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Food Science and Human Wellness 2023, 12(5): 1557-1570 https://doi.org/10.1016/j.fshw.2023.02.003
Research Article | Open Access | Issue | Published: 21 March 2023

Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation

Show Author's Information Wenqiang Wanga,  Yunfeng Pub,  Hao Wena,  Dengyang Lub,  Min Yanb,  Minzhe Liub,  Minyu Wua,  Hongjin Baib,  Lirong Shena( ),  Cuiyun Wub( )
Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, China
College of Horticulture and Forestry, Tarim University, Alar 843300, China

Peer review under responsibility of KeAi Communications Co., Ltd.

Keywords:
Hub genes, Transcriptome analysis, WGCNA, Jujube, Proanthocyanidin
Cite this article:
Wang W, Pu Y, Wen H, et al. Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation. Food Science and Human Wellness, 2023, 12(5): 1557-1570. https://doi.org/10.1016/j.fshw.2023.02.003
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Abstract Full text About this article

Proanthocyanidin (PA) is an important bioactive compound with multiple physiological benefits in jujube (Ziziphus jujube Mill.). However, the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated. Here, the profiling of PA, (+)-catechin and (–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed. The levels of total PAs and catechin exhibited a decreased trend over jujube ripening, and epicatechin content of two jujube cultivars increased first and then declined. Transcriptome analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in ribosome, glycolysis/gluconeogenesis, fructose and mannose metabolism. 17 DEGs encoding PAL, CHS, CHI, CHS, F3'H, LAR, ANR, C4Hs, 4CLs, FLSs, DFRs and UFGTs involved in PA biosynthesis were relatively abundant. The highly transcribed LAR gene may greatly contribute to epicatechin accumulation. A weighted gene co-expression network analysis (WGCNA) was performed, and a network module including 1620 genes highly correlated with content of Pas and catechin was established. We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module. Sixteen genes encoding 9 families of transcriptional factors (i.e., MYB, bHLH, ERF, bZIP, NAC, SBP, MIKC, HB, WRKY) were considered as hub genes. The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data. These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding.


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About this article

Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation

Show Author's information Wenqiang Wanga, Yunfeng Pub, Hao Wena, Dengyang Lub, Min Yanb, Minzhe Liub, Minyu Wua, Hongjin Baib, Lirong Shena( ), Cuiyun Wub( )
Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, China
College of Horticulture and Forestry, Tarim University, Alar 843300, China

Peer review under responsibility of KeAi Communications Co., Ltd.

Abstract

Proanthocyanidin (PA) is an important bioactive compound with multiple physiological benefits in jujube (Ziziphus jujube Mill.). However, the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated. Here, the profiling of PA, (+)-catechin and (–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed. The levels of total PAs and catechin exhibited a decreased trend over jujube ripening, and epicatechin content of two jujube cultivars increased first and then declined. Transcriptome analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in ribosome, glycolysis/gluconeogenesis, fructose and mannose metabolism. 17 DEGs encoding PAL, CHS, CHI, CHS, F3'H, LAR, ANR, C4Hs, 4CLs, FLSs, DFRs and UFGTs involved in PA biosynthesis were relatively abundant. The highly transcribed LAR gene may greatly contribute to epicatechin accumulation. A weighted gene co-expression network analysis (WGCNA) was performed, and a network module including 1620 genes highly correlated with content of Pas and catechin was established. We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module. Sixteen genes encoding 9 families of transcriptional factors (i.e., MYB, bHLH, ERF, bZIP, NAC, SBP, MIKC, HB, WRKY) were considered as hub genes. The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data. These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding.

Keywords: Hub genes, Transcriptome analysis, WGCNA, Jujube, Proanthocyanidin

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Publication history

Received: 30 March 2021
Revised: 26 May 2021
Accepted: 07 June 2021
Published: 21 March 2023
Issue date: September 2023

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© 2023 Beijing Academy of Food Sciences.

Acknowledgements

This work was supported by Major scientific and technological projects of Xinjiang Production and Construction Corps (2017DB006 and 2020KWZ-012). We would like to thank Prof. Liang Liu from Department of Statistics, The University of Georgia, United States for his help on writing and revising the manuscript, Prof. Qikang Gao of Center of Analysis and Measurement, Faculty of Agriculture, Life and Environment Science, Zhejiang University for his assistance in experiment of quantitative RT-PCR analysis.

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