Data from: A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids

Rapid identification of Populus L. species and hybrids can be achieved with relatively little effort through the use of primer extension-based single nucleotide polymorphism (SNP) genotyping assays. We present an optimized set of 36 SNP markers from 28 gene regions that diagnose eight poplar species (Populus angustifolia James, Populus balsamifera L., Populus deltoides Bartram, Populus fremontii Watson, Populus laurifolia Ledeb., Populus maximowiczii Henry, Populus nigra L., and Populus trichocarpa Torr. & Gray). A total of 700 DNA sequences from six Populus species (1–15 individuals per species) were used to construct the array. A set of flanking and probe oligonucleotides was developed and tested. The accuracy of the SNP assay was validated by genotyping 448 putatively “pure” individuals from 14 species of Populus. Overall, the SNP assay had a high success rate (97.6 %) and will prove useful for the identification of all Aigeiros Duby and Tacamahaca Spach. species and their early-generation hybrids within natural populations and breeding programs. Null alleles and intraspecific polymorphisms were detected for a few locus/species combinations in the Aigeiros and Tacamahaca sections. When we attempted to genotype aspens of the section Populus (Populus alba L., Populus grandidentata Michx., Populus tremula L., and Populus tremuloides Michx.), the success rate of the SNP array decreased by 13 %, demonstrating moderate cross-sectional transferability.

借助基于引物延伸的单核苷酸多态性（single nucleotide polymorphism, SNP）基因分型检测技术，仅需较少工作量即可实现杨属（Populus L.）物种及其杂交种的快速鉴定。本研究开发了一套源自28个基因区域的优化36个SNP标记组合，可精准鉴定8个杨树物种：小叶杨（Populus angustifolia James）、香脂杨（Populus balsamifera L.）、美洲黑杨（Populus deltoides Bartram）、弗里蒙特杨（Populus fremontii Watson）、朝鲜杨（Populus laurifolia Ledeb.）、大青杨（Populus maximowiczii Henry）、黑杨（Populus nigra L.）以及毛果杨（Populus trichocarpa Torr. & Gray）。本研究共采集并使用来自6个杨属物种（每个物种包含1~15个个体）的700条DNA序列，用于构建该SNP分型芯片。研究团队同步开发并验证了一套侧翼寡核苷酸引物与探针寡核苷酸序列。通过对来自14个杨属物种的448株推定"pure"个体开展基因分型实验，验证了该SNP检测技术的准确性。总体而言，该SNP检测技术的分型成功率高达97.6%，可有效应用于自然种群与育种项目中黑杨组（Aigeiros Duby）、青杨组（Tacamahaca Spach）的所有物种及其早期世代杂交种的鉴定工作。在黑杨组与青杨组的少数位点-物种组合中，研究人员检测到了无效等位基因与种内多态性。当尝试对杨组（section Populus）的白杨类物种（银白杨Populus alba L.、大齿杨Populus grandidentata Michx.、欧洲山杨Populus tremula L.以及美洲山杨Populus tremuloides Michx.）进行基因分型时，该SNP分型芯片的成功率下降了13%，表明其具备中等程度的跨组转移能力。