Genome-wide Mapping of Inherited Resilience Reveals Genetic Loci for Combined Salinity-Waterlogging Tolerance in Barley.

Combined salinity and waterlogging severely constrain barley productivity, yet the genetic basis of inherited resilience to this stress combination remains poorly understood. Here, we investigated intergenerational and transgenerational stress memory in a barley diversity panel of 138 genotypes evaluated across three successive generations under four treatment-history groups (C→C, C→S, S→C, and S→S). Morphophysiological, ionic, biochemical, and recovery-related traits were measured, and stress-memory indices were derived from first-stage accession best linear unbiased estimates (BLUEs) to avoid unnecessary shrinkage before GWAS. Primary stress exposure caused strong reductions in growth, water status, chlorophyll retention, and photosynthetic efficiency, together with increased Na+ accumulation, membrane injury, and oxidative damage. In contrast, progeny derived from stressed lineages and re-exposed to stress showed improved biomass, relative water content, SPAD, Fv/Fm, and K+/Na+ ratio, accompanied by reduced Na+, electrolyte leakage, malondialdehyde and H2O2. Stress-memory indices confirmed intergenerational and cumulative repeated-stress gains, with low mean carryover penalties under non-stress conditions. Correlation analysis resolved a tolerance module associated with growth, photosynthetic stability, and ion homeostasis, and a damage module associated with Na+ accumulation, oxidative stress, and membrane leakage. Genome-wide association analysis using 19 K genotyping-by-sequencing SNPs identified 128 candidate marker-trait associations at the exploratory threshold of -log10(P) ≥ 4. The strongest candidate signals were detected for transgenerational memory gain and intergenerational memory, particularly for Fv/Fm, proline, K+, and K+/Na+. Haplotype and linkage disequilibrium visualization supported the major candidate loci and their local haplotype structure. Candidate genes implicated calcium signalling, redox regulation, transcriptional control and ion transport as key components of stress-memory regulation. These findings indicate that combined salinity-waterlogging stress memory in barley is an inherited and genetically complex response; however, formal broad- or narrow-sense heritability was not estimated in the present study.