Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.
State Key Laboratory for Biology of Plant Diseases & Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Biotechniques. 2019 Jul;67(1):6-10. doi: 10.2144/btn-2019-0012. Epub 2019 May 24.
SNPs and single base pair (SBP) insertion/deletions (indels) are not only the most abundant genetic markers for genetic mapping and breeding selection, but also always occur in the mutants generated from chemical mutagenesis or CRISPR/Cas9-mediated genome editing. Most of the current SNP and SBP indel genotyping methods are time-consuming and/or require special equipment or reagents. Here, we describe an improved heteroduplex analysis method, named iHDA, that can readily discriminate SNP and SBP indel alleles with specially designed DNA probes that harbor a couple of nucleotides adjacent to the SNP site. By hybridizing with the same probe, SNP and SBP indel alleles form different heteroduplexes, differing in bulge size, which show different mobility on a polyacrylamide gel. Therefore, iHDA is an easy, fast and inexpensive method for SNP and SBP indel genotyping.
单核苷酸多态性（SNP）和单碱基对（SBP）插入/缺失（indels）不仅是遗传图谱和育种选择的最丰富的遗传标记，而且经常出现在化学诱变或 CRISPR/Cas9 介导的基因组编辑产生的突变体中。目前大多数 SNP 和 SBP indel 基因型分析方法耗时且/或需要特殊设备或试剂。在这里，我们描述了一种改进的异源双链分析方法，称为 iHDA，它可以通过设计含有紧邻 SNP 位点的几个核苷酸的特殊 DNA 探针来轻松区分 SNP 和 SBP indel 等位基因。通过与相同的探针杂交，SNP 和 SBP indel 等位基因形成不同的异源双链体，在凸起大小上有所不同，在聚丙烯酰胺凝胶上显示出不同的迁移率。因此，iHDA 是 SNP 和 SBP indel 基因型分析的一种简单、快速且廉价的方法。
