Dynamic molecular regulation of salt stress responses in maize ( <i>Zea mays</i> L.) seedlings

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Abstract

Introduction

Maize ranks among the most essential crops globally, yet its growth and yield are significantly hindered by salt stress, posing challenges to agricultural productivity. To utilize saline-alkali soils more effectively and enrich maize germplasm resources, identifying salt-tolerant genes in maize is essential.

Methods

In this study, we used a salt-tolerant maize inbred line, SPL02, and a salt-sensitive maize inbred line, Mo17. We treated both lines with 180 mmol/L sodium chloride (NaCl) for 0 days, 3 days, 6 days, and 9 days at the three-leaf growth stage (V3). Through comprehensive morphological, physiological, and transcriptomic analyses, we assessed salt stress effects and identified hub genes and pathways associated with salt tolerance.

Results

Our analysis identified 25,383 expressed genes, with substantial differences in gene expression patterns across the salt treatment stages. We found 8,971 differentially expressed genes (DEGs)—7,111 unique to SPL02 and 4,791 unique to Mo17—indicating dynamic gene expression changes under salt stress. In SPL02, the DEGs are primarily associated with the MAPK signaling pathway, phenylpropanoid biosynthesis, and hormone signaling under salt treatment conditions. In Mo17, salt stress responses are primarily mediated through the abscisic acid-activated signaling pathway and hormone response. Additionally, our weighted gene co-expression network analysis (WGCNA) pinpointed five hub genes that likely play central roles in mediating salt tolerance. These genes are associated with functions including phosphate import ATP-binding protein, glycosyltransferase, and WRKY transcription factors.

Discussion

This study offers valuable insights into the complex regulatory networks governing the maize response to salt stress and identifies five hub genes and pathways for further investigation. These findings contribute valuable knowledge for enhancing agricultural resilience and sustainability in saline-affected environments.

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Most cited references 120

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Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

Kenneth Livak, Thomas D. Schmittgen (2001)

The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).

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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Yoav Benjamini, Yosef Hochberg (1995)

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Is Open Access

The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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Author and article information

Contributors

Atikaimu Maimaiti: URI : https://loop.frontiersin.org/people/1988122Role: Role: Role: Role: Role: Role: Role:

Wei Gu: Role: Role: Role: Role: Role: Role: Role:

Diansi Yu: Role: Role: Role: Role:

Yuan Guan: Role: Role:

Jingtao Qu: Role: Role: Role: Role:

Tao Qin: Role: Role:

Hui Wang: Role: Role:

Jiaojiao Ren: Role: Role: Role: Role: Role:

Hongjian Zheng: URI : https://loop.frontiersin.org/people/2370064Role: Role: Role: Role: Role: Role: Role: Role: Role: Role: Role: Role: Role:

Penghao Wu: URI : https://loop.frontiersin.org/people/2906956Role: Role: Role: Role: Role: Role: Role: Role: Role: Role: Role:

Journal

Journal ID (nlm-ta): Front Plant Sci

Journal ID (iso-abbrev): Front Plant Sci

Journal ID (publisher-id): Front. Plant Sci.

Title: Frontiers in Plant Science

Publisher: Frontiers Media S.A.

ISSN (Electronic): 1664-462X

Publication date (Electronic): 25 February 2025

Publication date Collection: 2025

Volume: 16

Electronic Location Identifier: 1535943

Affiliations

[1] ¹ College of Agriculture, Xinjiang Agricultural University , Urumqi, China

[2] ² Crop Breeding, Cultivation Research Institution/Centro Internacional de Mejoramientode Maizy Trigo (CIMMYT)-China Specialty Maize Research Center, Shanghai Engineering Research Center of Specialty Maize, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences , Shanghai, China

Author notes

Edited by: Muhammad Waseem, Hainan University, China

Reviewed by: Anket Sharma, Texas Tech University, United States

Elsayed Nishawy, Desert Research Center, Egypt

*Correspondence: Penghao Wu, wupenghao@ 123456xjau.edu.cn ; Hongjian Zheng, hjzh6188@ 123456163.com ; Wei Gu, guwei@ 123456saas.sh.cn

†These authors have contributed equally to this work

Article

DOI: 10.3389/fpls.2025.1535943

PMC ID: 11893837

PubMed ID: 40070712

SO-VID: f123f7a3-19d7-45cc-9733-43681e6ef87e

License:

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) and the copyright owner(s) 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.

History

Date received : 28 November 2024

Date accepted : 31 January 2025

Page count

Figures: 11, Tables: 2, Equations: 2, References: 120, Pages: 19, Words: 9438

Funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the National Natural Science Foundation of China (grant numbers: 32172033, 32060484, U2003304, and 32001561), STI2030-Major Projects (grant number: 2023ZD0403004-02), National Agricultural Science and Technology Major Projects (grant number: NK202307040404), Tianshan Yingcai (grant number: 2022TSYCJU0003), Xinjiang Uygur Autonomous Region Natural Science Foundation key project (grant number: 2022D01D34), Xinjiang Uygur Autonomous Region Major Science and Technology Special Projects (grant number: 2022A02003-4), Xinjiang Agriculture Research System (grant number: XJARS-02), and Tianshan innovation team funding (grant number: 2022D14017).

Custom metadata

section-in-acceptance Plant Abiotic Stress

ScienceOpen disciplines: Plant science & Botany

Keywords: maize,salt stress,transcriptome analysis,degs,wgcna

Data availability:

ScienceOpen disciplines: Plant science & Botany

Keywords: maize, salt stress, transcriptome analysis, degs, wgcna

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Dynamic molecular regulation of salt stress responses in maize ( Zea mays L.) seedlings

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Abstract

Introduction

Methods

Results

Discussion

Related collections

Plant MYBs

Most cited references 120

Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

The Sequence Alignment/Map format and SAMtools

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