DURUM WHEAT GENE NETWORK ANALYSIS REVEALED MODULES AND CANDIDATE GENES CONTROLLING DEVELOPMENT AND STRESS RESPONSE

The new Platinum-quality durum wheat reference genome (Svevo Rel.2) represents an exceptional tool for studying the transcriptional landscapes of wheat development and stress responses. Gene expression data from 30 tissues at multiple developmental time points along with 28 shoot and root seedling samples subjected to abiotic or biotic stress treatments were combined for the construction of both supervised and unsupervised Gene Regulatory Networks (GRNs). Inferred GRNs were then integrated with time-course transcriptome profiling, tissue-specific gene expression, and transcription factor (TF) target predictions. This allowed us to identify TFs acting as master switches and their downstream targets for a variety of plant processes, including response to heat, nitrogen metabolism, Fusarium graminearum infection response, inflorescences and kernels development. For example, the ten inflorescence development modules include known regulators of wheat spike development (like SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes, MADS TFs and hormone signaling and metabolism-related genes), while among the nine kernel expression modules we focused on the identification of TFs regulating seed storage protein and carotenoid biosynthetic genes. Similarly, the four identified modules associated to heat stress response in roots and shoots include specific Heat Shock Protein (HSP) genes and Heat Stress Transcription Factors (HSFs), which in turn regulate the HSP genes. On the other hand, Fusarium infection modulates a large set of gene families involved in pathogen resistance, biotic and oxidative stress, and MADS, WRKY and AP2/ERF response TFs. Beyond known regulators, the identified modules include new key transcription factors acting as potential candidate regulators of the studied biological and developmental processes. The characterization and validation of the most promising ones is underway, using independent transcriptome datasets and analysing their co-localization with known (e)QTLs. Our results provide valuable insights into transcriptional changes, gene regulative networks and cross-talks that orchestrate developmental pathways, laying the groundwork to understand the biological control of complex traits and response to environmental cues. Moreover, key TFs represent new gene resources for gene-editing or molecular marker-assisted selection in breeding programs aimed at increasing yield, quality and stress resistance in both durum and bread wheat.