SNP high-throughput screening in grapevine using the SNPlex genotyping system.
SNP high-throughput screening in grapevine using the SNPlex genotyping system.
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SNP使用SNPLEX基因分型系统在葡萄藤中进行高通量筛选。
DOI：
10.1186/1471-2229-8-12
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发表时间：
2008-01-28
影响因子：
5.3
通讯作者：
Troggio, Michela
中科院分区：
文献类型：
--
作者：
Pindo, Massimo;Vezzulli, Silvia;Coppola, Giuseppina;Cartwright, Dustin A.;Zharkikh, Andrey;Velasco, Riccardo;Troggio, Michela
直到最近，只有少数低和中等通量的方法已被用于单核苷酸多态性（SNP）的发现和基因分型葡萄（葡萄属vinifera L.）。然而，在完成黑比诺高度杂合基因组的序列之后，已经可以识别数百万个电子SNP（eSNP），从而为高通量基因分型方法提供有价值的来源。在此，我们报道了SNIGHTM基因分型系统在葡萄藤中的首次应用，旨在锚定真核基因组。该方法将稳健的SNP检测与自动化测定读出和数据分析相结合。从黑比诺基因组非重复重叠群中筛选出813个候选eSNPs，并在90个西拉×黑比诺杂交后代中进行检测。获得并定位了563个新的SNP标记。当采用多重置换扩增（MDA）方法制备SNPs检测的基因组DNA时，效率从69%提高到80%。与用于研究少数基因型中的数千个SNP或约一千个基因型中的几个SNP的其他SNP基因分型方法不同，SNPs基因分型系统代表了同时研究一百个或更多样品中的数百个SNP的良好折衷。因此，SNPs检测结合全基因组扩增（WGA）的使用是未来在设备齐全的实验室中应用的一个很好的解决方案。
Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP) discovery and genotyping in grapevine (Vitis vinifera L.). However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs) thus providing a valuable source for high-throughput genotyping methods. Herein we report the first application of the SNPlex™ genotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah × Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA) methods were used for preparation of genomic DNA for the SNPlex assay. Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA), is a good solution for future applications in well-equipped laboratories.
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影响因子：
7
作者：
Hosono, S;Faruqi, AF;Lasken, RS
通讯作者：
Lasken, RS
影响因子：
30.8
作者：
Syvänen, AC
通讯作者：
Syvänen, AC
影响因子：
3.1
作者：
Salmaso, M;Faes, G;Velasco, R
通讯作者：
Velasco, R
影响因子：
14.9
作者：
Paez, JG;Lin, M;Sellers, WR
通讯作者：
Sellers, WR
影响因子：
3.3
作者：
Troggio, Michela;Malacarne, Giulia;Velasco, Riccardo
通讯作者：
Velasco, Riccardo