REGULAR ARTICLE Fine-mapping QTLs and the validation of candidate genes for Aluminum tolerance using a high-density genetic map Zhandong Cai & Yanbo Cheng & Peiqi Xian & Rongbin Lin & Qiuju Xia & Xueke He & Qiwen Liang & Tengxiang Lian & Qibin Ma & Hai Nian Received: 22 April 2019 /Accepted: 11 August 2019 # Springer Nature Switzerland AG 2019 Abstract Aims Aluminium (Al) stress is one of the most adverse abiotic factors limiting the growth and productivity of crops in acidic soils. Fine-mapping and cloning of quan- titative trait loci (QTLs) provides an effective tool in analysing the genetic mechanisms underlying Al toler- ance and in breeding Al-tolerant soybean varieties. Methods Soybean cultivar Huachun2 in South China has been reported to be highly tolerant to multiple abiotic stresses in acidic soils, including Al stress. Here, we em- ploy a recombinant inbred line (RIL) population derived from a cross of Huachun2 and Wayao to investigate the Al-tolerance QTLs. The prioritization method and qRT- PCR were applied to predict candidate genes in each QTL. Additionally, the functions of GmGSTU9 and GmPrx145 were investigated in transgenic soybean hairy roots. Results In total, five QTLs associated with relative root elongation and Al content were identified by using the high-density genetic map in hydroponics. GmGSTU9, which encodes a glutathione S-transferase gene in qAl06, and GmPrx145, which encodes a class III per- oxidase gene in qAl-HC2, were selected to further study the gene functions by using transgenic soybean hairy roots. In transgenic soybean hairy roots, the MDA, H 2 O 2 and O 2 - contents in GmGSTU9 - and GmPrx145-overexpressing hairy roots were lower than Plant Soil https://doi.org/10.1007/s11104-019-04261-0 Zhandong Cai and Yanbo Cheng contributed equally to this work. Responsible Editor: Jian Feng Ma. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11104-019-04261-0) contains supplementary material, which is available to authorized users. Z. Cai : Y. Cheng : P. Xian : R. Lin : X. He : Q. Liang : T. Lian : Q. Ma : H. Nian (*) The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, No.483 Wushan Road, Guangzhou, Guangdong 510642, People’ s Republic of China e-mail: hnian@scau.edu.cn Z. Cai : Y. Cheng : P. Xian : R. Lin : X. He : Q. Liang : T. Lian : Q. Ma : H. Nian The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, People’ s Republic of China Z. Cai : Y. Cheng : P. Xian : R. Lin : X. He : Q. Liang : T. Lian : Q. Ma : H. Nian The Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, People’ s Republic of China Q. Xia Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen 518086, People’ s Republic of China