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Volume 13
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10.3390/genes13101851
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Article

Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine

by
Tengfei Wang
1,2,3,
Huixiang Peng
1,2,3,
Yingying Cao
1,2,3,
Jing Xu
1,2,3,
Yuhong Xiong
1,2,3,
Kangchen Liu
1,2,3,
Jing Fang
1,2,3,
Fang Liu
1,2,
Aidi Zhang
1,2 and
Xiujun Zhang
1,2,*
1
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
2
Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
3
University of Chinese Academy of Sciences, Beijing 100049, China
*
Author to whom correspondence should be addressed.
Genes 2022, 13(10), 1851; https://doi.org/10.3390/genes13101851
Submission received: 16 September 2022 / Revised: 9 October 2022 / Accepted: 10 October 2022 / Published: 13 October 2022
(This article belongs to the Topic Complex Systems and Artificial Intelligence)
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Abstract

Grapevine (Vitisvinifera L.) fruit ripening is a complex biological process involving a phase transition from immature to mature. Understanding the molecular mechanism of fruit ripening is critical for grapevine fruit storage and quality improvement. However, the regulatory mechanism for the critical phase transition of fruit ripening from immature to mature in grapevine remains poorly understood. In this work, to identify the key molecular events controlling the critical phase transition of grapevine fruit ripening, we performed an integrated dynamic network analysis on time-series transcriptomic data of grapevine berry development and ripening. As a result, we identified the third time point as a critical transition point in grapevine fruit ripening, which is consistent with the onset of veraison reported in previous studies. In addition, we detected 68 genes as being key regulators involved in controlling fruit ripening. The GO (Gene Ontology) analysis showed that some of these genes participate in fruit development and seed development. This study provided dynamic network biomarkers for marking the initial transcriptional events that characterizes the transition process of fruit ripening, as well as new insights into fruit development and ripening.
Keywords: systems biology; network analysis; dynamic network biomarker; phase transition; fruit development systems biology; network analysis; dynamic network biomarker; phase transition; fruit development

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MDPI and ACS Style

Wang, T.; Peng, H.; Cao, Y.; Xu, J.; Xiong, Y.; Liu, K.; Fang, J.; Liu, F.; Zhang, A.; Zhang, X. Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine. Genes 2022, 13, 1851. https://doi.org/10.3390/genes13101851

AMA Style

Wang T, Peng H, Cao Y, Xu J, Xiong Y, Liu K, Fang J, Liu F, Zhang A, Zhang X. Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine. Genes. 2022; 13(10):1851. https://doi.org/10.3390/genes13101851

Chicago/Turabian Style

Wang, Tengfei, Huixiang Peng, Yingying Cao, Jing Xu, Yuhong Xiong, Kangchen Liu, Jing Fang, Fang Liu, Aidi Zhang, and Xiujun Zhang. 2022. "Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine" Genes 13, no. 10: 1851. https://doi.org/10.3390/genes13101851

APA Style

Wang, T., Peng, H., Cao, Y., Xu, J., Xiong, Y., Liu, K., Fang, J., Liu, F., Zhang, A., & Zhang, X. (2022). Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine. Genes, 13(10), 1851. https://doi.org/10.3390/genes13101851

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