中国水产科学2018，Vol.25Issue(3)：485-493,9.DOI:10.3724/SP.J.1118.2018.17340
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
Genome-wide genetic analysis of cultured rainbow trout (Oncorhyn-chus mykiss) populations in China
摘要
Abstract
The present study aimed to perform a genome-wide genetic evaluation of representative aquaculture populations of rainbow trout (Oncorhynchus mykiss) 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), Heilong-jiang 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 popula-tions. 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 popula-tions, 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.关键词
虹鳟/SNP芯片/遗传多态性/群体结构Key words
Oncorhynchus mykiss/SNP array/genetic polymorphism/population structure分类
农业科技引用本文复制引用
赵紫霞,许建,白庆利,杨世勇,蒋立坤,陈葆华,PaltiYniv,GaoGuangtu,徐鹏..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[J].中国水产科学,2018,25(3):485-493,9.基金项目
国家科技支撑计划项目(2015BAD25B01) （2015BAD25B01）
中国水产科学研究院基本科研业务费专项(2015C007). （2015C007）
