Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants
Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants
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DOI：
10.1007/s00122-006-0213-6
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发表时间：
2006-04-01
影响因子：
5.4
通讯作者：
Brunel, D
中科院分区：
文献类型：
--
作者：
Giancola, S;McKhann, HI;Brunel, D
高通量SNP基因分型技术的应用是植物遗传学领域许多研究项目面临的巨大挑战。用于质谱分析的GOOD检测试剂盒、Amplifluor（R）和TaqMan（R）是三种依赖于不同原理的等位基因鉴别和检测方法，分别是引物延伸、等位基因特异性PCR和杂交。首先，通过SNP基因分型评估等位基因频率的目标，我们比较了这些方法对一组三个SNP存在于除草剂抗性基因CSR，AXR1和IXR 1的拟南芥。在该比较中，我们基于PCR特异性、引物设计的灵活性和成功率获得了TaqMan（R）的最佳结果。我们还使用质谱对多倍体物种进行基因分型。最后，这三种方法的组合被用于在许多不同的植物物种中进行中高通量基因分型。在这里，我们表明，所有这三种基因分型技术是成功的，在不同的植物物种中的等位基因的歧视和讨论的因素，必须考虑在评估使用哪种方法用于给定的应用程序。
The application of high-throughput SNP genotyping is a great challenge for many research projects in the plant genetics domain. The GOOD assay for mass spectrometry, Amplifluor(R) and TaqMan(R) are three methods that rely on different principles for allele discrimination and detection, specifically, primer extension, allele-specific PCR and hybridization, respectively. First, with the goal of assessing allele frequencies by means of SNP genotyping, we compared these methods on a set of three SNPs present in the herbicide resistance genes CSR, AXR1 and IXR1 of Arabidopsis thaliana. In this comparison, we obtained the best results with TaqMan(R) based on PCR specificity, flexibility in primer design and success rate. We also used mass spectrometry for genotyping polyploid species. Finally, a combination of the three methods was used for medium- to high-throughput genotyping in a number of different plant species. Here, we show that all three genotyping technologies are successful in discriminating alleles in various plant species and discuss the factors that must be considered in assessing which method to use for a given application.