<b>Low-cost SNP array for genotype imputation optimized for breeding programs in the fish pacu </b><b><i>Piaractus mesopotamicus</i></b>

Pacu (<i>Piaractus mesopotamicus</i>) is one of the main native fish species for aquaculture in South America. Cost-effective genotyping strategies, involving low-density SNP arrays followed by genotype imputation, can facilitate the broader adoption of genomic selection for this species. In this study, we developed a 1K SNP array to be applied with genotype imputation strategies in breeding program of pacu. First, we assessed imputation accuracy across various SNP densities (9K, 7K, 5K, 2K, 1K, and 0.5K) from the commercial <i>Axiom 30 K SerraSNP</i> array to select the best subset for further analysis. Then, 15,166 (91.1%) imputed SNPs with high accuracy were obtained when we selected 1,068 SNPs to comprise the 1K SNP array (average accuracies of 0.90 ± 0.12 at the SNP level and 0.92 ± 0.06 for 290 genotyped individuals). The 1K SNP array was developed using the <i>Agriseq tGBS</i> platform. In the evaluation of array performance using 95 individuals, no discordant genotyping was observed between the <i>Agriseq tGBS</i> platform and the <i>Axiom 30 K SerraSNP</i> array. Ninety-one individuals had a call rate of 90% and above, and 92% of the SNPs were identified in at least 90% of the samples. Additionally, an average minor allele frequency (MAF) of 0.356 (± 0.108) and individual heterozygosity values ranging from 0.321 to 0.470 were found. The results showed that the constructed low-density SNP array exhibited high imputation accuracies and can explore genetic variations within pacu populations, making it a cost-effective tool for enhancing pacu production through genomic selection.帕库鱼（*Piaractus mesopotamicus*）是南美地区主要的本土养殖鱼类之一。采用低密度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片结合基因型填充的低成本基因分型策略，可推动该物种基因组选择技术的大范围应用。本研究针对帕库鱼的育种程序，开发了一款可配合基因型填充策略使用的1K SNP芯片。首先，我们以商用Axiom 30 K SerraSNP芯片为参考，针对不同SNP密度（9K、7K、5K、2K、1K及0.5K）的基因型填充准确率进行评估，以筛选出最适合后续分析的SNP子集。随后，我们筛选出1068个SNP构成这款1K SNP芯片，最终获得15166个（占比91.1%）高精度填充后的SNP；在SNP层面，其平均填充准确率为0.90±0.12，针对290个基因分型个体的平均准确率为0.92±0.06。该1K SNP芯片依托Agriseq tGBS平台开发完成。针对95个个体的芯片性能评估结果显示，Agriseq tGBS平台与Axiom 30 K SerraSNP芯片的基因分型结果无不一致情况。其中91个个体的分型成功率达到90%及以上，92%的SNP可在至少90%的样本中被检测到。此外，本研究还检测到平均次要等位基因频率（Minor Allele Frequency, MAF）为0.356±0.108，个体杂合度取值范围为0.321至0.470。研究结果表明，本研究构建的低密度SNP芯片具有优异的基因型填充准确率，可有效解析帕库鱼种群内的遗传变异，是一款通过基因组选择技术提升帕库鱼养殖产量的低成本高效工具。