Salt stress severely constrains wheat growth and yield by inducing osmotic imbalance, ion toxicity, and excessive accumulation of reactive oxygen species (ROS). Although salt-tolerant cultivars can adapt through rapid signaling transduction and maintenance of cellular homeostasis, the underlying dynamic regulatory networks remain insufficiently characterized. In this study, we reanalyzed publicly available time-series RNA-seq data (0, 1, 3, 6, 12, and 24 h) from the salt-tolerant wheat cultivar Xiaoyan22 under salt stress and constructed a time-series-based co-expression network using weighted gene co-expression network analysis (WGCNA). Multiple gene modules were identified, among which the black module showed significant positive correlations with both salt treatment (treatment_bin) and stress duration (time_h). This module displayed a progressively increasing eigengene expression pattern throughout the stress period. Gene significance (GS) was positively correlated with module membership (MM), facilitating the identification of highly connected hub genes within this module. Functional enrichment analysis indicated that genes in the black module were primarily associated with DNA replication and genome stability maintenance, RNA metabolic regulation, phenylpropanoid metabolism, and cuticle/suberin/wax biosynthesis. Physiological analysis further revealed enhanced activities of superoxide (SOD), peroxide (POD), and catalase (CAT), enhanced accumulation of proline and soluble sugars, and a time-dependent increase in MDA under salt stress. qRT-PCR confirmed significant induction of candidate genes, including a ZAR1-like receptor kinase, Remorin, and NETWORKED 1D. Collectively, these findings integrate co-expression network inference with physiological and molecular validation, providing candidate regulators and pathways for understanding salt tolerance and supporting future molecular breeding efforts.

Salt stress is a major constraint on wheat production, particularly in arid and semi-arid regions such as Xinjiang, China. Understanding the phenotypic variation and genetic basis of salt tolerance at the seedling stage is essential for improving wheat breeding efficiency. A total of 134 wheat accessions from Xinjiang were evaluated under control (0 mM Na₂SO₄) and salt stress (120 mM Na₂SO₄) conditions. Seedling traits including plant height (PH), root length (RL), and germination rate (GR) were measured. Salt tolerance indices (STIs) were calculated to quantify stress responses. Genome-wide association studies (GWAS) were performed using resequencing-derived SNP data and linear mixed models (LMMs). Transcriptome data from salt-tolerant and salt-sensitive genotypes were integrated to prioritize candidate genes. Significant phenotypic variation was observed among accessions under salt stress. GWAS identified multiple SNPs significantly associated with salt tolerance traits, which were clustered into 18 robust QTL intervals, including major hotspots on chromosomes 2A and 2B. Transcriptome analysis further supported the identification of candidate genes showing differential expression between tolerant and sensitive genotypes. The integration of GWAS and transcriptomic data provided a more comprehensive understanding of the genetic architecture underlying seedling-stage salt tolerance in wheat. The identified QTLs and candidate genes offer valuable resources for functional validation and molecular breeding of salt-tolerant wheat varieties.

Introduction: Salt stress is a major constraint on wheat growth and productivity, necessitating efficient methods for identifying salt-tolerant germplasm. Methods: In this study, 120 wheat varieties were evaluated at the seedling stage under four NaCl concentrations (0, 50, 100, and 150 mM). Key traits, including plant height, root length, germination rate, and salt tolerance index (STI), were measured across two independent replicates. Statistical analyses, including ANOVA, correlation analysis, principal component analysis (PCA), hierarchical clustering, and TOPSIS, were applied to assess phenotypic variation and rank salt tolerance. Representative tolerant and sensitive varieties were further validated through physiological and molecular analyses. Results: Increasing salinity significantly inhibited growth and germination, with the greatest variation observed at 100–150 mM NaCl. Salt concentration, genotype, and their interaction significantly affected all traits. STI showed strong positive correlations with growth traits. Multivariate analyses revealed stable phenotypic groupings and identified tolerant and sensitive varieties. Physiological and molecular validation demonstrated that tolerant varieties maintained better ion homeostasis, higher antioxidant activity, lower membrane damage, and favorable K⁺/Na⁺ ratios under salt stress. Discussion: This study establishes an integrated framework combining multi-gradient phenotyping, statistical analysis, comprehensive ranking, and mechanistic validation. The approach provides a reliable and scalable strategy for identifying salt-tolerant wheat germplasm and supports future genetic research and breeding programs.