Marker–trait associations for physiological responses to irrigation and terminal drought stress in bread wheat using SSR and iPBS markers

As global food demand rises, ensuring wheat (Triticum aestivum L.) production under intensifying climate change is critical. Late drought stress is one of the major environmental constraints limiting wheat productivity and yield stability worldwide. This study aimed to characterize drought tolerance in bread wheat by integrating physiological traits with molecular marker analysis. A panel of 64 bread wheat genotypes was evaluated in an 8 × 8 lattice design with two replications under highly controlled irrigated and rain-shelter terminal drought stress conditions over two growing seasons. Bread wheat genotypes were evaluated over two growing seasons using simple sequence repeat (SSR) and inter-primer binding site (iPBS) retrotransposon markers. Physiological assessments included canopy temperature difference (CTD), leaf senescence rate (LSR), SPAD chlorophyll content, chlorophyll fluorescence parameters (Fo, Fm, Fv, and Fv/Fm), as well as leaf and grain ash content. Significant phenotypic variation was observed among genotypes under both irrigated and drought-stressed environments. Drought stress generally increased phenotypic and genotypic variances for most investigated traits, with coefficients of variation ranging from 0.97% to 26.85%. Moreover, elevated phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) values under drought conditions indicate enhanced genetic expression in response to water deficit. Broad-sense heritability estimates were particularly high for senescence and chlorophyll fluorescence traits and were generally greater under drought stress than under irrigated conditions, suggesting stronger genetic regulation under stress environments. Association mapping identified 25 iPBS markers and 108 SSR loci significantly associated with physiological responses to drought stress. Notably, iPBS-2376 and iPBS-2390 were associated with multiple physiological traits, whereas SSR loci such as BARC 78 and CFA 2187 exhibited strong associations with chlorophyll stability and canopy temperature regulation. The findings demonstrate that integrating physiological characterization with SSR and iPBS marker systems is an effective strategy for identifying drought-tolerant wheat genotypes and detecting genomic regions valuable for marker-assisted breeding aimed at improving drought adaptation and yield stability.