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

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.

Transcriptomic Analysis of Melatonin-Mediated Salt Stress Response in Germinating Alfalfa

“…Studies have shown that melatonin can stimulate the synthesis of GSH [58]. In this study, 18 and 41 differentially expressed genes were enriched in the glutathione pathway in the NaCl and MT treatment groups, among which 16 and 27 genes were related to GST, respectively, which have been proven to play a key role in combating salt stress [59][60][61]. In the melatonin-treated group, genes related to GST were significantly upregulated, which may be because melatonin promotes the expression of GST, thereby catalyzing GSH to neutralize reactive oxygen species.…”

Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy in Wheat

“…A set of wheat germplasm comprising 97 hexaploid accessions (Triticum aestivum L.) [38], including 38 landraces and 59 modern cultivars (Table S1), was used to estimate the adaptability and the allele distribution of QTL. All the plant materials were planted in the greenhouse at Shanxi Agricultural University (Taiyuan, China) in 2022.…”