Molecular insights into salinity tolerance in Thymus daenensis: Scot and ISSR marker discovery in polycross-derived genotypes

Thymus daenensis is a valuable medicinal plant known for its potent therapeutic properties. This study aimed to identify genetic loci (markers) associated with important morpho-physiological traits under both non-stress (control) and saline conditions, with the goal of detecting stable marker–trait associations in a diverse panel of polycross-derived T. daenensis genotypes. Association analysis was conducted using 111 SCoT and 121 ISSR markers under both the general linear model (GLM) and mixed linear model (MLM). Population structure analysis classified the genotypes into three distinct subpopulations, which did not correspond to their geographical origins. Under non-stress conditions, 42 significant marker–trait associations were identified through the GLM (18 SCoT and 24 ISSR), while the MLM detected 11 associations (five SCoT and six ISSR). Under salinity stress, the GLM revealed 44 significant associations (18 SCoT and 26 ISSR), and the MLM detected 16 associations (six SCoT and ten ISSR). Among these, several markers—particularly SC36 and UBC835—consistently demonstrated strong associations with traits across environments and models, underscoring their potential value for marker–assisted selection (MAS) and trait-targeted breeding. These findings enhance our understanding of the genetic mechanisms underlying salinity tolerance in T. daenensis and offer valuable molecular markers for the development of salt-tolerant cultivars.