Pines are some of the most ecologically and economically important tree species in the world, and many have enormous natural distributions or have been extensively planted. However, a lack of rapid genotyping capability is hampering progress in understanding the molecular basis of genetic variation in these species. Here, we deliver an efficient tool for genotyping thousands of single nucleotide polymorphism (SNP) markers across the genome that can be applied to genetic studies in pines. Polymorphisms from resequenced candidate genes and transcriptome sequences of P. sylvestris, P. mugo, P. uncinata, P. uliginosa and P. radiata were used to design a 49,829 SNP array (Axiom_PineGAP, Thermo Fisher). Over a third (34.68%) of the unigenes identified from the P. sylvestris transcriptome were represented on the array, which was used to screen samples of four pine species. The conversion rate for the array on all samples was 42% (N = 20,795 SNPs) and was similar for SNPs sourced from resequenced candidate gene and transcriptome sequences. The broad representation of gene ontology terms by unigenes containing converted SNPs reflected their coverage across the full transcriptome. Over a quarter of successfully converted SNPs were polymorphic among all species, and the data were successful in discriminating among the species and some individual populations. The SNP array provides a valuable new tool to advance genetic studies in these species and demonstrates the effectiveness of the technology for rapid genotyping in species with large and complex genomes.

中文翻译：

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开发用于四种欧洲松树物种种群基因组研究的 SNP 阵列。

松树是世界上在生态和经济上最重要的树种之一，许多松树具有巨大的自然分布或已被广泛种植。然而，快速基因分型能力的缺乏阻碍了了解这些物种遗传变异的分子基础的进展。在这里，我们提供了一种有效的工具，用于对整个基因组中的数千个单核苷酸多态性 (SNP) 标记进行基因分型，可应用于松树的遗传研究。P. sylvestris、P. mugo、P. uncinata、P. uliginosa和P. radiata 的重测序候选基因和转录组序列的多态性用于设计 49,829 SNP 阵列（Axiom_PineGAP，Thermo Fisher）。超过三分之一 (34.68%) 从P. sylvestris转录组鉴定的unigenes出现在阵列上，用于筛选四种松树物种的样本。阵列在所有样品上的转化率为 42% ( N = 20,795 个 SNP），并且与来自重测序候选基因和转录组序列的 SNP 相似。包含转换的 SNP 的 unigenes 对基因本体术语的广泛表示反映了它们在整个转录组中的覆盖范围。超过四分之一的成功转换的 SNP 在所有物种中都是多态的，并且数据成功地区分了物种和一些个体种群。SNP 阵列为推进这些物种的遗传研究提供了一种有价值的新工具，并证明了该技术对具有大型复杂基因组的物种进行快速基因分型的有效性。