Plant Cell, Tissue and Organ Culture (PCTOC)

, Volume 123, Issue 2, pp 389–404 | Cite as

Transcriptome profiling reveals auxin suppressed anthocyanin biosynthesis in red-fleshed apple callus (Malus sieversii f. niedzwetzkyana)

  • Xiao-Hao Ji
  • Rui Zhang
  • Nan Wang
  • Long Yang
  • Xue-Sen ChenEmail author
Original Article


Anthocyanin biosynthesis in callus culture in vitro is strongly influenced by exogenous auxin concentrations. However, the mechanisms by which auxin regulates anthocyanin biosynthesis are largely unknown. To understand the molecular basis of this phenomenon, global gene expression was analyzed in red-fleshed apple calli treated with 1-naphthaleneacetic acid (NAA; 0.3 and 10 mg/L) and 2,4-dichlorophenoxyacetic acid (2,4-D; 0.03 and 0.6 mg/L) using RNA-seq. A total of 3070 and 2533 genes were differently expressed (log2 ratio ≥ 2 at P < 0.0001) in the 2,4-D and NAA treatments, respectively. Thereof, 937 genes were up-regulated and 902 genes were both down-regulated. Genes involved in anthocyanin and flavonoid synthesis and transport into the vacuole were generally down-regulated. Higher concentrations of 2,4-D and NAA facilitated the transport of auxin and induced the expressions of genes involved in the homeostatic feedback regulatory loop. In the auxin signaling pathway, nine Aux/IAA family genes and seven ARF family genes were up-regulated. Moreover, 298 transcription factors were differentially expressed in the NAA and 2,4-D treatments. Among them, some members of MYB, bHLH, and WD40 families that directly regulate anthocyanin and flavonoid synthesis, such as MYB75 (MdMYB10), MYB12, MYB111, MYB113, TT2, and TT8 (MdbHLH3), were down-regulated by NAA and 2,4-D. Auxin also affected gene expression in other plant hormone signaling pathways, such as the cytokinin, ethylene, and gibberellic acid pathways, which also influenced anthocyanin biosynthesis. This study provides a valuable overview of transcriptome changes and gives insight into the molecular mechanism by which auxin inhibits anthocyanin biosynthesis in red-fleshed apple calli.


Transcriptome Auxin Anthocyanin biosynthesis Malus sieversii f. niedzwetzkyana 



2,4-Dichlorophenoxyacetic acid


Naphthalene acetic acid




Murashige and skoog



The authors are grateful to professor Zhang-Jun Fei for reviewing this paper. This work was supported by Special Fund for Agro-scientific Research in the Public Interest (201303093), Natl. Natural Science Foundation of China (Grant No. 31171932) and National Key Basic Research Program of China (2011CB100606).

Authors contribution

Conceived and designed the experiments: XHJ RZ XSC. Performed the experiments: XHJ RZ NW. Analyzed the data: XHJ RZ. Contributed to the writing of the manuscript: XHJ RZ LY XSC.

Supplementary material

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Supplementary material 1 (DOC 104 kb)
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Supplementary material 2 (XLS 22 kb)
11240_2015_843_MOESM3_ESM.xls (740 kb)
Supplementary material 3 (XLS 739 kb)
11240_2015_843_MOESM4_ESM.xls (92 kb)
Supplementary material 4 (XLS 91 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Xiao-Hao Ji
    • 1
    • 2
    • 3
  • Rui Zhang
    • 1
    • 2
    • 3
  • Nan Wang
    • 1
    • 2
    • 3
  • Long Yang
    • 1
    • 2
    • 4
  • Xue-Sen Chen
    • 1
    • 2
    • 3
    Email author
  1. 1.National Key Laboratory of Crop BiologyShandong Agricultural UniversityTai-AnChina
  2. 2.National Research Center for Apple Engineering and TechnologyShandong Agricultural UniversityTai-AnChina
  3. 3.College of Horticulture Science and EngineeringShandong Agricultural UniversityTai-AnChina
  4. 4.Tobacco LaboratoryShandong Agricultural UniversityTai-AnChina

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