Comparative Transcriptomics Reveals Epigenetic and Transcriptional Regulatory Genes Associated with Drought Stress Memory in Winter Wheat.

Wheat is a staple crop vital to global food security, yet its productivity is increasingly threatened by drought stress. The extent to which contrasting wheat genotypes exhibit stress memory, and how this influences morpho-physiological adjustments during repeated drought exposures, remains unclear. Through integrated analyses of morpho-physiological responses, gene expression patterns, and key regulatory pathways, we examined intergenerational and transgenerational drought memory in drought-tolerant "Intro" and drought-sensitive "Sonalika". Under repeated stress, seedlings of both genotypes with drought history showed enhanced resilience. Transcriptome profiling identified drought memory genes exhibiting consistent differential expression between initial and repeated stress exposures in seeds and leaves. Gene ontology analysis revealed enrichment of "Intro" seed memory genes in transcripts linked to H3K36me3, while its leaf memory genes were enriched in pathways related to ABA signaling, osmoprotectant accumulation, protein synthesis, and antioxidant activity. By contrast, "Sonalika" showed enrichment of seed transcripts associated with H3K9ac and H3K14ac, and leaf memory genes linked to transcriptional activity, proteostasis, and immune-related pathways. The functional drought memory exhibited by "Sonalika", despite the absence of transcripts associated with canonical methylation-based chromatin marks, suggests alternative regulatory strategies. Together, these results indicate that wheat seedlings exhibit genotype-specific drought stress memory involving distinct transcriptional programs and putative epigenetic regulators. Although histone modifications were not directly assessed, the enrichment of histone-related genes suggests their potential involvement in mediating these responses. Direct chromatin-level analyses will be required to validate these mechanisms and support future efforts to enhance drought resilience through targeted breeding.