Integrated transcriptomics and metabolomics analyses provide insights into salt-stress response in germination and seedling stage of wheat (Triticum aestivum L.)

Wang, Wei; Cao, Jinfeng; Huang, Sufang; Wang, Zhi; Wang, Weiwei; Zou, Jingwei; Wang, Fengzhi; Luo, Meng; Zhang, Jingjian

doi:10.1016/j.cpb.2023.100274

Cited by 6 publications

(3 citation statements)

References 60 publications

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“…Metabolomics analysis is an effective method for studying plant metabolites. In previous studies, the mechanisms underlying the responses of soybean [43], wheat [44], tomato [45] to Saline-Alkali stress have been investigated using metabolomics. In the present study, a broad-targeted metabolomics approach was employed to determine metabolites present in five stages of jujube fruit development under conditions of lowsalinity stress, high-salinity stress, and no stress.…”

Section: Discussionmentioning

confidence: 99%

Effects of Saline-Alkali Stress on Sugar Metabolism of Jujube Fruit: A Metabolomic Analysis

Wang,

Feng,

Yan

et al. 2023

Agronomy

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There have been numerous studies on the effects of salt stress on jujube fruit; however, only a few studies have reported the changes in fruit quality, particularly sugar content, under conditions of combined salt and alkali stress. Therefore, the present study aimed to investigate the performance of jujube fruits under Saline-Alkali stress and the changes in sugar content in fruits. To achieve this, jujube fruits were treated with varying concentrations of salt and alkali during five developmental periods. The content of relevant sugar components was determined, and metabolomics data were analyzed in combination with relevant quantitative gene data. The results indicated that 100 days after flowering, the surface color of jujube fruit gradually turned red, and the cell structure of the fruit gradually loosened with increasing salt and alkali concentration. The content of sugar components at each stage showed that glucose and fructose primarily accumulate in the early stage of development, while sucrose is the main component in the later stage of development. Metabolomic correlation network maps showed that six differentially accumulated metabolites were closely related to specific genes. Among these metabolites, sucrose was identified as the core metabolite in the metabolic pathway. Quantitative analysis of the related genes revealed that ZjvINV2 and ZjHK2 exhibited prolonged adaptability to stress. Additionally, the expression levels of ZjSS1 and ZjSPS2 under Saline-Alkali stress were consistent with the trend of sucrose content during the same period. In conclusion, the variations in sugar content in jujube fruits during different growth stages and under Saline-Alkali treatment conditions were recorded as reference data, and the primary metabolic substances and related regulatory genes produced in jujube fruits under Saline-Alkali stress were preliminarily identified.

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Section: Discussionmentioning

confidence: 99%

Effects of Saline-Alkali Stress on Sugar Metabolism of Jujube Fruit: A Metabolomic Analysis

Wang,

Feng,

Yan

et al. 2023

Agronomy

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“…RNA-seq can be used to analyze the mechanisms of drought, salt, and cold tolerance, and also to uncover the role of lncRNA and the identification of candidate genes [23,24,26,[28][29][30].…”

Section: Discussionmentioning

confidence: 99%

Exploring the Role of TaPLC1-2B in Heat Tolerance at Seedling and Adult Stages of Wheat through Transcriptome Analysis

Li,

Zhao,

et al. 2023

IJMS

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Heat stress is a major abiotic stress that can cause serious losses of a crop. Our previous work identified a gene involved in heat stress tolerance in wheat, TaPLC1-2B. To further investigate its mechanisms, in the present study, TaPLC1-2B RNAi-silenced transgenic wheat and the wild type were comparatively analyzed at both the seedling and adult stages, with or without heat stress, using transcriptome sequencing. A total of 15,549 differentially expressed genes (DEGs) were identified at the adult stage and 20,535 DEGs were detected at the seedling stage. After heat stress, an enrichment of pathways such as phytohormones and mitogen-activated protein kinase signaling was mainly found in the seedling stage, and pathways related to metabolism, glycerophospholipid metabolism, circadian rhythms, and ABC transporter were enriched in the adult stage. Auxin and abscisic acid were downregulated in the seedling stage and vice versa in the adult stage; and the MYB, WRKY, and no apical meristem gene families were downregulated in the seedling stage in response to heat stress and upregulated in the adult stage in response to heat stress. This study deepens our understanding of the mechanisms of TaPLC1-2B in regard to heat stress in wheat at the seedling and adult stages.

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“…193 showed that 5829 genes were differentially expressed in the roots, whereas 3495 genes were identified in the shoots, of which eight DEGs were validated [ 11 ]. Moreover, RNA-Seq data from other salt-tolerant germplasm, such as the Chinese cultivars Qingmai 6 [ 12 ], Xiaoyan 60 [ 13 ], Jimai 22 [ 14 ], and Cangmai 6005 [ 15 ], as well as Iranian cultivar Arg [ 16 ], also revealed many DEGs responding to salt stress, helping to further identify salt-tolerance genes in wheat. However, most of the previously reported RNA-Seq analyses have been based solely on DEGs and use simple qRT-PCR to validate candidate genes, which cannot uncover more useful information.…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq-Based WGCNA and Association Analysis Reveal the Key Regulatory Module and Genes Responding to Salt Stress in Wheat Roots

Chen,

Zhang,

Liu

et al. 2024

Plants

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Soil salinization is the main abiotic stressor faced by crops. An improved understanding of the transcriptional response to salt stress in roots, the organ directly exposed to a high salinity environment, can inform breeding strategies to enhance tolerance and increase crop yield. Here, RNA-sequencing was performed on the roots of salt-tolerant wheat breeding line CH7034 at 0, 1, 6, 24, and 48 h after NaCl treatment. Based on transcriptome data, a weighted gene co-expression network analysis (WGCNA) was constructed, and five gene co-expression modules were obtained, of which the blue module was correlated with the time course of salt stress at 1 and 48 h. Two GO terms containing 249 differentially expressed genes (DEGs) related to osmotic stress response and salt-stress response were enriched in the blue module. These DEGs were subsequently used for association analysis with a set of wheat germplasm resources, and the results showed that four genes, namely a Walls Are Thin 1-related gene (TaWAT), an aquaporin gene (TaAQP), a glutathione S-transfer gene (TaGST), and a zinc finger gene (TaZFP), were associated with the root salt-tolerance phenotype. Using the four candidate genes as hub genes, a co-expression network was constructed with another 20 DEGs with edge weights greater than 0.6. The network showed that TaWAT and TaAQP were mainly co-expressed with fifteen interacting DEGs 1 h after salt treatment, while TaGST and TaZFP were mainly co-expressed with five interacting DEGs 48 h after salt treatment. This study provides key modules and candidate genes for understanding the salt-stress response mechanism in wheat roots.

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Integrated transcriptomics and metabolomics analyses provide insights into salt-stress response in germination and seedling stage of wheat (Triticum aestivum L.)

Cited by 6 publications

References 60 publications

Effects of Saline-Alkali Stress on Sugar Metabolism of Jujube Fruit: A Metabolomic Analysis

Effects of Saline-Alkali Stress on Sugar Metabolism of Jujube Fruit: A Metabolomic Analysis

Exploring the Role of TaPLC1-2B in Heat Tolerance at Seedling and Adult Stages of Wheat through Transcriptome Analysis

RNA-Seq-Based WGCNA and Association Analysis Reveal the Key Regulatory Module and Genes Responding to Salt Stress in Wheat Roots

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