Plant and Soil

, Volume 444, Issue 1–2, pp 119–137 | Cite as

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 NianEmail author
Regular Article



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 quantitative trait loci (QTLs) provides an effective tool in analysing the genetic mechanisms underlying Al tolerance and in breeding Al-tolerant soybean varieties.


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 employ 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.


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 peroxidase 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, H2O2 and O2 contents in GmGSTU9- and GmPrx145-overexpressing hairy roots were lower than those in the control and RNA-interference-exposed hairy roots under Al stress.


GmGSTU9 and GmPrx145 detected in qAl06 and qAl-HC2, respectively, positively regulate Al tolerance in soybean hairy roots by improving the antioxidant activity. These Al tolerance genes and molecular markers will be useful for marker-assisted selection to improve the Al tolerance of soybeans in acidic soils.


Soybean Aluminum stress High-density genetic map QTL mapping Antioxidant ability 



composite interval mapping method


Inductively coupled plasma-atomic emission spectrometry


glutathione S-transferase




marker-assisted selection


National Center for Biotechnology Information


real-time quantitative polymerase chain reaction


quantitative trait loci


restriction-site associated DNA sequencing


Recombinant inbred line


reverse transcription-polymerase chain reaction


single nucleotide polymorphism



This work was supported by the Projects of Science and Technology of Guangzhou (201804020015); the National Key R&D Program of China (2018YFD0201006); the China Agricultural Research System (CARS-04-PS09) and the Research Project of the State Key Laboratory of Agricultural and Biological Resources Protection and Utilization in Subtropics.

Author contributions

Y. C., T. L., Q. M. and H. N. provided the soybean materials used in this study. P. X., R. L., X. H., Q. L., and Z. C. performed the experiments and date analyses. Q. X. performed QTL mapping. Z. C. and H. N. prepared the manuscript. H. N. planned, supervised and financed this work, as well as edited the manuscript. All authors have read and approved the final version of the manuscript to be published.

Compliance with ethical standards

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary material

11104_2019_4261_MOESM1_ESM.pdf (130 kb)
ESM 1 (PDF 130 kb)
11104_2019_4261_MOESM2_ESM.pdf (11.6 mb)
ESM 2 (PDF 11874 kb)


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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesSouth China Agricultural UniversityGuangzhouPeople’s Republic of China
  2. 2.The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouPeople’s Republic of China
  3. 3.The Guangdong Subcenter of the National Center for Soybean Improvement, College of AgricultureSouth China Agricultural UniversityGuangzhouPeople’s Republic of China
  4. 4.Beijing Genomics Institute (BGI)-ShenzhenShenzhenPeople’s Republic of China

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