些疫苗和诊断方法可应用于鲑鱼水产养殖业，以降低与疾病相关的死亡率。与鲑鱼养殖公司Landcatch Natural Selection Ltd的合作确保了成果开发的明确路线。

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.