ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Nutrition
This article is part of the Research TopicExploring Mechanisms and Alleviation Strategies for Ammonium Toxicity in Plants, with a Focus on Abiotic Stress InteractionsView all 5 articles
Transcriptional Reprogramming and Co-expression Network Underlying Enhanced Ammonium Uptake in Intraspecific Hybrids of Saccharum spontaneum
Provisionally accepted
Feiyan Zhao1
Sisi Zhang1Yinyong Li1
Ting Yang2
Zongtao Yang2Jiayong Liu2
Fenggang Zan2
Jun Deng2Jianmin Wu3
Yong Zhao1,2*Zuhu Deng1*
Xinwang Zhao1*Yuebin Zhang1,2- 1Fujian Agriculture and Forestry University, Fuzhou, China
- 2Yunnan Academy of Agricultural Sciences Yunnan Sugarcane Research Institute, Kaiyuan, China
- 3Guangxi Academy of Agricultural Sciences Sugarcane Research Institute, Nanning, China
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In sugarcane production, nitrogen utilization efficiency is generally suboptimal, averaging only 30– 40%. Saccharum spontaneum, the wild progenitor of sugarcane, harbors abundant genetic resources for high nitrogen efficiency, which remain largely untapped. Notably, the application of intraspecific hybridization in S. spontaneum for improving nitrogen efficiency in sugarcane breeding remains unexplored. Against this background, in March 2024, an initial investigation was conducted at the Sugarcane Research Institute of the Yunnan Academy of Agricultural Sciences, China, focusing on four S. spontaneum germplasm materials (YN82, GSM22, GSM12, YN2) and two intraspecific F1 hybrids (A2, B1), to explore the mechanisms underlying heterosis in nitrogen use efficiency in S. spontaneum. Physiological assays revealed that the hybrids specifically enhanced ammonium (15NH4+) uptake capacity but not nitrate uptake. Comparative transcriptomics and weighted gene co-expression network analysis (WGCNA) unveiled a systemic transcriptional reprogramming in hybrids. This reprogramming involved the coordinated downregulation of nitrate assimilation genes and the rewiring of starch/sucrose metabolism, facilitating carbon skeleton supply for energetically favorable ammonium assimilation. WGCNA identified key modules significantly correlated with ammonium uptake. From these modules, we pinpointed 14 core candidate genes constituting a multi-layered regulatory network, encompassing transcription factors (e.g., AP2/EREBP, bHLH, MYB), nitrogen assimilation enzymes (GAD), carbon metabolism providers (TPP, TPS), and root development regulators (HCT, CYP84A1). Our work deciphers how intraspecific hybridization triggers systemic optimization to improve NUE and provides novel gene resources for breeding nitrogen-efficient sugarcane.
Keywords: Nitrogen-efficient, Saccharum spontaneum, sugarcane, Transcriptome, WGCNA
Received: 03 Dec 2025; Accepted: 06 Feb 2026.
Copyright: © 2026 Zhao, Zhang, Li, Yang, Yang, Liu, Zan, Deng, Wu, Zhao, Deng, Zhao and Zhang. 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:
Yong Zhao
Zuhu Deng
Xinwang Zhao
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