Development of a high-density salmon SNP chip: a key tool for improving the competitiveness and sustainability of the UK salmon farming industry

开发高密度鲑鱼SNP芯片：提高英国鲑鱼养殖业竞争力和可持续性的关键工具

• 批准号: 100965
• 金额: $ 41.42万
• 依托单位: LANDCATCH NATURAL SELECTION LTD
• 依托单位国家: 英国
• 项目类别: Collaborative R&D
• 财政年份: 2011
• 资助国家: 英国
• 起止时间: 2011 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=100965
• 关键词: Development; density; salmon; SNP; chip

Salmon farming is a key economic contributor to the UK (£0.5bn p.a.) and provides healthy, high quality food. The competitiveness and sustainability of this rural industry depend upon selective breeding. While cutting-edge genomics tools such as high density (HD) SNP chips are now routinely employed for livestock breeding decisions, salmon aquaculture has no access to such tools. This project addresses this technology gap by developing an HD salmon SNP chip for selective breeding. The project will; 1) use high-throughput sequencing to detect genome-wide SNP variation; 2) develop an HD SNP chip; 3) use the chip to perform association mapping of loci affecting resistance to sea lice; 4) verify trait-associated SNPs in a commercial context; 5) implement strategies for SNP use in breeding programmes to improve resistance to sea lice, a paradigm for other key economic traits.Sea louse infestation is the most serious disease affecting salmon farming worldwide. In the northern hemisphere, the salmon louse Lepeophtheirus salmonis is particularly problematic. L. salmonis infection of salmon can cause surface lesions, osmotic imbalance, and susceptibility to other pathogens because of host immunomodulation and lesions.Almost all salmon farms require sea lice control strategies, usually involving frequent chemotherapeutant treatment. Sea lice treatment costs vary from 0.10 Euros to 0.25 Euro per kg of fish, amounting to losses of 34M Euros per annum in the UK and 305M Euros per annum worldwide. However, without such treatment the existing salmon aquaculture industry would not be viable.Through a pilot sea louse infection trial in collaboration with the University of Glasgow and the Institute of Aquaculture at the University of Stirling, LNS have demonstrated there is widespread genetic variation for resistance to sea lice across their broodstock and that heritability for resistance to sea lice in LNS families is c30 percent.However sea lice challenge trials are an expensive and laborious means of identifying the best selection candidate fish in each generation. The approach of direct selection based on genomic information that has been applied in several agricultural sectors has been shown to be a more cost-effective and accurate means of selection, particularly for difficult/expensive to measure traits.Association of genetic markers with disease resistance requires identification of markers in population-wide linkage disequilibrium. Although a proprietary salmon SNP chip is currently available through CIGENE (Norway), its marker density (3K) is insufficient for genomic association mapping.This project aims to overcome this limitation through development of high-throughput genotyping tools for the identification of genetic markers associated with sea lice resistance and other economically important traits in farmed salmon.Key steps are firstly identifying genome-wide SNP variation across the LNS breeding stock by utilising massively parallel sequencing platforms (Illumina GAIIx and HiSeq2000) and bioinformatic analyses of reduced representation (RR) and restriction site-associated DNA (RAD) libraries.Secondly the design and manufacture of a custom HD (~200K) SNP genotyping tool for LNS fish using Affymetrix high-throughput array technology.Thirdly use of this tool for identification of SNP variants associated with resistance to sea lice by HD SNP chip genotyping and association mapping of accurate phenotypes in LNS families infected under controlled conditions.Subsequently the identified subset of informative and trait-associated markers markers will be incorporated into a lower cost genotyping platform which will be used for verification of SNPs associated with reduced levels of lice infestation in fish exposed to aquaculture conditions.Breeding strategies will be developed to apply these SNPs in selection for sea lice resistance, which will permit genetic improvement without the need for further disease challenge.Further, through use of the High Density chip for identification of markers in linkage disequilibrium with other economically important traits, these strategies will be extended to introduce genotypic selection for other traits, significantly accelerating genetic progress achieved via the LNS breeding programme.

鲑鱼养殖是英国的主要经济贡献者（每年5亿英镑）提供健康优质的食物。这一农村产业的竞争力和可持续性取决于选择性育种。虽然尖端的基因组学工具，如高密度（HD）SNP芯片，现在经常用于牲畜育种决策，鲑鱼水产养殖没有获得这样的工具。该项目通过开发用于选择性育种的HD鲑鱼SNP芯片来解决这一技术差距。该项目将; 1）使用高通量测序来检测全基因组SNP变异; 2）开发HD SNP芯片; 3）使用该芯片来进行影响对海虱的抗性的基因座的关联作图; 4）在商业背景下验证性状相关SNP; 5）实施在育种计划中使用SNP的策略，以提高对海虱的抗性，海虱感染是影响世界范围内鲑鱼养殖的最严重疾病。在北方，鲑鱼虱（Lepeophtheirus salmonis）是特别成问题的。L.由于宿主的免疫调节和病变，鲑鱼的salmonis感染可引起表面病变、渗透压失衡和对其它病原体的易感性。几乎所有的鲑鱼养殖场都需要海虱控制策略，通常涉及频繁的化学治疗剂治疗。海虱治疗费用从每公斤鱼0.10欧元到0.25欧元不等，相当于英国每年损失3400万欧元，全球每年损失3.05亿欧元。然而，如果没有这种处理，现有的鲑鱼养殖业将无法生存。通过与格拉斯哥大学和斯特林大学水生生物研究所合作进行的一项试点海虱感染试验，LNS已经证明，在它们的亲鱼中，对海虱的抗性存在广泛的遗传变异，并且LNS家族中对海虱的抗性的遗传率为30%。挑战试验是在每一代中鉴定最佳选择候选鱼的昂贵且费力的手段。基于基因组信息的直接选择方法已被应用于许多农业领域，是一种更经济、更准确的选择方法，特别是对于难以/昂贵测量的性状。遗传标记与抗病性的关联需要在群体范围内连锁不平衡中识别标记。虽然目前可通过CIGENE（挪威）获得专有的鲑鱼SNP芯片，其标记密度（3 K）不足以进行基因组关联作图。本项目旨在通过开发高通量基因分型工具来识别与养殖鲑鱼抗海虱和其他重要经济性状相关的遗传标记，以克服这一限制。关键步骤是首先识别基因组-通过利用大规模平行测序平台，（Illumina GAIIx和HiSeq 2000）和简化代表性（RR）和限制性位点相关DNA（RAD）文库的生物信息学分析。第三，通过HD SNP芯片基因分型和在受控条件下感染的LNS家族中精确表型的关联作图，使用该工具鉴定与海虱抗性相关的SNP变体。相关的标记物标记物将被纳入一个低成本的基因分型平台，该平台将用于验证与暴露于以下物质的鱼类中虱子感染水平降低相关的SNP。将开发育种策略以将这些SNPs应用于海虱抗性的选择，这将允许遗传改良而不需要进一步的疾病挑战。此外，通过使用高密度芯片来鉴定与其他经济上重要的性状连锁不平衡的标记，这些策略将扩展到引入其他性状的基因型选择，通过LNS育种计划显著加快遗传进展。