Phenotypic variation and genetic architecture of seedling salt tolerance in Xinjiang wheat revealed by GWAS and resequencing

Introduction: 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. Methods: 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. Results: 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. Discussion: 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.