Comparative gene network analysis reveals drought resistance mechanisms in Aegilops tauschii genotypes

Wheat (Triticum aestivum) production faces growing threats from drought caused by climate change, which endangers global food security. Aegilops tauschii, the diploid ancestor of bread wheat, holds vital genetic resources for drought resistance. To decode the molecular basis of this resilience, we employed an integrated systems biology approach to analyze RNA-Seq data from drought-tolerant (XJ098) and drought-sensitive (XJ002) Aegilops tauschii genotypes. Differentially expressed genes (DEGs) under drought conditions were utilized to reconstruct genotype-specific protein-protein interaction (PPI) networks, facilitating the identification of central hub genes, functional modules, and cis-regulatory promoter motifs. Our network topology analysis revealed that XJ098 has a highly cohesive, modular network optimized for rapid stress signaling, in contrast to the decentralized, less cohesive network observed in XJ002. In XJ098, identified hub genes were significantly upregulated in coordinated pathways governing abscisic acid (ABA) signaling, cell wall remodeling (via expansins), osmotic adjustment (via aquaporins), and mitochondrial energy metabolism. Conversely, homologous hubs in XJ002 exhibited reduced connectivity and downregulation. Promoter analysis in XJ098 highlighted a significant enrichment of drought-responsive cis-regulatory elements, including ABRE, DREB, NAC, and MYB motifs, enabling a robust transcriptional response that was less pronounced in XJ002. Functional clustering indicated that XJ098 effectively coordinates these biological modules to enhance the biosynthesis of secondary metabolites, such as flavonoids, thereby fortifying antioxidant defenses and cellular integrity during water deficit. In summary, this research deciphers the complex regulatory networks governing drought tolerance in A. tauschii. The characterized hub genes and promoter motifs provide promising targets for functional validation and precision breeding, laying a crucial groundwork for developing climate-resilient wheat varieties.