DOI: 10.5683/sp3/ohbwux
title: High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p class="paragraph" style="line-height:150%;vertical-align:baseline;"&gt;&lt;span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;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, &lt;/span&gt;&lt;span class="normaltextrun"&gt;&lt;span lang="EN-GB" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;we developed a linkage map relying on 21,570 SNP makers in &lt;/span&gt;&lt;/span&gt;&lt;span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;Sitka spruce (&lt;em&gt;Picea sitchensis&lt;/em&gt; [Bong.] Carr.)&lt;/span&gt;&lt;span class="normaltextrun"&gt;&lt;em&gt;&lt;span lang="EN-GB" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;, &lt;/span&gt;&lt;/em&gt;&lt;/span&gt;&lt;span class="normaltextrun"&gt;&lt;span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. &lt;/span&gt;&lt;/span&gt;&lt;span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;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 evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for &lt;em&gt;P. sitchensis&lt;/em&gt; and &lt;em&gt;P. glauca&lt;/em&gt; based on 27,052 makers and 11,609 gene sequences. Altogether, these two linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed herein opens new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.&lt;/span&gt;&lt;/p&gt;
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p class="MsoNormal"&gt;The data included in this dataset is genotypic data for two full-sib families of Sitka spruce (&lt;em&gt;Picea sitchensis&lt;/em&gt;) 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 (&lt;a href="https://github.com/HayleyTumas/SitkaLinkageMap"&gt;https://github.com/HayleyTumas/SitkaLinkageMap&lt;/a&gt;).&lt;/p&gt;
description: &lt;b&gt;Usage notes&lt;/b&gt;&lt;br /&gt;&lt;p class="MsoNormal"&gt;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.&lt;/p&gt;
description: <b>Dryad version number:</b> 7
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.ghx3ffbv6
<b>Storage size:</b> 149206418
<b>Visibility:</b> public