Application of genetic markers to improve resistance to herpes virus in commercial oyster populations

背景：太平洋牡蛎（C.牡蛎（Oyster herpes virus，OsHV）是世界上最重要的水产养殖物种之一，但其可持续生产受到牡蛎疱疹病毒（OsHV）爆发的威胁，该病毒可导致高死亡率。在养殖种群中，抗性存在大量宿主遗传变异。因此，通过选择性育种提高存活率有可能成为疾病控制的一个主要组成部分。然而，英国牡蛎生产还没有能力生产更具抗性的种群，因为贝类的结构化选择性育种计划还不存在。作为正在进行的BBSRC-NERC可持续水产养殖奖的一部分，罗斯林研究所，Cefas和爱丁堡基因组公司开发了第一个牡蛎高密度单核苷酸多态性（SNP）阵列。同时，成功进行了实验室病毒攻毒实验。来自该试验的抗性和易感牡蛎正在进行基因分型，以绘制牡蛎基因组中的抗性位点。主要的实际成果将是SNP标记，可以预测哪些牡蛎对疾病有抵抗力。项目合作伙伴和挑战：英国缺乏贝类的选择性育种，这带来了重大挑战（和机会）英国生产;即（1 -短期）从对OsHV-1具有高抗性的亲本牡蛎中鉴定和育种，（2 -长期）转向管理良好的牡蛎选择性育种，利用遗传变异来改善关键性状。罗斯林研究所将与Cefas和英国牡蛎孵化场Guersey Sea Farms Ltd和Seasalter Shellfish Ltd合作，以应对这些挑战。他们还将与Cawthron研究所（新西兰）合作，该研究所在贝类育种和繁殖方面处于世界领先地位，但尚未在其育种方案中应用现代基因组工具。该项目直接促进了呼吁中关于“种群增殖的育种和遗传学方法”和“健康和疾病的监测和控制”的主题。目的和目标：本项目的主要目的是应用遗传标记在养殖场环境中培育对牡蛎疱疹病毒具有更高抗性的牡蛎。该项目的具体目标是：（i）使用来自野外爆发期间商业牡蛎种群的样品和数据来验证与OsHV抗性相关的SNP标记。(ii)在商业孵化场内建立一个利用亲本牡蛎进行抗性标记辅助选择的过程。(iii)在具有系谱和性状记录的牡蛎群体中检验OsHV抗性育种值的基因组预测。(iv)项目成果和影响：项目团队将与商业伙伴密切合作，提供切实的成果，帮助应对上述挑战。在田间爆发中在独立群体中对发现群体的抗性的SNP标记的测试将使得能够创建OsHV抗性的遗传测试。这将通过与商业孵化场合作伙伴合作，并开发一种对亲牡蛎进行基因分型以进行标记辅助选择的系统，应用于牡蛎水产养殖业。同时，将在不同的标记密度下评估基因组预测（使用全基因组标记来预测育种值）的效用。这将导致一份关于使用遗传标记进行牡蛎抗病育种的最（成本）有效方法的报告。项目工期和成本：该项目将持续24个月，总成本为199，741英镑。

Background:Pacific oyster (C. gigas) is one of the most important aquaculture species in the world, but sustainable production is threatened by outbreaks of Oyster herpes virus (OsHV), which can cause high mortality rates. There is substantial host genetic variation in resistance within farmed stocks. Therefore, improvement of survival rates via selective breeding has the potential to form a major component of disease control. However, UK oyster production does not yet have the capacity to produce more resistant stocks, because structured selective breeding schemes for shellfish do not exist. As part of an ongoing BBSRC-NERC sustainable aquaculture award, the Roslin Institute, Cefas and Edinburgh Genomics have developed the first high density single nucleotide polymorphism (SNP) array for oysters. In parallel, a laboratory virus challenge experiment has been successfully performed. The resistant and susceptible oysters from this trial are being genotyped to map resistance loci in the oyster genome. The major practical outcome will be SNP markers that can predict which oysters are resistant to the disease.Project Partners and Challenges:The lack of selective breeding for shellfish in the UK presents significant challenges (and opportunities) for UK production; namely (1 - short term) to identify and breed from parent oysters with high resistance to OsHV-1, and (2 - long term) to move towards well-managed selective breeding of oysters to harness genetic variation to improve key traits. The Roslin institute will work with Cefas and UK oyster hatcheries Guersey Sea Farms Ltd and Seasalter Shellfish Ltd to address these challenges. They will also work with the Cawthron Institute (New Zealand), who are world leaders in shellfish breeding and reproduction, but do not yet apply modern genomic tools in their breeding programmes. The project directly contributes to the themes of the call relating to "Breeding and genetics approaches for stock enhancement" and "Monitoring and control of health and disease". Aims and Objectives:The primary aim of this project is to apply genetic markers to breed oysters with improved resistance to oyster herpes virus in the farm environment. The specific objectives of the proposed project are:(i) To verify SNP markers associated with OsHV resistance using samples and data from commercial oyster populations during field outbreaks.(ii) To establish a process within a commercial hatchery for marker-assisted selection for resistance using parental oysters. (iii) To test genomic prediction of breeding values for OsHV resistance in an oyster population with pedigree and trait records.(iv) To determine the most (cost) effective method of using genetic markers in oyster breeding to improve disease resistance.Project Outputs and Impacts:The project team will work closely with commercial partners to deliver tangible outputs that will help address the aforementioned challenges. Testing of SNP markers of resistance in field outbreaks in independent populations to the discovery population will enable a genetic test for OsHV resistance to be created. This will be applied to the oyster aquaculture industry by working with commercial hatchery partners, and developing a system to genotype parent oysters for marker-assisted selection. Concurrently, the utility of genomic prediction (use of genome-wide markers to predict breeding values) will be assessed at different marker densities. This will result in a report on the most (cost) effective means of using genetic markers to breed for disease resistance in oysters.Project Duration and Cost:The project will last 24 months and will have a total cost of £199,741.