Bioinformatics approaches for deciphering molecular mechanisms of plant stress responses

Abiotic stresses are among the most important factors limiting plant growth and production worldwide. Plant responses to stresses such as salinity, drought, temperature, and metal toxicity involve a complex network of interactions and molecular, biochemical, and physiological changes. In this regard, advances in genomics, proteomics, and bioinformatics tools have enabled a comprehensive study of the molecular mechanisms of stress tolerance. In general, analyses based on gene networks, biological pathways, and molecular responses play an important role in understanding the complex mechanisms of plant adaptation to environmental stresses. Also, modern bioinformatics approaches using genomic data, especially data from RNA-sequencing, have enabled the identification of differentially expressed genes, key regulatory genes, and expression patterns related to stress tolerance. In addition, gene regulatory network analysis provides a deeper insight into how plant defense responses are regulated by identifying the interrelationships between transcription factors, target genes, and signaling pathways. On the other hand, studying miRNA–mRNA interactions, as one of the most important layers of post-transcriptional regulation, allows the identification of small regulatory molecules affecting processes such as growth regulation, oxidative balance, hormonal pathways, and stress resistance. Overall, the integration of these analyses can help identify candidate genes, key metabolic pathways, and molecular networks related to stress tolerance, paving the way for the development of genetic engineering strategies and breeding resistant plants.