TY - JOUR
T1 - Dynamic network biomarker analysis discovers IbNAC083 in the initiation and regulation of sweet potato root tuberization
AU - He, Shutao
AU - Wang, Hongxia
AU - Hao, Xiaomeng
AU - Wu, Yinliang
AU - Bian, Xiaofeng
AU - Yin, Minhao
AU - Zhang, Yandi
AU - Fan, Weijuan
AU - Dai, Hao
AU - Yuan, Ling
AU - Zhang, Peng
AU - Chen, Luonan
N1 - Publisher Copyright:
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd
PY - 2021/11
Y1 - 2021/11
N2 - 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.
AB - 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.
KW - IbNAC083
KW - Ipomoea batatas
KW - co-expression network
KW - dynamic network biomarker
KW - storage root development
KW - tipping point
KW - transcriptome dynamics
UR - http://www.scopus.com/inward/record.url?scp=85115191063&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85115191063&partnerID=8YFLogxK
U2 - 10.1111/tpj.15478
DO - 10.1111/tpj.15478
M3 - Article
C2 - 34460981
AN - SCOPUS:85115191063
SN - 0960-7412
VL - 108
SP - 793
EP - 813
JO - Plant Journal
JF - Plant Journal
IS - 3
ER -