Applying genomics to establish mechanisms of disease resistance against a virus impacting on a globally farmed fish, the Common Carp (Cyprinus carpio)

应用基因组学建立针对影响全球养殖鱼类鲤鱼（Cyprinus carpio）的病毒的抗病机制

• 批准号: BB/R010870/1
• 负责人: Jackie Lighten
• 金额: $ 38.84万
• 依托单位: UNIVERSITY OF EXETER
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR010870%2F1
• 关键词: Applying; genomics; establish; mechanisms; disease

With a growing global population, the demand for food is increasing rapidly. Wild fish stocks have been subjected to unsustainable over exploitation, resulting in major population declines, and we are increasingly reliant on aquaculture (the farming of fish) to meet our global needs. Aquaculture provides over 50% of the supply of harvested aquatic organisms for consumption (over 70 million tons), and is an important source of animal protein for billions of people. The contribution of aquaculture is predicted to rise to over 60% by 2030. However, further intensification will increase the risk of disease due to high stocking densities, low genetic diversity in brood-stocks, and increased pathogen dispersal associated with international trade. Traditionally, disease in farming is managed by pesticides/antibiotics or vaccines. These however offer only a short term and unsustainable solution to disease prevention as pathogens/vectors can evolve resistance to medications, resulting in re-emerging infectious diseases. The security of aquaculture is of paramount importance and so new disease control methods must be developed to ensure global food security.Cutting edge DNA research offers an approach to help manage disease in aquaculture. DNA provides the blueprint for how living cells function and interact, and DNA variation results in the diversity of life we observe, controlling key biological characteristics such as appearance, behaviour, and disease susceptibility. The objective of my research proposal is to identify the differences in DNA between individuals of an important aquaculture fish species, the Common Carp (Cyprinus carpio), that are either resistant or susceptible to the deadly Koi Herpesvirus (KHV). Importantly, this is the first project to characterize global DNA variation in carp and KHV, which is an essential component in understanding and managing disease. Understanding host defence systems and the variable genomic components in the DNA that confer disease resistance, may offer part of the solution to the problems facing aquaculture, enabling farmers to create diverse brood-stocks with resistance to local pathogens. The analysis tools developed in this BBSRC fellowship can be applied to other emerging infectious diseases of carp, and the research can be used as a blueprint for other species in aquaculture.Common Carp is the third most farmed fish globally and is worth billions of pounds per annum. Aside from its global importance as a protein source for millions of people, it is also farmed in the UK and Europe for angling and as an ornamental strain (Koi). Alone, the carp fishing industry in the UK is worth over two billion pounds per annum. Huge financial losses have occurred in the carp industry through the rapid global spread of KHV. Despite the global value of carp and its vulnerability to viral outbreaks, genetically informed selective breeding is non-existent. This is a major limitation for the expansion of the industry and surprising given strong recommendations from the Food and Agriculture Organization (FAO) for intensified understanding and control of carp diseases (2004), and the fact that genomic techniques are now available to apply to such problems.By testing individuals from around the world for gene variants that promote resistance, and understanding the geographic patters of viral diversity, carp can be artificially selected by farmers to produce fish that are robust to infection from local strains of deadly viruses. Research focused purely on controlled laboratory infection trials in single host and viral strains, will produce findings that may be of little relevance to real-world aquaculture that comprises many strains of both host and pathogen. As such, I will pioneer a global plan for immuno-genomics informed selective breeding in carp aquaculture, which will contribute to promoting food security in this important species of fish.

随着全球人口的增长，对粮食的需求正在迅速增加。野生鱼类资源受到不可持续的过度开发，导致种群数量大幅下降，我们越来越依赖水产养殖（鱼类养殖）来满足我们的全球需求。水产养殖提供了50%以上的水生生物供应（超过7000万吨），是数十亿人动物蛋白的重要来源。预计到2030年，水产养殖的贡献将上升到60%以上。然而，由于放养密度高、种鱼遗传多样性低以及与国际贸易有关的病原体扩散加剧，进一步的集约化将增加疾病风险。传统上，农业中的疾病是通过杀虫剂/抗生素或疫苗来控制的。然而，这些措施只能为疾病预防提供短期和不可持续的解决办法，因为病原体/媒介可能对药物产生耐药性，导致传染病重新出现。水产养殖的安全至关重要，因此必须开发新的疾病控制方法，以确保全球粮食安全。尖端的DNA研究提供了一种帮助管理水产养殖疾病的方法。DNA为活细胞的功能和相互作用提供了蓝图，DNA变异导致了我们观察到的生命的多样性，控制着关键的生物特征，如外观、行为和疾病易感性。我的研究计划的目的是确定一种重要的水产养殖鱼类——鲤鱼（Cyprinus carpio）个体之间的DNA差异，这种鱼类要么对致命的锦鲤疱疹病毒（KHV）具有抗性，要么易受感染。重要的是，这是第一个描述鲤鱼和KHV全球DNA变异的项目，这是理解和管理疾病的重要组成部分。了解宿主防御系统和DNA中赋予抗病能力的可变基因组成分，可能为解决水产养殖面临的问题提供部分解决方案，使农民能够培育出对当地病原体具有抗性的多样化种鱼。本研究开发的分析工具可应用于其他新出现的鲤鱼传染病，并可作为其他水产养殖物种的研究蓝图。鲤鱼是全球第三大养殖鱼类，每年价值数十亿英镑。除了作为数百万人的蛋白质来源在全球具有重要意义外，它还在英国和欧洲养殖，用于垂钓和作为观赏品种（锦鲤）。单是英国的鲤鱼捕捞业，每年的产值就超过20亿英镑。由于KHV在全球的迅速传播，鲤鱼产业遭受了巨大的经济损失。尽管鲤鱼具有全球价值，而且易受病毒爆发的影响，但不存在遗传知情的选择性育种。鉴于粮食及农业组织（粮农组织）关于加强了解和控制鲤鱼疾病的强烈建议（2004年），以及基因组技术现已可用于解决这类问题，这是该行业发展的一个主要限制。通过对来自世界各地的个体进行基因变异测试，并了解病毒多样性的地理模式，农民可以人工选择鲤鱼，以生产对当地致命病毒株感染具有抵抗力的鱼。研究仅仅集中在单一宿主和病毒株的受控实验室感染试验上，将产生的发现可能与现实世界中包含许多宿主和病原体菌株的水产养殖没有什么关系。因此，我将率先制定一项全球计划，在鲤鱼养殖中利用免疫基因组学进行选择性育种，这将有助于促进这一重要鱼类的粮食安全。

项目成果

Genetic variation in resistance and high fecundity impede viral biocontrol of invasive fish

抗性和高繁殖力的遗传变异阻碍了入侵鱼类的病毒生物防治

• DOI: 10.1111/1365-2664.13762
• 发表时间: 2020
• 期刊: Journal of Applied Ecology
• 影响因子: 5.7
• 作者: Mintram K

Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication.

在四倍体鲤鱼中编码保守抗病毒反应的ohnologs的对称表达表明在全基因组复制后不存在亚基因组优势。

• DOI: 10.1016/j.ygeno.2023.110723
• 发表时间: 2023
• 期刊: Genomics
• 影响因子: 4.4
• 作者: Blasweiler A