An Axiom SNP genotyping array for Douglas-fir
An Axiom SNP genotyping array for Douglas-fir
复制标题
DOI：
10.1186/s12864-019-6383-9
复制
发表时间：
2020-01-03
期刊：
影响因子：
4.4
通讯作者：
McEvoy, Susan
中科院分区：
文献类型：
--
作者：
Howe, Glenn T.;Jayawickrama, Keith;McEvoy, Susan
在森林树木中，遗传标记已被用于了解自然种群的遗传结构、鉴定数量性状位点、推断基因功能和加强树木育种。近年来，对成千上万的单核苷酸多态性（snp）进行基因分型的新型高效技术终于使遗传标记的大规模应用变得广泛。这些方法对于改善杉木的选育和了解杉木的生态遗传学具有重要的意义。我们设计了55,766个潜在SNP的SNP检测，这些SNP来自之前的转录组测序项目。我们对来自俄勒冈州和华盛顿州的2300棵相关和不相关的沿海道格拉斯杉树（门齐杉树）和13棵内陆道格拉斯杉树（门齐杉树）进行了测试。根据选择的SNP调用率，多达28k的SNP是可靠的基因型和多态性。为了增加SNP的数量并提高基因组覆盖率，我们制定了“拯救”未通过默认Affymetrix质量控制标准（例如，97% SNP调用率）的SNP的方案。将SNP呼叫率阈值从97%降低到60%，成功的SNP数量从20,669个增加到28,094个。我们使用395棵不相关树的子集来计算沿海道格拉斯冷杉的SNP群体遗传统计。在呼出率阈值范围内（97% ~ 60%），Hardy-Weinberg平衡中SNPs的呼出率中位数为99.2 ~ 99.7%，次要等位基因频率中位数为0.198 ~ 0.233。成功的snp在道格拉斯冷杉内部也有很好的效果。基于原始转录组组装和与道格拉斯杉木参考基因组1.0版本的比较，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。Axiom基因分型阵列将为研究道格拉斯冷杉种群基因组学和实施基因组选择提供良好的基础。我们目前正在使用该阵列构建连锁图谱，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。
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 similar to 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 similar to 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.