Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)

Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programs for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97 075 highly reliable in silico SNPs. These SNPs were distributed across 14 909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2%, for in silico SNPs compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.黑云杉（Picea mariana）是加拿大境内分布广泛的北方针叶树种，同时亦是多项先进育种计划的核心研究对象，相关研究正开发群体基因组学（population genomics）与基因组选择（genomic selection）技术方法。本研究借助源自远缘亲缘物种白云杉（Picea glauca）测序转录组（transcriptome）设计的探针，完成了黑云杉外显子组（exome）的捕获与靶向测序（targeted sequencing）。尽管云杉属物种基因组结构复杂且规模庞大，基因序列间夹杂多处长内含子（intron），但本研究仍实现了75.9%的高捕获效率。研究结果证实，利用同属物种的探针可成功开展云杉属内的种间外显子组捕获，该方案具备显著应用价值。本研究开发了一套搭载严格筛选标准的生物信息学流程（bioinformatics pipeline），成功鉴定得到97075个高可靠性的计算机预测单核苷酸多态性（in silico SNP）位点，这些位点分布于14909个功能基因中。本研究使用Infinium iSelect基因分型芯片（Infinium iSelect array）的一部分，对4267个计算机预测单核苷酸多态性位点开展黑云杉群体个体的基因分型（genotyping）实验，以验证其真阳性率（true positive rate）。结果显示，计算机预测单核苷酸多态性的真阳性率达96.2%；而从既往基因分型芯片中复用的1115个黑云杉对照单核苷酸多态性位点的基因分型成功率为96.7%。上述结果表明，本研究所构建的基因分型芯片具备较高的分型成功率，同时也证实了筛选新型黑云杉计算机预测单核苷酸多态性资源所采用的标准具备充分合理性。此外，计算机预测单核苷酸多态性位点在自然群体中普遍呈现中等至高频率的分布特征，可为未来群体基因组学研究提供较高的信息价值。