Single Nucleotide Polymorphisms in Common Bean: Their Discovery and Genotyping Using a Multiplex Detection System
Single Nucleotide Polymorphisms in Common Bean: Their Discovery and Genotyping Using a Multiplex Detection System
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DOI：
10.3835/plantgenome2008.04.0204
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发表时间：
2008-11-01
期刊：
影响因子：
4.2
通讯作者：
Tohme, J.
中科院分区：
文献类型：
--
作者：
Gaitan-Solis, E.;Choi, I. -Y.;Tohme, J.
单核苷酸多态性（SNP）标记是迄今为止基因组中最常见的DNA多态性形式。本研究的目的是发现普通菜豆（Phaseolus vulgaris L.）通过比较从GenBank和基因组DNA获得的编码区和非编码区的序列，并将测序结果与在Luminex-100系统上使用单碱基延伸（SBE）测定获得的结果进行比较，以用于高通量种质评价。我们使用SBE作为评估方法，评估了47个菜豆DNA片段中SNP的频率。我们进行了10个基因型的栽培和野生豆类属于中美洲和安第斯山脉的遗传库的P. vulgaris的序列分析。对于评估的10种基因型，在每个基因型中分析并比较总共20，964 bp的序列，导致发现239个SNP和133个InDel，得到平均SNP频率为每88 bp一个，InDel频率为每157 bp一个。这相当于核苷酸多样性（theta）为6.27 x 10（-3）。与先前通过直接测序获得的SNP基因型的比较表明，在Luminex-100上的SBE测定是准确的，2.5%被误判，1%显示没有信号。这些结果表明，Luminex-100提供了一种高通量系统，可用于分析基因型大样本中的SNP，既用于评估多样性，也用于作图研究。
Single nucleotide polymorphism (SNP) markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean (Phaseolus vulgaris L.) by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA and to compare sequencing results with those obtained using single base extension (SBE) assays on the Luminex-100 system for use in high-throughput germplasm evaluation. We assessed the frequency of SNPs in 47 fragments of common bean DNA, using SBE as the evaluation methodology. We conducted a sequence analysis of 10 genotypes of cultivated and wild beans belonging to the Mesoamerican and Andean genetic pools of P. vulgaris. For the 10 genotypes evaluated, a total of 20,964 bp of sequence were analyzed in each genotype and compared, resulting in the discovery of 239 SNPs and 133 InDels, giving an average SNP frequency of one per 88 bp and an InDel frequency of one per 157 bp. This is the equivalent of a nucleotide diversity (theta) of 6.27 x 10(-3). Comparisons with the SNP genotypes previously obtained by direct sequencing showed that the SBE assays on the Luminex-100 were accurate, with 2.5% being miscalled and 1% showing no signal. These results indicate that the Luminex-100 provides a high-throughput system that can be used to analyze SNPs in large samples of genotypes both for purposes of assessing diversity and also for mapping studies.