Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome‐wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS‐based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two‐step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high‐confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high‐quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.

中文翻译：

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通过全基因组重测序为挪威云杉（Picea abies L. Karst）的大型复杂基因组开发高效的 50K 单核苷酸多态性基因分型阵列及其向其他云杉物种的可转移性

挪威云杉 ( Picea abiesL. Karst) 是欧洲最重要的森林树种之一，具有显着的经济和生态影响。几十年来，挪威云杉的基因组和遗传研究一直具有挑战性，因为基因组庞大且重复（19.6 Gb，重复率超过 70%）。为了加速挪威云杉和相关物种的基因组研究，包括群体遗传学、全基因组关联研究 (GWAS) 和基因组选择 (GS)，我们在此报告了 50K 单核苷酸多态性 (SNP) 基因分型阵列的设计和性能对于挪威云杉。该阵列是基于全基因组重测序 (WGS) 开发的，使其成为迄今为止任何针叶树物种中第一个基于 WGS 的 SNP 阵列。在使用来自北欧收集的 29 棵树的基因组重测序数据识别 SNP 后，我们采用了两步法来设计阵列。首先，我们构建了一个 450K 筛选阵列，并使用它对从挪威云杉分布范围内的自然和繁殖种群中采样的 480 棵树木种群进行基因分型。然后使用这些样本选择高置信度的探针，并放置在最终的 50K 阵列上。选择的 SNP 分布在 45,552 个支架上P. abies 1.0 版基因组组装和目标 19,954 个独特的基因模型，均匀覆盖了挪威云杉的 12 个连锁群。我们表明该阵列具有 99.5% 的探针特异性、> 98% 的孟德尔等位基因遗传一致性、96.30% 的平均样本检出率和 98.90% 的家族三重奏和单倍体组织的 SNP 检出率。我们还观察到，可以在其他三种云杉物种（白云杉 [ Picea glauca ]、黑云杉 [ P. mariana ] 和 Sitka spruce [ P. sitchensis ]）中以高可信度鉴定 23,797 个探针（50% ）。高质量的基因分型芯片将成为挪威云杉以及同属其他针叶树物种遗传和基因组研究的宝贵资源。