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.

中文翻译：

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QTL-BSA：用于QTL-seq的散装分离剂分析和可视化管道。

近年来，全基因组测序（WGS）在植物上的应用已经产生了足够的数据来鉴定与性状相关的基因组位点或基因。高通量的基因组辅助QTL-seq策略，结合来自表型特征值相反的分离后代的两个群体的群体隔离分析和WGS，在研究界越来越受欢迎。但是，没有公开可用的用户友好软件来进行标识和可视化。因此，我们开发了一种名为QTL-BSA（QTL批量隔离分析和可视化管道）的工具，该工具可以帮助快速识别和可视化来自QTL-seq的候选QTL。作为概念验证研究，我们已经将该工具用于水稻的局部抗稻瘟病相关基因的快速发现和鉴定。在6号染色体上鉴定出的主要QTL的基因组区域位于1.52和4.32 Mb之间，与先前的研究（2.39-4.39 Mb）一致。我们还获得了该区域的基因和QTL功能注释。QTL-BSA提供了一个全面的解决方案，以促进QTL-seq分析中的各种编程和可视化任务，预计将被研究界广泛使用。