Stable genetic loci orchestrate redox networks and grain traits in polyploid wheat (Triticum aestivum L.) under combined salinity and drought stress.

Combined drought and secondary salinization threaten wheat production in arid and semi-arid regions. While trans- and inter-generational patterns of enhanced tolerance have been reported, their genomic underpinnings remain unclear. Here, we combined multi-environment phenotyping across three successive generations with high-density (90K) single nucleotide polymorphism (SNP) genotyping of 111 bread wheat accessions to map loci associated with performance under recurrent drought–salinity. Multi-trait, multi-generation genome-wide association analyses identified five genomic regions on chromosomes 1B, 2A, 2B, 6B, and 7A that were repeatedly associated with grain-yield stability, antioxidant capacity, and water-use efficiency. Gene annotations within these regions highlight plausible mechanisms including flavonoid-directed reactive oxygen species (ROS) scavenging, organellar RNA processing, proteostasis and hormone signaling, sucrose partitioning, and Ca2⁺-linked signaling, which transmit rapid stress signals to the cell cycle. Nevertheless, the repeatedly detected regions and their lead SNPs provide practical markers for breeding (e.g., KASP assays) and entry points for functional validation. Future work should fine-map these intervals and test causative roles through near-isogenic lines, genome editing, expression and metabolite profiling, and transgenerational designs.