We adapted and tested a Rapture assay as an enhancement of genotyping-by-sequencing (GBS) in oat (Avena sativa). This assay was based on an additional bait-based capture of specific DNA fragments representing approximately 10,000 loci within the enzyme-based complexity reduction provided by GBS. By increasing the specificity of GBS to include only those fragments that provided effective polymorphic markers, it was possible to achieve deeper sequence coverage of target markers, while simultaneously sequencing a greater number of samples on a single unit of next-generation sequencing. The Rapture assay consistently out-performed the GBS assay when filtering markers at 80% completeness or greater, even though the total number of reads per sample was only 25% that of GBS. The reduced sequencing cost per sample for Rapture more than compensated for the increased cost of the capture reaction. Thus, Rapture generated a more repeatable set of marker data at a cost per sample that was approximately 40% less than GBS. Additional advantages of Rapture included accurate identification of heterozygotes, and the possibility to increase the depth or length of sequence reads with less impact on the cost per sample. We tested Rapture for genomic selection and diversity analysis and concluded that it is an effective alternative to GBS or other SNP assays. We recommend the use of Rapture in oat and the development of similar assays in other crops with large complex genomes.

中文翻译：

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一种靶向基因分型测序工具（Rapture），用于燕麦中的基因组学辅助育种。

我们改编并测试了Rapture检测方法，以增强燕麦（Avena sativa）的基因分型（GBS）基因分型。此测定法是基于GBS提供的基于酶的复杂性降低中代表大约10,000个基因座的特定DNA片段的基于诱饵的额外捕获。通过提高GBS的特异性，使其仅包括那些提供有效多态性标记的片段，就有可能实现更深的目标标记序列覆盖率，同时在下一代测序的单个单元上对大量样品进行测序。当以80％或更高的完整性过滤标记时，Rapture测定始终优于GBS测定，即使每个样品的读数总数仅为GBS的25％。Rapture降低了每个样品的测序成本，足以弥补捕获反应成本的增加。因此，Rapture生成了一组更具可重复性的标记数据，每个样品的成本比GBS大约低40％。Rapture的其他优点包括准确鉴定杂合子，并可能增加序列读取的深度或长度，而对每个样品的成本影响较小。我们测试了Rapture的基因组选择和多样性分析，并得出结论，它是GBS或其他SNP分析的有效替代方法。我们建议在燕麦中使用Rapture，并在具有复杂基因组的其他农作物中开发类似的测定方法。Rapture生成了一组更具可重复性的标记数据，每个样品的成本比GBS大约低40％。Rapture的其他优点包括准确鉴定杂合子，并可能增加序列读取的深度或长度，而对每个样品的成本影响较小。我们测试了Rapture的基因组选择和多样性分析，并得出结论，它是GBS或其他SNP分析的有效替代方法。我们建议在燕麦中使用Rapture，并在具有复杂基因组的其他农作物中开发类似的测定方法。Rapture生成了一组更具可重复性的标记数据，每个样品的成本比GBS大约低40％。Rapture的其他优点包括准确鉴定杂合子，并可能增加序列读取的深度或长度，而对每个样品的成本影响较小。我们测试了Rapture的基因组选择和多样性分析，并得出结论，它是GBS或其他SNP分析的有效替代方法。我们建议在燕麦中使用Rapture，并在具有复杂基因组的其他农作物中开发类似的测定方法。我们测试了Rapture的基因组选择和多样性分析，并得出结论，它是GBS或其他SNP分析的有效替代方法。我们建议在燕麦中使用Rapture，并在具有复杂基因组的其他农作物中开发类似的测定方法。我们测试了Rapture的基因组选择和多样性分析，并得出结论，它是GBS或其他SNP分析的有效替代方法。我们建议在燕麦中使用Rapture，并在具有复杂基因组的其他农作物中开发类似的测定方法。