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 evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and P. glauca 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.对于基因组庞大且结构复杂的针叶树等物种而言，高密度遗传连锁图谱（linkage map）可有效辅助基因组组装，并为基因组在结构、群体及功能层面的研究奠定基础。 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，这极大制约了高密度遗传连锁图谱的构建。 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.）为材料——该树种在不列颠群岛广泛种植以开展商业化林业生产——利用21570个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记构建了遗传连锁图谱。 我们采用单步作图法（single-step mapping approach），将来自两个全同胞家系的528个个体的限制性位点相关DNA测序（Restriction-site Associated DNA Sequencing, RAD-Seq）数据与基因分型芯片（genotyping array）SNP数据进行高效整合。 正如云杉属类群的预期结果，该饱和图谱包含12个连锁群（linkage group），总长度达2142厘摩（centimorgan, cM）。 我们对5414个独特基因编码序列进行了定位，借此将本图谱与其他松科（Pinaceae）物种的图谱进行比对，结果证实松科物种间存在高度的共线性（synteny）与基因顺序保守性。 随后，我们基于27052个标记与11609个基因序列，构建了西加云杉与白云杉（*Picea glauca*）的整合图谱。 综上，本研究构建的两张遗传连锁图谱、配套的286159个SNP目录集，以及本研究开发的基因分型芯片，为一系列基础与应用研究目标提供了全新的研究视角：例如优化云杉属基因组组装，或是实现西加云杉及其近缘物种遗传资源的标记辅助可持续管理。