Abstract Single nucleotide polymorphism (SNP) arrays are a powerful genotyping tool used in genetic research and genomic breeding programs. Japanese flounder (Paralichthys olivaceus) is an economically-important aquaculture flatfish in many countries. However, the lack of high-efficient genotyping tools has impeded the genomic breeding programs for Japanese flounder. We developed a 50K Japanese flounder SNP array, “Yuxin No. 1”, and report its utility in genomic selection (GS) for disease resistance to bacterial pathogens. We screened more than 42.2 million SNPs from the whole-genome resequencing data of 1099 individuals and selected 48 697 SNPs that were evenly distributed across the genome to anchor the array with Affymetrix Axiom genotyping technology. Evaluation of the array performance with 168 fish showed that 74.7% of the loci were successfully genotyped with high call rates (> 98%) and that the polymorphic SNPs had good cluster separations. More than 85% of the SNPs were concordant with SNPs obtained from the whole-genome resequencing data. To validate “Yuxin No. 1” for genomic selection, the arrayed genotyping data of 27 individuals from a candidate population and 931 individuals from a reference population were used to calculate the genomic estimated breeding values (GEBVs) for disease resistance to Edwardsiella tarda. There was a 21.2% relative increase in the accuracy of GEBV using the weighted genomic best linear unbiased prediction (wGBLUP), compared to traditional pedigree-based best linear unbiased predictions (ABLUP), suggesting good performance of the “Yuxin No. 1” SNP array for genomic selection. In summary, we developed the “Yuxin No. 1” 50K SNP array, which provides a useful platform for high-quality genotyping that may be beneficial to the genomic selective breeding of Japanese flounder.

中文翻译：

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日本比目鱼50K SNP阵列的研制及其在抗病基因组选择中的应用

摘要 单核苷酸多态性 (SNP) 阵列是一种强大的基因分型工具，用于遗传研究和基因组育种计划。日本比目鱼 (Paralichthys olivaceus) 在许多国家是经济上重要的水产养殖比目鱼。然而，缺乏高效的基因分型工具阻碍了日本比目鱼的基因组育种计划。我们开发了一种 50K 日本比目鱼 SNP 阵列“Yuxin 1 号”，并报告了其在基因组选择 (GS) 中对细菌病原体抗病性的效用。我们从 1099 个人的全基因组重测序数据中筛选了超过 4220 万个 SNP，并选择了 48697 个均匀分布在基因组中的 SNP，以使用 Affymetrix Axiom 基因分型技术锚定阵列。对 168 条鱼的阵列性能评估表明，74. 7% 的基因座以高检出率 (> 98%) 成功进行基因分型，并且多态性 SNP 具有良好的簇分离。超过 85% 的 SNP 与从全基因组重测序数据中获得的 SNP 一致。为了验证“育新 1 号”的基因组选择，使用候选群体 27 个个体和参考群体 931 个个体的阵列基因分型数据计算迟发爱德华氏菌抗病性的基因组估计育种值 (GEBV)。与传统的基于谱系的最佳线性无偏预测 (ABLUP) 相比，使用加权基因组最佳线性无偏预测 (wGBLUP) 的 GEBV 准确度相对提高了 21.2%，表明“育新 1 号”SNP 的性能良好用于基因组选择的阵列。综上所述，我们开发了“宇信一号”。