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

背景：太平洋牡蛎（C. gigas）是世界上最重要的水产养殖物种之一，但牡蛎疱疹病毒（OsHV）的爆发威胁着其可持续生产，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主要组成部分。然而，英国的牡蛎生产还没有能力生产出更具抗性的种群，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，成功地进行了实验室病毒挑战实验。该试验中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这种疾病有抵抗力。项目合作伙伴和挑战：英国贝类缺乏选择性育种，为英国生产带来了重大挑战（和机遇）；即（1 -短期）鉴定和培育对OsHV-1具有高抗性的亲本牡蛎，以及（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，但尚未在其育种计划中应用现代基因组工具。该项目直接促进了有关“增加种群的育种和遗传学方法”和“监测和控制健康和疾病”的呼吁主题。目的和目标：本项目的主要目的是应用遗传标记在养殖环境中培育对牡蛎疱疹病毒有更好抵抗力的牡蛎。拟议项目的具体目标是：(i)利用野外暴发期间商业牡蛎种群的样本和数据，验证与OsHV抗性相关的SNP标记。（ii）在商业孵化场内建立利用亲本牡蛎进行标记辅助抗性选择的程序。（iii）对具有系谱和性状记录的牡蛎群体进行抗OsHV育种价值的基因组预测测试。（iv）确定在牡蛎育种中利用遗传标记提高抗病性的最（成本）有效的方法。项目产出和影响：项目团队将与商业伙伴密切合作，提供有助于应对上述挑战的切实产出。在独立种群对发现种群的现场暴发中检测耐药性的SNP标记，将有助于建立OsHV耐药性的基因检测。这将应用于牡蛎养殖业，与商业孵化场合作伙伴合作，并开发一种系统，对亲本牡蛎进行基因型标记辅助选择。同时，基因组预测的效用（使用全基因组标记来预测育种值）将在不同的标记密度下进行评估。这将产生一份关于利用遗传标记进行牡蛎抗病育种的最有效（成本）方法的报告。项目持续时间和成本：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.