Development and Evaluation of a Barley 50k iSelect SNP Array.
Development and Evaluation of a Barley 50k iSelect SNP Array.
复制标题
DOI：
10.3389/fpls.2017.01792
复制
发表时间：
2017
影响因子：
5.6
通讯作者：
Waugh R
中科院分区：
文献类型：
--
作者：
Bayer MM;Rapazote-Flores P;Ganal M;Hedley PE;Macaulay M;Plieske J;Ramsay L;Russell J;Shaw PD;Thomas W;Waugh R
高通量基因分型阵列仍然是一个有吸引力的，具有成本效益的替代基于测序的方法。我们开发了一种新的50k Illumina Infinium iSelect基因分型阵列，用于大麦，这是一种具有重要国际意义的谷物作物。该阵列上的大多数snp都是从广泛的欧洲大麦种质的外显子组捕获数据中提取的变体。我们使用最近发表的大麦假分子组装来绘制外显子组捕获数据，这使我们能够生成具有准确物理位置和详细基因注释的标记。现有的和广泛使用的大麦9k Infinium iSelect阵列的标记被转移到50k芯片上以向后兼容。该阵列设计具有49,267个SNP标记，转化为44,040个工作分析，其中43,461个在GenomeStudio中可评分。在工作分析中，6251个来自9k iSelect平台。我们通过比较来自新阵列和遗留数据集的基因型调用来验证snp。遗留的9k iSelect SNP集（Comadran等人，）和外显子组捕获SNP的一致性平均分别为98.1和93.9%。为了测试50k芯片在遗传定位方面的效用，我们对来自Golden Promise × Morex杂交的分离群体进行了基因分型（Liu et al.,），并将超过14,000个snp定位到与已知物理位置几乎完全对应的遗传位置。对基因型评分的解释软件所使用的聚类文件进行人工调整，大大改善了结果，但聚类文件在站点之间的迁移导致结果恶化，这表明需要在每个站点的基础上对聚类文件进行局部调整。有关芯片上的标记的信息可在https://ics.hutton.ac.uk/50k上在线获得。
High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al.,) and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise × Morex cross (Liu et al.,) and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at https://ics.hutton.ac.uk/50k.
登录
查看更多内容
影响因子：
3.7
作者：
Sim SC;Durstewitz G;Plieske J;Wieseke R;Ganal MW;Van Deynze A;Hamilton JP;Buell CR;Causse M;Wijeratne S;Francis DM
通讯作者：
Francis DM
DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Fan, JB;Oliphant, A;Chee, MS
通讯作者：
Chee, MS
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
3.7
作者：
Bianco L;Cestaro A;Sargent DJ;Banchi E;Derdak S;Di Guardo M;Salvi S;Jansen J;Viola R;Gut I;Laurens F;Chagné D;Velasco R;van de Weg E;Troggio M
通讯作者：
Troggio M
影响因子：
2.3
作者：
Shaw, Paul D.;Raubach, Sebastian;Marshall, David F.
通讯作者：
Marshall, David F.