Uncovering the potential MTAs, candidate genes and microRNAs regulatory networks involved in salinity stress tolerance triggered in Iranian Aegilops tauschii

This study evaluated the molecular diversity and identified marker-trait associations (MTAs), candidate genes, and microRNAs (miRNAs) regulatory networks in Iranian Aegilops tauschii ecotypes under salinity stress during the seedling stage. The results demonstrated that ISJ9 exhibited the highest values for polymorphic information content (PIC), effective number of alleles (Ne), gene diversity (h), Shannon's information index (I). Similarly, OPE03-Xgwm44-7DF displayed the highest Ne and I values. Therefore, ISJ9 and OPE03-Xgwm44-7DF markers demonstrated the greatest discriminatory power for distinguishing Aegilops tauschii ecotypes. Association analysis under salinity stress identified 115 MTAs, including iPBS44-D and OPB01-Xgwm44-7DR-3. Subsequent bioinformatics analyses revealed 254 candidate genes and 107 regulatory microRNAs associated with salinity tolerance. Several important candidate genes and their regulatory miRNAs identified in this study function significantly in salinity stress response. Gene ontology analysis determined the most significant biological processes, cellular components, and molecular functions, while pathway analysis revealed genes involved in glutathione metabolism pathways. Protein-protein interaction networks indicated that interacting genes were physically or functionally related. The identified candidate genes and miRNAs provide valuable resources for breeding programs, including marker-assisted selection (MAS) and genome editing, to develop salinity stress-tolerant wheat varieties.