Ophir Ron, Sherman Amir
Institute of Plant Sciences, Agricultural Research Organization, Volcani Research Center, Bet Dagan 50250, Israel.
Methods Mol Biol. 2012;815:39-47. doi: 10.1007/978-1-61779-424-7_4.
Successful genetic mapping is dependent upon a high-density set of markers. Therefore, tools for high-throughput discovery of genetic variation are essential. The most abundant genetic marker is the single-nucleotide polymorphism (SNP). However, except for model organisms, genomic information is still limited. Although high-throughput genomic sequencing technologies are becoming relatively inexpensive, only low-throughput genetic markers are accessible (e.g., simple sequence repeats). The use of sequencing for the discovery and screening of high-density genetic variation in whole populations is still expensive. Alternatively, hybridization of genomic DNA (gDNA) on a reference (either genome or transcriptome) is an efficient approach for genetic screening without knowing the alleles in advance (Borevitz et al. Proc Natl Acad Sci USA 104:12057-12062). We describe a protocol for the design of probes for a high-throughput genetic-marker discovery microarray, termed single feature polymorphism (SFP) array. Starting with consensus cDNA sequences (UniGenes), we use OligoWiz to design T (m)-optimized 50-bp long oligonucleotide probes (Ophir et al. BMC Genomics 11:269, 2010). This design is similar to expression arrays and we point out the differences.
成功的基因定位依赖于高密度的标记集。因此，用于高通量发现遗传变异的工具至关重要。最丰富的遗传标记是单核苷酸多态性（SNP）。然而，除了模式生物外，基因组信息仍然有限。尽管高通量基因组测序技术正变得相对便宜，但目前只能获得低通量的遗传标记（例如简单序列重复）。利用测序来发现和筛选全群体中的高密度遗传变异仍然成本高昂。另外，将基因组DNA（gDNA）与参考物（基因组或转录组）杂交是一种无需预先知晓等位基因的高效遗传筛选方法（Borevitz等人，《美国国家科学院院刊》104:12057 - 12062）。我们描述了一种用于设计高通量遗传标记发现微阵列（称为单特征多态性（SFP）阵列）探针的方案。从共有cDNA序列（单基因簇）开始，我们使用OligoWiz设计Tm优化的50个碱基长的寡核苷酸探针（Ophir等人，《BMC基因组学》11:269，2010）。这种设计类似于表达阵列，我们也指出了其中的差异。
