DataSheet1_Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping.PDF

Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2–10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50–100 kb which are usual distances between markers of the medium-density chip.

单核苷酸多态性（Single Nucleotide Polymorphism，SNP）阵列，又称“SNP芯片”，可实现对大量个体的基因分型，能够靶向检测数千个经全基因组鉴定的分子标记。本研究依托美国农业部（USDA）已有的变异数据集、法国商业虹鳟品系，以及INRAE同基因系的30倍覆盖度全基因组测序数据，为虹鳟开发了一款Affymetrix 665K SNP阵列（高密度芯片，HD chip）。最终，我们在USDA与INRAE数据库中共鉴定出32,372,492个具有多态性的SNP位点。研究人员从已鉴定的SNP位点中筛选出部分位点用于芯片设计，筛选优先级如下：侧翼序列可唯一比对至Swanson参考基因组、在全基因组中均匀分布，且在USDA与法国数据库中均具备最高的最小等位基因频率（Minimum Allele Frequency）。在通过Affymetrix质量过滤并被纳入HD芯片的664,531个SNP位点中，分别有65.3%与60.9%的位点通过了后续过滤标准，且在另外两个独立的法国商业虹鳟种群中呈现多态性；这两个种群分别对288尾与175尾采样个体完成了基因分型。仅有576,118个SNP位点可同时唯一比对至Swanson与Arlee参考基因组，另有12,071个SNP位点完全无法比对至Arlee参考基因组。在这576,118个SNP位点中，有38,948个位点来自已商业化的中等密度57K SNP芯片。本研究通过对比虹鳟基因组中2–10kb区间内的连锁不平衡（Linkage Disequilibrium）水平与中等密度芯片标记间常规间距（50–100kb）对应的连锁不平衡水平，验证了该HD芯片的应用价值。