Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University, Hangzhou, China.
Department of Agronomy and James D Watson Institute of Genome Science, Zhejiang University, Hangzhou, China.
Interdiscip Sci. 2019 Dec;11(4):730-737. doi: 10.1007/s12539-019-00344-9. Epub 2019 Aug 6.
In recent years, the application of Whole Genome Sequencing (WGS) on plants has generated sufficient data for the identification of trait-associated genomic loci or genes. A high-throughput genome-assisted QTL-seq strategy, combined with bulked-segregant analysis and WGS of two bulked populations from a segregating progeny with opposite phenotypic trait values, has gained increasing popularities in research community. However, there is no publicly available user friendly software for the identification and visualization. Hence, we developed a tool named QTL-BSA (QTL-bulked segregant analysis and visualization pipeline), which could facilitate the rapid identification and visualization of candidate QTLs from QTL-seq. As a proof-of-concept study, we have applied the tool for the rapid discovery and the identification of genes related with the partial blast resistance in rice. Genomic region of the major QTL identified on chromosome 6, is located between 1.52 and 4.32 Mb, which is consistent with previous studies (2.39-4.39 Mb). We also derived the gene and QTLs functional annotation of this region. QTL-BSA offers a comprehensive solution to facilitate a wide range of programming and visualization tasks in QTL-seq analysis, is expected to be used widely by the research community.
近年来，全基因组测序（WGS）在植物中的应用已经产生了足够的数据，用于鉴定与性状相关的基因组位点或基因。一种高通量的基于基因组的 QTL-seq 策略，结合了两个来自具有相反表型性状值的分离后代群体的混池分离分析和 WGS，在研究界越来越受欢迎。然而，目前还没有公开的用户友好的软件用于鉴定和可视化。因此，我们开发了一个名为 QTL-BSA（QTL-混池分离分析和可视化管道）的工具，它可以方便地从 QTL-seq 中快速鉴定和可视化候选 QTL。作为概念验证研究，我们已经应用该工具快速发现和鉴定了与水稻部分抗穗瘟性相关的基因。在第 6 号染色体上鉴定到的主要 QTL 的基因组区域位于 1.52 到 4.32Mb 之间，与之前的研究结果一致（2.39-4.39Mb）。我们还推导出了该区域的基因和 QTL 功能注释。QTL-BSA 提供了一个全面的解决方案，以方便 QTL-seq 分析中的各种编程和可视化任务，预计将在研究界得到广泛应用。
