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Chen J, Zhang L, Liu Y, Shen X, Guo Y, Ma X, Zhang X, Li X, Cheng T, Wen H, Qiao L, Chang Z. RNA-Seq-Based WGCNA and Association Analysis Reveal the Key Regulatory Module and Genes Responding to Salt Stress in Wheat Roots. PLANTS (BASEL, SWITZERLAND) 2024; 13:274. [PMID: 38256827 PMCID: PMC10818790 DOI: 10.3390/plants13020274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
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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Affiliation(s)
- Jiating Chen
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Lei Zhang
- Department of Biology, Taiyuan Normal University, Taiyuan 030031, China;
| | - Yingxi Liu
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Xinyao Shen
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Yujing Guo
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Xiaofei Ma
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Xiaojun Zhang
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Xin Li
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Tianling Cheng
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Huiqin Wen
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Linyi Qiao
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
| | - Zhijian Chang
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (J.C.); (X.Z.); (X.L.); (T.C.); (H.W.)
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