Molecular Genetics and Genomics

, Volume 293, Issue 6, pp 1523–1534 | Cite as

Transcriptome analysis in Malus halliana roots in response to iron deficiency reveals insight into sugar regulation

  • Ya Hu
  • Yan-fang Zhu
  • Ai-xia Guo
  • Xu-mei Jia
  • Li Cheng
  • Tong Zhao
  • Yan-xiu WangEmail author
Original Article


Iron (Fe) deficiency is a frequent nutritional problem limiting apple production in calcareous soils. The utilization of rootstock that is resistant to Fe deficiency is an effective way to solve this problem. Malus halliana is an Fe deficiency-tolerant rootstock; however, few molecular studies have been conducted on M. halliana. In the present work, a transcriptome analysis was combined with qRT-PCR and sugar measurements to investigate Fe deficiency responses in M. halliana roots at 0 h (T1), 12 h (T2) and 72 h (T3) after Fe deficiency stress. Total of 2473, 661, and 776 differentially expressed genes (DEGs) were identified in the pairs of T2 vs. T1, T3 vs. T1, and T3 vs. T2, respectively. Several DEGs were enriched in the photosynthesis, glycolysis and gluconeogenesis, tyrosine metabolism and fatty acid degradation pathways. The glycolysis and photosynthesis pathways were upregulated under Fe deficiency. In this experiment, sucrose accumulated in Fe-deficient roots and leaves. However, the glucose content significantly decreased in the roots, while the fructose content significantly decreased in the leaves. Additionally, 15 genes related to glycolysis and sugar synthesis and sugar transport were selected to validate the accuracy of the transcriptome data by qRT-PCR. Overall, these results indicated that sugar synthesis and metabolism in the roots were affected by Fe deficiency. Sugar regulation is a way by which M. halliana responds to Fe deficiency stress.


RNA-Seq Fe deficiency Sugar Glycolysis Apple Malus halliana 



This work was supported by Gansu Agricultural University Youth Postgraduate Tutor Support Fund Project (project No. GAU-2NDS-201710), Gansu Education Department University Research Project (project No. 2018A-035) and Lanzhou Science and Technology Bureau Program (project No. 2015-3-76).

Compliance with ethical standards

Conflict of interest

All authors declare that we have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

438_2018_1479_MOESM1_ESM.xlsx (9 kb)
Supplementary material 1 (XLSX 9 KB)
438_2018_1479_MOESM2_ESM.xlsx (14 kb)
Supplementary material 2 (XLSX 14 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Ya Hu
    • 1
    • 2
  • Yan-fang Zhu
    • 1
  • Ai-xia Guo
    • 1
  • Xu-mei Jia
    • 1
  • Li Cheng
    • 1
  • Tong Zhao
    • 1
  • Yan-xiu Wang
    • 1
    Email author
  1. 1.College of HorticultureGansu Agricultural UniversityLanzhouChina
  2. 2.Northwest Institute of Eco-Environment and ResourcesChinese Academy of ScienceLanzhouChina

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