DeepBSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits  

作　　者：Zhao Li Xiaoxuan Chen Shaoqiang Shi Hongwei Zhang Xi Wang Hong Chen Weifu Li Lin Li 

机构地区：[1]National Key Laboratory of Crop Genetic Improvement,Huazhong Agricultural University,Wuhan 430070,China [2]Hainan Yazhou Bay Seed Lab,Hainan,China [3]College of Science,Huazhong Agricultural University,Wuhan 430070,China [4]Institute of Crop Science,Chinese Academy of Agricultural Sciences,Beijing 100081,China

出　　处：《Molecular Plant》2022年第9期1418-1427,共10页分子植物（英文版）

基　　金：supported by the National Natural Science Foundation of China(31922068);HainanYazhouBay Seed Lab(B21HJ8102);themajor Program of Hubei Hongshan Laboratory(2021hszd008);Huazhong 3 Agricultural University Scientific&Technological Self-innovation Foundation(2021ZKPY001);Fundamental Research Funds for the Central Universities of China(2662020LXQD002).

摘　　要：Bulked segregant analysis(BSA)is a rapid,cost-effective method for mapping mutations and quantitative trait loci(QTLs)in animals and plants based on high-throughput sequencing.However,the algorithms currently used for BSA have not been systematically evaluated and are complex and fallible to operate.We developed a BSA method driven by deep learning,DeepBSA,for QTL mapping and functional gene cloning.DeepBSA is compatible with a variable number of bulked pools and performed well with various simulated and real datasets in both animals and plants.DeepBSA outperformed all other algorithms when comparing absolute bias and signal-to-noise ratio.Moreover,we applied DeepBSA to an F2 segregating maize population of 7160 individuals and uncovered five candidate QTLs,including three well-known plant-height genes.Finally,we developed a user-friendly graphical user interface for DeepBSA,by integrating five widely used BSA algorithms and our two newly developed algorithms,that is easy to operate and can quickly map QTLs and functional genes.The DeepBSA software is freely available to noncommercial users at http://zeasystemsbio.hzau.edu.cn/tools.html and https://github.com/lizhao007/DeepBSA.

关 键 词：QTL mapping bulked segregant analysis BSA deep learning DL functional genomics plant height 

分 类 号：Q94[生物学—植物学]