High-throughput genotyping with the GoldenGate assay in the complex genome of soybean
High-throughput genotyping with the GoldenGate assay in the complex genome of soybean
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DOI：
10.1007/s00122-008-0726-2
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发表时间：
2008-05-01
影响因子：
5.4
通讯作者：
Cregan, Perry B.
中科院分区：
文献类型：
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作者：
Hyten, David L.;Song, Qijian;Cregan, Perry B.
大量的单核苷酸多态性（SNP）标记现在可用于许多作物物种。然而，用于多重SNP测定的高通量方法尚未在具有高比例旁系同源基因的复杂基因组（例如大豆）中测试。Illumina GoldenGate检测试剂盒能够在3天的时间内在单个反应中多重检测96至1，536个SNP。我们在大豆中测试了GoldenGate测定法，以确定将经验证的SNP转化为工作测定法的成功率。定制384-SNP GoldenGate测定使用通过对作为三个重组近交系（RIL）作图群体的亲本的五个不同种质进行重测序而发现的SNP来设计。预测选择用于该定制测定的384个SNP在一个或多个RIL作图群体中分离。等位基因数据成功地产生了89%的SNP位点（384个中的342个），当它被用于三个RIL作图群体时，表明大豆基因组的复杂性对发现的SNP转化为可用的测定几乎没有影响。此外，当该测定用于亚洲地方品种种质资源的多样化样品时，342个作图的SNP中的80%具有> 10%的次要等位基因频率。GoldenGate分析的高成功率使其成为在SNP标记迅速变得可用的物种中快速创建高密度遗传图谱的有用技术。
Large numbers of single nucleotide polymorphism (SNP) markers are now available for a number of crop species. However, the high-throughput methods for multiplexing SNP assays are untested in complex genomes, such as soybean, that have a high proportion of paralogous genes. The Illumina GoldenGate assay is capable of multiplexing from 96 to 1,536 SNPs in a single reaction over a 3-day period. We tested the GoldenGate assay in soybean to determine the success rate of converting verified SNPs into working assays. A custom 384-SNP GoldenGate assay was designed using SNPs that had been discovered through the resequencing of five diverse accessions that are the parents of three recombinant inbred line (RIL) mapping populations. The 384 SNPs that were selected for this custom assay were predicted to segregate in one or more of the RIL mapping populations. Allelic data were successfully generated for 89% of the SNP loci (342 of the 384) when it was used in the three RIL mapping populations, indicating that the complex nature of the soybean genome had little impact on conversion of the discovered SNPs into usable assays. In addition, 80% of the 342 mapped SNPs had a minor allele frequency > 10% when this assay was used on a diverse sample of Asian landrace germplasm accessions. The high success rate of the GoldenGate assay makes this a useful technique for quickly creating high density genetic maps in species where SNP markers are rapidly becoming available.