ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Combined transcriptome, metabolome, and miRNA analysis reveals the genetic regulatory network of sweet corn pericarp thickness
Provisionally accepted
Xiaming Wu1*
Ruixiang Liu2Meijing Zhang2
Min Yang1
Chenping Zhou1Ruibin Kuang1
Chen Yanping2Yuerong Wei1- 1State Key Laboratory of Livestock and Poultry Breeding; Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition; Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou,Guangdong, China
- 2Jiangsu Institute of Agricultural Sciences, Nantong, China
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The thickness of the pericarp is a complex characteristic that determines sweet corn's palatability. However, the molecular mechanisms in forming pericarp thickness differences have not been clarified. In this study, we conducted transcriptomics, miRNA analysis, and metabolomics to explore the underlying molecular mechanisms. Scanning electron microscopy (SEM) revealed that the disparity in pericarp thickness is primarily due to variations in the number of cell layers. Our combined multi-omics analysis discovered 6,054 differentially expressed genes (DEGs), 73 differentially expressed miRNAs, 113 differentially accumulated metabolites (DAMs), and several key miRNAs, such as zma-miR164, zma-miR166, zma-miR827, and zma-miR171b were identified, which modulate the expression of different transcription factors and regulate the signal transduction of various plant hormones, thereby influencing pericarp thickness. Additionally, our integrated transcriptomic and metabolomic analysis revealed that genes and metabolites involved in plant hormone signal transduction and phenylpropanoids biosynthesis pathway play a significant role in regulating pericarp growth and development. Furthermore, we observed that in the thick pericarp line (M08), the content of cytokinins was significantly reduced, while phenylpropanoid compounds such as 5-O-feruloylquinic acid glucoside, berberine, scopoletin, sinapic alcohol, sinapic acid and 3-O-feruloylquinic acid glucoside accumulated considerably. These findings provide valuable theoretical support and genetic resources.
Keywords: Metabolism, miRNA, Pericarp thickness, sweet corn, Transcriptome
Received: 03 Sep 2025; Accepted: 27 Nov 2025.
Copyright: © 2025 Wu, Liu, Zhang, Yang, Zhou, Kuang, Yanping and Wei. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Xiaming Wu
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