Introgression browser: high-throughput whole-genome SNP visualization
Introgression browser: high-throughput whole-genome SNP visualization
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DOI：
10.1111/tpj.12800
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发表时间：
2015-04-01
期刊：
影响因子：
7.2
通讯作者：
Peters, Sander A.
中科院分区：
文献类型：
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作者：
Aflitos, Saulo Alves;Sanchez-Perez, Gabino;Peters, Sander A.
导入杂交育种是拓宽作物遗传基础的关键策略。通常，通过标记辅助选择在连续的杂交世代中监测所需的性状，但他们的分析在交叉重组子罕见或不可行的染色体区域失败。在这里，我们介绍了介绍浏览器(IBrowser)，这是一个生物信息学工具，旨在可视化导入核苷酸或SNP(单核苷酸多态)的准确性。该软件从可变呼叫格式(VCF)信息中选择纯合子SNPs，并筛选出杂合子SNPs、多核苷酸多态(MNPs)和插入-缺失(Indels)。对于数据分析，iBrowser使用滑动窗口，但如果需要，它可以通过通用要素格式(GFF)信息生成任何所需的碎片模式。在番茄(Solanum Lycopsicum)材料的一个例子中，我们显示了SNP模式，并阐明了导入的位置和边界。我们还表明，我们的工具能够通过检测番茄中导入片段的系统发育关系来识别一组密切相关的pimpinellifolium中的外源DNA。在第三个例子中，我们在一组597份拟南芥材料中展示了iBrowser的功能，检测了4号染色体短臂上一个多态的1.17 Mbp反向片段周围的无SNP区域的边界。iBrowser的结构和功能使该软件适合于广泛的分析，包括SNP挖掘、基因组结构分析和系谱分析。它的功能，再加上处理大型数据集的能力和高效的序列变异可视化，使iBrowser成为一个有价值的育种工具。
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (iBrowser), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, multi-nucleotide polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis iBrowser makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S.pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the iBrowser in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of iBrowser makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes iBrowser a valuable breeding tool.