鲑鳟通用型低通量单核苷酸多态性芯片的开发

Development of a Universal 96 Single Nucleotide Polymorphism Array for Salmonid Fishes

中文关键词: 鲑科鱼类  单核苷酸多态性芯片  亲权鉴定  群体遗传

英文关键词: Salmonid fishes  Single nucleotide polymorphism array  Pedigree assignment  Population genetics

中文摘要:

      为开发常见鲑鳟养殖物种通用的遗传分析工具，本研究利用Affymetrix虹鳟(Oncorhynchus mykiss) 57K高通量单核苷酸多态性(Single nucleotide polymorphism, SNP)芯片，对国内代表性鲑鳟养殖群体开展了分型检测，包括山女鳟(Oncorhynchus masou masou)、银鲑(Oncorhynchus kisutch)、美洲红点鲑(Salvelinus fontinalis)、白斑红点鲑(Salvelinus leucomaenis) 4个物种，从57,501个SNP标记中筛选出96个共享多态性标记，应用Fluigidm 96.96动态芯片平台，构建了大麻哈鱼属(Oncorhynchus)和红点鲑属(Salvelinus)通用型低通量SNP芯片。该芯片分型结果准确性较高，与Affymetrix高通量芯片分型一致性达到96.55%。使用该芯片对来自6个家系的48尾银鲑个体及其候选亲本进行检测，应用Cervus 3.0.7软件进行亲权鉴定，结果能够准确重现复杂家系的真实系谱。在用于单亲本亲权鉴定时，第一亲本非排除率(Non-exclusion probability for first parent, NE-1P)为4.120×10–4；用于双亲本亲权鉴定时，双亲非排除率(Non-exclusion probability for parent pair, NE-PP)低至6.219×10–12，表明该芯片在鲑鳟养殖群体系谱鉴定应用中具有较高的准确性。使用该芯片开展4个鲑鳟养殖群体遗传结构分析，样本分群聚类结果与其所属的分类阶元相符，能够准确反映群体遗传组分构成和遗传关系。本研究构建的低通量SNP芯片在常见鲑鳟养殖物种中具有良好的通用性，将其应用于养殖群体遗传分析，能够为鲑鳟制种、育种和引种等科学决策提供基因组信息参考。

英文摘要:

      This study aimed to develop a universal genotyping tool for common salmonid species cultured in China. Using an Affymetrix rainbow trout (Oncorhynchus mykiss) 57 K single nucleotide polymorphism (SNP) array, four representative aquaculture salmonid populations were genotyped, including Oncorhynchus masou masou, Oncorhynchus kisutch, Salvelinus fontinalis, and Salvelinus leucomaenis. A total of 96 shared polymorphism markers was screened out of 57,501 SNPs, then a low-density SNP array was constructed based on a Fluigidm 96.96 dynamic array, which is universal for the genera Oncorhynchus and Salvelinus. Reliability of the genotyping results was high because the identity of results with those of the Affymetrix 57 K array reached 96.55%. Parentage assignment for 48 Oncorhynchus kisutch offspring was performed with Cervus 3.0.7 software, based on genotyping data by the 96 SNP array. The results matched perfectly with the true pedigrees among complicated families, proving high accuracy in the pedigree assignment application of the 96 SNP array. The non-exclusion probability for the first parent (NE-1P) was 4.120×10–4 during single parent assignment, whereas the non-exclusion probability for the parent pair (NE-PP) was as low as 6.219×10–12. Genetic structure analysis for four salmonid populations was also performed using genotyping data of the 96 SNP array. Clustering results were in accordance with the taxonomic categories of the samples, whereas certain degrees of genetic introgression were observed among the populations, indicating that the genetic composition and relationships among populations were properly demonstrated in the analysis. All these results suggested that the developed 96 SNP array has great potential in genetic analyses for salmonid populations, which might provide helpful genome-wide information for plasm resource evaluation, selective breeding, high-quality fry production, and reasonable foreign strain introduction in the Chinese salmonid aquaculture.