Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27606, USA.
Sci Rep. 2023 Dec 15;13(1):22488. doi: 10.1038/s41598-023-49462-x.
Single nucleotide polymorphism (SNP) markers are powerful tools for investigating population structures, linkage analysis, and genome-wide association studies, as well as for breeding and population management. The availability of SNP markers has been limited to the most commercially important timber species, primarily due to the cost of genome sequencing required for SNP discovery. In this study, a combination of reference-based and reference-free approaches were used to identify SNPs in Nordmann fir (Abies nordmanniana), a species previously lacking genomic sequence information. Using a combination of a genome assembly of the closely related Silver fir (Abies alba) species and a de novo assembly of low-copy regions of the Nordmann fir genome, we identified a high density of reliable SNPs. Reference-based approaches identified two million SNPs in common between the Silver fir genome and low-copy regions of Nordmann fir. A combination of one reference-free and two reference-based approaches identified 250 shared SNPs. A subset of 200 SNPs were used to genotype 342 individuals and thereby tested and validated in the context of identity analysis and/or clone identification. The tested SNPs successfully identified all ramets per clone and five mislabeled individuals via identity and genomic relatedness analysis. The identified SNPs will be used in ad hoc breeding of Nordmann fir in Denmark.
单核苷酸多态性（SNP）标记是研究种群结构、连锁分析和全基因组关联研究以及育种和种群管理的有力工具。SNP 标记的可用性仅限于最具商业重要性的木材物种，主要是由于 SNP 发现所需的基因组测序成本。在这项研究中，结合了基于参考和无参考的方法来鉴定冷杉（Abies nordmanniana）中的 SNP，这是一个以前缺乏基因组序列信息的物种。使用亲缘关系密切的银冷杉（Abies alba）物种的基因组组装和冷杉基因组低拷贝区的从头组装的组合，我们鉴定出了高密度的可靠 SNP。基于参考的方法在银冷杉基因组和冷杉低拷贝区之间鉴定出了两百万个共同 SNP。一种参考无和两种参考的组合方法鉴定出了 250 个共享 SNP。选择了 200 个 SNP 的一个子集对 342 个个体进行基因分型，从而在身份分析和/或克隆鉴定的背景下进行了测试和验证。通过身份和基因组相关性分析，测试的 SNP 成功地鉴定了每个克隆的所有半同胞个体和五个标记错误的个体。所鉴定的 SNP 将用于丹麦的冷杉特定育种。
