Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.
Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.
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通过整个基因组重新配置的挪威云杉（picea abies L. karst）的大型且复杂的基因组的高效50K单核苷酸多态性基因分型阵列及其转移到其他云杉物种。
DOI：
10.1111/1755-0998.13292
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发表时间：
2021-04
影响因子：
7.7
通讯作者：
Wu HX
中科院分区：
文献类型：
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作者：
Bernhardsson C;Zan Y;Chen Z;Ingvarsson PK;Wu HX
挪威云杉Picea abies L.喀斯特）是欧洲最重要的森林树种之一，具有重要的经济和生态影响。几十年来，挪威云杉的基因组和遗传研究一直具有挑战性，因为它的基因组庞大且重复（19.6 Gb，超过70%是重复的）。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），我们在这里报告了挪威云杉50K单核苷酸多态性（SNP）基因分型阵列的设计和性能。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。在使用从北方收集的29棵树的基因组重测序数据鉴定SNP后，我们采用两步法设计阵列。首先，我们建立了一个450K的筛选阵列，并使用这个基因型的480棵树的人口从整个挪威云杉分布范围内的自然和繁殖种群采样。然后使用这些样本选择高置信度探针，并将其置于最终50K阵列上。选择的SNP分布在来自P.abies版本1.0基因组组装的45，552个支架上，并靶向19，954个独特的基因模型，均匀覆盖挪威云杉中的12个连锁群。结果表明，该芯片在家系三倍体和单倍体组织中具有99.5%的探针特异性，>98%的孟德尔等位基因遗传一致性，平均样本识别率为96.30%，SNP识别率为98.90%。我们还观察到，23，797个探针（50%）可以在其他三种云杉物种（白色云杉[Picea glauca]，黑云杉[P. mariana]和锡特卡云杉[P. sitchensis]）中以高置信度进行鉴定。高质量的基因分型阵列将是挪威云杉以及同一属的其他针叶树物种的遗传和基因组研究的宝贵资源。
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.
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影响因子：
2.6
作者：
Bernhardsson, Carolina;Vidalis, Amaryllis;Ingvarsson, Par K.
通讯作者：
Ingvarsson, Par K.
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影响因子：
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作者：
Bartholomé J;Van Heerwaarden J;Isik F;Boury C;Vidal M;Plomion C;Bouffier L
通讯作者：
Bouffier L
影响因子：
7.2
作者：
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通讯作者：
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影响因子：
4.4
作者：
Howe, Glenn T.;Jayawickrama, Keith;McEvoy, Susan
通讯作者：
McEvoy, Susan
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
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