, Volume 206, Issue 1, pp 117–131 | Cite as

Mining for low-nitrogen tolerance genes by integrating meta-analysis and large-scale gene expression data from maize

  • Bowen Luo
  • Haitao Tang
  • Hailan Liu
  • Su Shunzong
  • Suzhi Zhang
  • Ling Wu
  • Dan Liu
  • Shibin Gao


Nitrogen (N) is the most important macronutrient for plant growth and development. Hence, understanding genetic architectures and functional genes involved in the response to N deficiency can greatly facilitate the development of low-N-tolerant cultivars. In this study, we collected 212 quantitative trait loci (QTL) of agronomically important traits under low-N stress conditions in maize. We then identified 21 consensus QTL (cQTL) strongly induced for low-N tolerance after excluding overlapping cQTL containing QTL simultaneously identified in meta-analyses of studies performed under other environmental conditions. Among the 21 cQTL, 30 candidate maize genes were identified from maize large-scale differential expression data derived from analyses of low-N stress, and the 12 most important maize orthologs were identified using homologous BLAST analyses of genes with known functions in N use efficiency in model plants. Furthermore, maize orthologs associated with low-N tolerance and metabolism were also predicted using large-scale expression data from other model plants. The present genetic loci and candidate genes indicate the molecular mechanisms of low-N tolerance in maize and may provide information for QTL fine mapping and molecular marker-assisted selection.


Low-N tolerance Maize Quantitative trait loci Consensus QTL Candidate genes 



This work was supported by the National Natural Science Foundation of China (31361140364 and 31471511), the 948 Project of Ministry of Agriculture of China (2011-G15-2 and 2013-Z38), and the Key Technologies R&D Program of China during the 12th Five-Year Plan period (2011BAD35B01).

Supplementary material

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Bowen Luo
    • 1
    • 2
  • Haitao Tang
    • 3
  • Hailan Liu
    • 1
    • 2
  • Su Shunzong
    • 1
    • 2
  • Suzhi Zhang
    • 1
    • 2
  • Ling Wu
    • 1
    • 2
  • Dan Liu
    • 1
    • 2
  • Shibin Gao
    • 1
    • 2
  1. 1.Maize Research InstituteSichuan Agricultural UniversityChengduChina
  2. 2.Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMinistry of AgricultureChengduChina
  3. 3.Crop Research InstituteSichuan Academy of Agricultural SciencesChengduChina

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