Conversion of array-based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum).
Conversion of array-based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum).
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DOI：
10.1111/pbi.12834
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发表时间：
2018-04
影响因子：
13.8
通讯作者：
Edwards KJ
中科院分区：
文献类型：
--
作者：
Burridge AJ;Wilkinson PA;Winfield MO;Barker GLA;Allen AM;Coghill JA;Waterfall C;Edwards KJ
小麦育种家和学者都使用单核苷酸多态性（SNPs）作为分子标记来表征六倍体小麦基因组内的感兴趣区域。许多基于SNP的基因分型平台是可用的，其效用取决于可用技术、所需数据点数量、预算和所需技术专长等因素。遗憾的是，标记物很少能在现有平台和新开发的平台之间交换，这意味着以前生成的数据无法与最近生成的数据集进行比较或组合。我们预测，通过测序进行基因分型将在未来5-10年内成为主要的基因分型技术。考虑到这一点，为了确保从当前基因分型平台生成的数据继续使用，我们从Axiom®和KASP™基因分型平台的数千个现有和公开可用的探针中设计并利用了基于SNP的捕获探针。我们已经使用31个先前基因分型的英国精英六倍体小麦种质通过测序方案在靶向基因分型中验证了我们的捕获探针。通过测序进行的靶向基因分型、Axiom®阵列基因分型和KASP™基因分型测定之间的数据比较鉴定了一组3256个探针，其可靠地将通过测序进行的靶向基因分型数据与先前可用的标记物数据集结合在一起。因此，这些探针可能对小麦社区具有相当大的价值。探针细节、完整探针序列和定制的分析管道可以从CerealsDB网站（http：//www.cerealsdb.uk.net/cerealgenomics/CerealsDB/sequence_capture.php）免费下载。
Wheat breeders and academics alike use single nucleotide polymorphisms (SNPs) as molecular markers to characterize regions of interest within the hexaploid wheat genome. A number of SNP‐based genotyping platforms are available, and their utility depends upon factors such as the available technologies, number of data points required, budgets and the technical expertise required. Unfortunately, markers can rarely be exchanged between existing and newly developed platforms, meaning that previously generated data cannot be compared, or combined, with more recently generated data sets. We predict that genotyping by sequencing will become the predominant genotyping technology within the next 5–10 years. With this in mind, to ensure that data generated from current genotyping platforms continues to be of use, we have designed and utilized SNP‐based capture probes from several thousand existing and publicly available probes from Axiom® and KASP™ genotyping platforms. We have validated our capture probes in a targeted genotyping by sequencing protocol using 31 previously genotyped UK elite hexaploid wheat accessions. Data comparisons between targeted genotyping by sequencing, Axiom® array genotyping and KASP™ genotyping assays, identified a set of 3256 probes which reliably bring together targeted genotyping by sequencing data with the previously available marker data set. As such, these probes are likely to be of considerable value to the wheat community. The probe details, full probe sequences and a custom built analysis pipeline may be freely downloaded from the CerealsDB website (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/sequence_capture.php).
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影响因子：
13.8
作者：
Allen AM;Winfield MO;Burridge AJ;Downie RC;Benbow HR;Barker GL;Wilkinson PA;Coghill J;Waterfall C;Davassi A;Scopes G;Pirani A;Webster T;Brew F;Bloor C;Griffiths S;Bentley AR;Alda M;Jack P;Phillips AL;Edwards KJ
通讯作者：
Edwards KJ
影响因子：
3.7
作者：
Holtz Y;Ardisson M;Ranwez V;Besnard A;Leroy P;Poux G;Roumet P;Viader V;Santoni S;David J
通讯作者：
David J
DOI：
10.1111/tpj.12307
发表时间：
2013-11
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Jupe F;Witek K;Verweij W;Sliwka J;Pritchard L;Etherington GJ;Maclean D;Cock PJ;Leggett RM;Bryan GJ;Cardle L;Hein I;Jones JD
通讯作者：
Jones JD
影响因子：
12.3
作者：
Parla JS;Iossifov I;Grabill I;Spector MS;Kramer M;McCombie WR
通讯作者：
McCombie WR
影响因子：
4.4
作者：
Chilamakuri CS;Lorenz S;Madoui MA;Vodák D;Sun J;Hovig E;Myklebost O;Meza-Zepeda LA
通讯作者：
Meza-Zepeda LA