Genome-wide genetic analysis of cultured rainbow trout ( Oncorhynchus mykiss ) populations in China

Abstract

PDF HTML阅读 XML下载 导出引用 引用提醒 国内虹鳟代表性养殖群体的高通量SNP芯片检测及遗传分析 DOI: 作者: 作者单位: 1. 中国水产科学研究院, 农业部水生动物基因组学重点实验室, 渔业生物技术北京市重点实验室, 北京 100141;2. 中国水产科学研究院黑龙江水产研究所, 黑龙江 哈尔滨 150070;3. 四川农业大学 动物科技学院, 四川 雅安 625014;4. National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV 25430, USA;5. 厦门大学 海洋与地球学院, 福建省海洋生物资源开发利用协同创新中心, 福建 厦门 361102 作者简介: 赵紫霞(1983-),女,博士,副研究员,从事水产生物技术研究. 通讯作者: 中图分类号: S917 基金项目: 国家科技支撑计划项目（2015BAD25B01）；中国水产科学研究院基本科研业务费专项（2015C007）. Genome-wide genetic analysis of cultured rainbow trout (Oncorhynchus mykiss) populations in China Author: Affiliation: 1. Key Laboratory of Aquatic Genomics, Ministry of Agriculture;Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China;2. Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China;3. College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, China;4. National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV 25430, USA;5. Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources;College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:本研究旨在对国内虹鳟（）代表性养殖群体开展全基因组水平的遗传评估。利用57K单核苷酸多态性（single nucleotide polymorphism，SNP）芯片，检测了来自不同地域的6个虹鳟养殖群体样本共计48尾，包括黑龙江虹鳟、黑龙江金鳟、四川虹鳟、四川金鳟、北京虹鳟和北京金鳟，共获得有效SNP位点50201个，在中国虹鳟中的多态比例达到97.7%，表明该芯片虽然基于美国和挪威虹鳟群体设计，但对中国群体同样具有良好的适用性。各群体最小等位基因频率均值为0.240~0.267，与国外主流养殖群体相近，黑龙江虹鳟、四川虹鳟和北京虹鳟群体内遗传多样性丰富，多态位点比例为83.6%~84.9%，与国外主流养殖群体相近，而黑龙江金鳟、四川金鳟和北京金鳟，多态位点比例相对较低，在60.2%~76.9%范围内。应用6个中国虹鳟群体和2个美国虹鳟群体数据开展系统发育分析、主成分分析和群体遗传结构STRUCTURE分析，结果显示8个群体可分为3个祖源类群，其中3个金鳟群体为遗传联系较紧密的一个类群，黑龙江虹鳟和北京虹鳟为一个类群，而四川虹鳟与2个美国虹鳟群体为一个类群，部分中国养殖群体中有显著离群个体存在，表明群体遗传背景不均一。本研究表明，高密度SNP芯片在我国虹鳟养殖群体遗传分析中具有广泛的应用前景，能够为种质资源评估、本土化良种培育、制种和引种工作提供基因组水平的参考信息。 Abstract:The present study aimed to perform a genome-wide genetic evaluation of representative aquaculture populations of rainbow trout () in China. A 57K single nucleotide polymorphism (SNP) array that was designed by the National Center for Cool and Cold Water Aquaculture (NCCCWA) was used to genotype 48 individuals from six aquaculture populations, which included the Heilongjiang rainbow trout (1HLJ), Heilongjiang golden trout (2gHLJ), Sichuan rainbow trout (3SC), Sichuan golden trout (4gSC), Beijing rainbow trout (5BJ), and Beijing golden trout (6gBJ). A total of 50,201 SNPs were successfully genotyped using a >97% call rate threshold, and the overall rate of polymorphism was 97.7%, which indicated that the SNP array was suitable for analyzing the Chinese rainbow trout populations, even though it was designed using USA and Norwegian populations. The average minor allele frequency of each population was between 0.240 and 0.267, which is similar to that reported for other major aquaculture populations. Genetic diversity was high in the 1HLJ, 3SC, and 5BJ populations, with rates of polymorphism ranging from 83.6% to 84.9%, which is similar to reported for other major aquaculture populations. However, genetic diversity was relatively low in the 2gHLJ, 4gSC, and 6gBJ populations, with rates of polymorphism ranging from 60.2% to 76.9%. Phylogenetic, principal components, and STRUCTURE analyses, which were performed using genotype data from the six Chinese populations and two USA populations, indicated that the eight populations could be clustered into three groups. The three golden trout groups and the 1HLJ and 5BJ populations formed respective clusters, whereas the 3SC population was placed in a third cluster with the two USA populations. Outliers were identified for the 3SC, 4gSC, and 6gBJ populations, which suggested that the populations possessed inhomogeneous genetic backgrounds. Together, these results demonstrate the promising potential of high-density SNP arrays for the genetic analysis of Chinese rainbow trout populations and that such analyses could provide genomic data for plasm resource evaluation, localized strain breeding, high-quality fry production, and reasonable foreign strain introduction. 参考文献 相似文献 引证文献