High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers

In species with large and complex genomes such as conifers, dense linkage maps are a useful for supporting genome assembly and laying the genomic groundwork at the structural, populational and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 SNP makers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-Seq and genotyping array SNP data for 528 individuals from two full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided eviden..., The data included in this dataset is genotypic data for two full-sib families of Sitka spruce (Picea sitchensis) in the United Kingdom and resulting linkage maps for the species. Samples for DNA extraction and genotyping were collected from two full-sib genetic field trials as described in the accompanying publication. A SNP Chip array was developed for this work using exome capture. A subset of the samples had been genotyped using RAD Seq from a previous project (Fuentes-Utrilla et al 2017). The dataset includes information on the SNP array developed for the project and genotype data that has been filtered for missingness and minor allele frequency. Final results are in the form of linkage maps stored in csv files. Further information on collection methods and processing are detailed in the accompanying manuscript and scripts for data processing are available on GitHub (https://github.com/HayleyTumas/SitkaLinkageMap)., All files should be able to be opened using open access, freely available software. All tabular data are CSV or text files for the larger genotype data files. Code files are stored as bash script and can be opened using any text editor or in .R files that can be opened using the freely available R software., File generated 01-17-2024 by Hayley Tumas

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Title: High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers

This is data and code accompanying the publication \"High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers\" in G3 (Tumas et al. 2024, Accepted, DOI pending).

PROJECT:
The project developed a high-density genetic linkage map for Sitka spruce using genotype data for two full sib families from the UK Sitka spruce breeding population. Samples were genotyped using both a SNP array developed for the project and RAD-Seq. These two genotype datasets were used separately to generate genetic maps and together in a single combined map using the software LepMap-3. This combined genetic map (RADChip map) was used along with a genetic map for white spruce (Pavy et al 2017) to create an integrated species map. The data includes information on the SNP arra...

对于基因组庞大且复杂的针叶树等物种而言，高密度遗传连锁图谱（dense linkage maps）可有效辅助基因组组装，并为结构基因组学、群体基因组学与功能基因组学层面的研究奠定基因组学基础。然而，现存的600余种针叶树中，多数仍缺乏充足的基因分型资源，这极大阻碍了高密度连锁图谱的构建。
本研究以北美西部原生的长寿命针叶树种西加云杉（*Picea sitchensis* [Bong.] Carr.）为研究对象，利用21570个SNP标记（SNP marker）构建了遗传连锁图谱；该树种在不列颠群岛被广泛种植以用于商业化林业生产。我们采用单步作图法（single-step mapping approach），整合了来自两个全同胞家系共528个个体的RAD-Seq与基因分型芯片（genotyping array）SNP数据，实现了高效的图谱构建。正如云杉属类群的预期结果，该饱和连锁图谱包含12个连锁群（linkage groups），总长度达2142 cM。通过对5414个独特基因编码序列的定位，我们得以将本研究构建的图谱与其他松科物种的连锁图谱进行比对，从而为相关研究提供依据……[原文截断]

本数据集包含英国境内西加云杉（*Picea sitchensis*）两个全同胞家系的基因型数据，以及该物种的遗传连锁图谱结果。用于DNA提取与基因分型的样本，取自两项全同胞遗传田间试验，具体细节参见随附的发表论文。本研究通过外显子组捕获技术开发了一款SNP芯片（SNP Chip array）。部分样本的基因型数据源自此前一项研究（Fuentes-Utrilla等，2017）的RAD-Seq分型结果。本数据集包含本项目开发的SNP芯片相关信息，以及经过缺失率与次要等位基因频率过滤后的基因型数据。最终结果以连锁图谱的形式存储于CSV文件中。关于样本采集方法与数据处理流程的更多细节，参见随附的研究论文；数据处理脚本可在GitHub平台（https://github.com/HayleyTumas/SitkaLinkageMap）获取。所有文件均可通过开源免费的软件打开。其中，大型基因型数据文件采用CSV或文本格式存储；代码文件以Bash脚本格式存储，可通过任意文本编辑器打开，或采用可通过免费R软件打开的.R格式文件。本数据集文件由Hayley Tumas于2024年1月17日生成。

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标题：西加云杉的高密度遗传连锁图谱构建推动松科植物基因组资源整合
本数据集与代码配套发表于《G3》期刊的论文《西加云杉的高密度遗传连锁图谱构建推动松科植物基因组资源整合》（Tumas等，2024，已接收，DOI待公布）。

项目概况：
本项目利用英国西加云杉育种群体中两个全同胞家系的基因型数据，为西加云杉构建了高密度遗传连锁图谱。研究采用本项目开发的SNP芯片与RAD-Seq两种技术对样本进行基因分型。两组基因型数据可分别用于构建遗传图谱，也可通过LepMap-3软件整合为一张联合遗传图谱（RADChip图谱）。本联合遗传图谱与白云杉的遗传图谱（Pavy等，2017）相结合，最终构建了跨物种整合图谱。本数据集包含本项目开发的SNP芯片相关信息……[原文截断]