Dynamic network biomarker analysis discovers IbNAC083 in the initiation and regulation of sweet potato root tuberization

Shutao He, Hongxia Wang, Xiaomeng Hao, Yinliang Wu, Xiaofeng Bian, Minhao Yin, Yandi Zhang, Weijuan Fan, Hao Dai, Ling Yuan, Peng Zhang, Luonan Chen

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


The initiation and development of storage roots (SRs) are intricately regulated by a transcriptional regulatory network. One key challenge is to accurately pinpoint the tipping point during the transition from pre-swelling to SRs and to identify the core regulators governing such a critical transition. To solve this problem, we performed a dynamic network biomarker (DNB) analysis of transcriptomic dynamics during root development in Ipomoea batatas (sweet potato). First, our analysis identified stage-specific expression patterns for a significant proportion (>9%) of the sweet potato genes and unraveled the chronology of events that happen at the early and later stages of root development. Then, the results showed that different root developmental stages can be depicted by co-expressed modules of sweet potato genes. Moreover, we identified the key components and transcriptional regulatory network that determine root development. Furthermore, through DNB analysis an early stage, with a root diameter of 3.5 mm, was identified as the critical period of SR swelling initiation, which is consistent with morphological and metabolic changes. In particular, we identified a NAM/ATAF/CUC (NAC) domain transcription factor, IbNAC083, as a core regulator of this initiation in the DNB-associated network. Further analyses and experiments showed that IbNAC083, along with its associated differentially expressed genes, induced dysfunction of metabolism processes, including the biosynthesis of lignin, flavonol and starch, thus leading to the transition to swelling roots.

Original languageEnglish
Pages (from-to)793-813
Number of pages21
JournalPlant Journal
Issue number3
StatePublished - Nov 2021

Bibliographical note

Funding Information:
This work was supported by National Key R&D Program of China (grant nos 2017YFA0505500 and 2018YFD1000705), Priority Research Program of the Chinese Academy of Sciences (grant no. XDB38040400), the National Natural Science Foundation of China (grant nos 31930022, 12026608 and 31771476) and Japan Science and Technology Agency Moonshot R&D (grant no. JPMJMS2021).

Publisher Copyright:
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd


  • IbNAC083
  • Ipomoea batatas
  • co-expression network
  • dynamic network biomarker
  • storage root development
  • tipping point
  • transcriptome dynamics

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology


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