Bernard Maria, Dehaullon Audrey, Gao Guangtu, Paul Katy, Lagarde Henri, Charles Mathieu, Prchal Martin, Danon Jeanne, Jaffrelo Lydia, Poncet Charles, Patrice Pierre, Haffray Pierrick, Quillet Edwige, Dupont-Nivet Mathilde, Palti Yniv, Lallias Delphine, Phocas Florence
INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France.
INRAE, SIGENAE, Jouy-en-Josas, France.
Front Genet. 2022 Jul 18;13:941340. doi: 10.3389/fgene.2022.941340. eCollection 2022.
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（SNP）阵列，也被称为“ SNP芯片”，能够对大量个体进行数千个全基因组鉴定标记的靶向基因分型。我们利用美国农业部的现有变异数据集、一个法国商业品系以及法国国家农业、食品与环境研究院（INRAE）近交系的30X覆盖度全基因组测序数据，开发了一种用于虹鳟的Affymetrix 665K SNP阵列（HD芯片）。我们总共鉴定出32,372,492个在美国农业部或法国国家农业、食品与环境研究院数据库中具有多态性的SNP。从鉴定出的SNP中选择了一部分纳入芯片，优先选择侧翼序列与斯旺森参考基因组唯一比对、在基因组上分布均匀且在美国农业部和法国数据库中具有最高最小等位基因频率（MAF）的SNP。在通过Affymetrix质量筛选并在HD芯片上制造的664,531个SNP中，65.3%和60.9%通过了筛选指标，并且在另外两个不同的法国商业群体中具有多态性，在这两个群体中分别对288条和175条采样鱼进行了基因分型。只有576,118个SNP在斯旺森和阿利参考基因组上都能唯一映射，而12,071个SNP在阿利参考基因组上根本无法映射。在这576,118个SNP中，38,948个SNP是从市售的中密度57K SNP芯片中保留下来的。我们通过描述虹鳟基因组中2 - 10kb处的连锁不平衡率较高，与中密度芯片标记之间通常的50 - 100kb距离处观察到的连锁不平衡情况相比，展示了HD芯片的实用性。
