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Journal of Integrative Agriculture  2021, Vol. 20 Issue (1): 132-146    DOI: 10.1016/S2095-3119(20)63399-8
Special Issue: 园艺-分子生物合辑Horticulture — Genetics · Breeding
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L.
FU Fang-fang1*, PENG Ying-shu1, 2*, WANG Gui-bin1, Yousry A. EL-KASSABY2, CAO Fu-liang1 
1 Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, P.R.China
2 Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, B.C., V6T 1Z4, Canada
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We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate (Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis (WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages.  In total, 489 metabolites were detected, including 40 differentially accumulated metabolites.  The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process.  Using WGCNA, we identified modules related to the various seed germination stages and hub genes.  In the initial imbibition stage (stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage (stage 4), the pivotal genes were involved in multiple metabolic pathways.  In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.
Keywords:  seed germination stages        weighted gene co-expression network analysis (WGCNA)        metabolome        transcriptome        flavonoid pathway  
Received: 15 March 2020   Accepted:
Fund: This work was supported by the Doctorate Fellowship Foundation of Nanjing Forestry University, China (163010550) and the Priority Academic Program Development of Jiangsu High Education Institutions, China (PAPD).
Corresponding Authors:  Correspondence CAO Fu-liang, Tel/Fax: +86-25-85427921, E-mail:; Yousry A. EL-KASSABY, Tel: +1-604-8221821, Fax: +1-604-8229102, E-mail:   
About author:  * These authors contributed equally to this study.

Cite this article: 

FU Fang-fang, PENG Ying-shu, WANG Gui-bin, Yousry A. EL-KASSABY, CAO Fu-liang. 2021. Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L.. Journal of Integrative Agriculture, 20(1): 132-146.

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