BACKGROUND In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, efficient technologies for genotyping thousands to millions of single nucleotide polymorphisms (SNPs) have finally made large-scale use of genetic markers widely available. These methods will be exceedingly valuable for improving tree breeding and understanding the ecological genetics of Douglas-fir, one of the most economically and ecologically important trees in the world. RESULTS We designed SNP assays for 55,766 potential SNPs that were discovered from previous transcriptome sequencing projects. We tested the array on ~ 2300 related and unrelated coastal Douglas-fir trees (Pseudotsuga menziesii var. menziesii) from Oregon and Washington, and 13 trees of interior Douglas-fir (P. menziesii var. glauca). As many as ~ 28 K SNPs were reliably genotyped and polymorphic, depending on the selected SNP call rate. To increase the number of SNPs and improve genome coverage, we developed protocols to 'rescue' SNPs that did not pass the default Affymetrix quality control criteria (e.g., 97% SNP call rate). Lowering the SNP call rate threshold from 97 to 60% increased the number of successful SNPs from 20,669 to 28,094. We used a subset of 395 unrelated trees to calculate SNP population genetic statistics for coastal Douglas-fir. Over a range of call rate thresholds (97 to 60%), the median call rate for SNPs in Hardy-Weinberg equilibrium ranged from 99.2 to 99.7%, and the median minor allele frequency ranged from 0.198 to 0.233. The successful SNPs also worked well on interior Douglas-fir. CONCLUSIONS Based on the original transcriptome assemblies and comparisons to version 1.0 of the Douglas-fir reference genome, we conclude that these SNPs can be used to genotype about 10 K to 15 K loci. The Axiom genotyping array will serve as an excellent foundation for studying the population genomics of Douglas-fir and for implementing genomic selection. We are currently using the array to construct a linkage map and test genomic selection in a three-generation breeding program for coastal Douglas-fir.

中文翻译：

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道格拉斯冷杉的Axiom SNP基因分型阵列。

背景技术在森林树木中，已经使用遗传标记来了解自然种群的遗传结构，鉴定数量性状基因座，推断基因功能并增强树木育种。近来，用于对成千上万的单核苷酸多态性（SNP）进行基因分型的新的有效技术终于广泛使用了遗传标记。这些方法对于改善树木育种和了解花旗松的生态遗传学将是极其有价值的。道格拉斯杉是世界上最经济和生态上最重要的树木之一。结果我们设计了从以前的转录组测序项目中发现的55,766个潜在SNP的SNP分析。我们在约2300个相关和不相关的沿海道格拉斯杉树（Pseudotsuga menziesii var。来自俄勒冈州和华盛顿的menziesii）和室内花旗松（P. menziesii var。glauca）的13棵树。可靠地将多达28 K个SNP进行基因分型和多态，这取决于所选的SNP检出率。为了增加SNP的数量并改善基因组覆盖范围，我们开发了“拯救”未通过默认Affymetrix质量控制标准（例如97％SNP检出率）的SNP的方案。将SNP呼叫率阈值从97％降低到60％，可以将成功的SNP数量从20,669增加到28,094。我们使用了395棵无关树的子集来计算海岸道格拉斯冷杉的SNP种群遗传统计。在一定范围的检出率门限（97％到60％）中，Hardy-Weinberg平衡中SNP的中位检出率在99.2％至99.7％之间，中位次要等位基因频率在0.198至0.233之间。成功的SNP在室内花旗松上也表现良好。结论基于原始的转录组组装和与道格拉斯冷杉参考基因组的1.0版的比较，我们得出结论，这些SNP可用于约10 K至15 K位点的基因分型。公理基因分型阵列将为研究道格拉斯冷杉的种群基因组学和实施基因组选择奠定良好的基础。我们目前正在使用该阵列来构建连锁图谱，并在沿海道格拉斯冷杉的三代育种计划中测试基因组选择。公理基因分型阵列将为研究道格拉斯冷杉的种群基因组学和实施基因组选择奠定良好的基础。目前，我们正在使用阵列构建连锁图谱，并在沿海道格拉斯冷杉的三代育种计划中测试基因组选择。公理基因分型阵列将为研究道格拉斯冷杉的种群基因组学和实施基因组选择奠定良好的基础。目前，我们正在使用阵列构建连锁图谱，并在沿海道格拉斯冷杉的三代育种计划中测试基因组选择。