Introduction
Association mapping is a widely utilized approach in crop science for identifying loci associated with quantitative traits. Among antibiotic stresses, salinity stress poses a significant challenge to global wheat production, severely impacting yield, particularly during sensitive developmental stages such as germination.  Exposure to salt stress can inhibit plant growth at various stages and, in extreme cases, result in complete crop loss. Consequently, the development and identification of salt-tolerant wheat cultivars is a critical strategy for mitigating the adverse effects of salinity and sustaining agricultural productivity.
Materials and Methods
This study evaluated 64 bread wheat (Triticum aestivum L.) cultivars under three growth conditions: control (normal), 60 mM NaCl, and 120 mM NaCl, to simulate increasing levels of salt stress. Experiments were conducted during the 2021 cropping season using a simple lattice design with two replications at the Genetics Laboratory, Faculty of Agriculture, Urmia University. Salinity treatments were administered using sodium chloride (NaCl). A comprehensive set of germination and early seedling traits were assessed, including seedling length, shoot length, root length, shoot-to-root length ratio, seedling fresh weight, seedling dry weight, germination percentage, germination index, germination speed, mean germination speed, mean germination time, germination energy, seed vigor, relative germination index, relative germination speed, and relative germination energy. Genome-wide association was performed using 36361 single nucleotide polymorphism (SNP) markers to identify genetic loci associated with these germination-related traits. Association analyses were conducted with TASSEL 5.0 software, employing a mixed linear model (MLM) method that incorporated principal component analysis (PCA) and Kinship matrices to control for population structure and relatedness. Manhattan plots and linkage disequilibrium (LD) plots were produced using R studio version 4.1.1 to visualize significant marker-trait associations and the underlying genomic architecture.
Results and Discussion
In this study, a total of 330, 153, and 116 marker-trait associations (MTAs) were identified under normal, 60 mM salinity stress, and 120 mM salinity stress conditions, respectively. Under normal conditions, 43 significant markers associated with germination indices were predominantly located on chromosomes 1B and 7B. Under 60 mM salinity stress 32 key markers were mapped to chromosomes 1B, 2B, 6A, 5A and 6B, while under 120 mM salinity stress, 14 important markers were identified on chromosomes 1B, 3A and 3B, all linked to control of germination-related traits. All significant marker sequences were analyzed using the Ensembl Plants Database, revealing that MTAs are involved in key biological and molecular processes, including signal transduction, kinase signaling pathways, defense responses, and response to biotic stimuli, hydrolase metabolism, and polysaccharide binding. Notably, in the 60 mM salinity stress condition, pathways related to proline, arginine, and beta-alanine metabolism were implicated. Under 120 mM salinity stress, the ABC transporter pathway emerged as particularly relevant.
Conclusion
The MTAs and metabolic pathways identified in this study provide valuable genetic resources for improving salinity tolerance I bread wheat. Following validation in biparental populations and further functional assays, these findings can be leveraged in marker-assisted selection and breeding programs aimed at enhancing wheat germination and early growth under saline conditions.