OcBSA: An NGS-based bulk segregant analysis tool for outcross populations

文献类型： 外文期刊

第一作者： Zhang, Lingkui

作者： Zhang, Lingkui;Duan, Yanfeng;Zhang, Zewei;Zhang, Lei;Chen, Shumin;Cai, Chengcheng;Duan, Shaoguang;Zhang, Kang;Li, Guangcun;Cheng, Feng

作者机构：

关键词： outcross; BSA; self-incompatible; F 1 population; QTL mapping; potato

期刊名称：MOLECULAR PLANT （ 影响因子：27.5； 五年影响因子：22.6 ）

ISSN： 1674-2052

年卷期： 2024 年 17 卷 4 期

页码：

收录情况： SCI

摘要： Constructing inbred lines for self -incompatible species and species with long generation times is challenging, making the use of F 1 outcross/segregating populations the main strategy for genetic studies of such species. However, there is a lack of dedicated algorithms/tools for rapid quantitative trait locus (QTL) mapping using the F 1 populations. To this end, we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F 1 populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F 1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F 1 population. Testing of OcBSA on 1800 simulated F 1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy. In addition, the broad applicability of OcBSA was validated by QTL mapping using seven reported F 1 populations of apple, pear, peach, citrus, grape, tea, and rice. We also used OcBSA to map the QTL for flower color in a newly constructed F 1 population of potato generated in this study. The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene, which regulates potato flower color. Taken together, these results highlight the power and broad utility of OcBSA for QTL mapping using F 1 populations and thus a great potential for functional gene mining in outcrossing species. For ease of use, we have developed both Windows and Linux versions of OcBSA, which are freely available at: https://gitee.com/Bioinformaticslab/OcBSA.

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