Computational Molecular Biology 2024, Vol.14, No.5, 191-201 http://bioscipublisher.com/index.php/cmb 197 6.3 Comparative analysis of PPI networks in different rice varieties under drought stress Comparative proteomic studies have revealed significant differences in the PPI networks of various rice genotypes under the conditions of drought stress. A study on eight diverse rice genotypes demonstrated that while some proteins were commonly induced in response to drought stress, others were unique to specific genotypes, indicating diversity in metabolic responses (Hamzelou et al., 2020). In another study, a network-based computational approach was employed to analyze seven drought-tolerant rice genotypes, with the objective of identifying co-expressed gene modules and potential candidate genes related to drought resistance. This study emphasised the pivotal function of the ABA signaling pathway and the distinct regulation of jasmonic acid (JA) phytohormones, within the PPI networks of different genotypes (Sircar and Parekh, 2018). The integration of these findings facilitates a more nuanced comprehension of the intricate dynamics of PPI networks in rice under drought stress. This, in turn, can inform the development of more effective breeding strategies and genetic engineering approaches to enhance drought tolerance in rice. 7 Application of PPI Network Analysis 7.1 Potential targets for genetic engineering and breeding for drought tolerance PPI networks offer a comprehensive insight into the molecular mechanisms that underpin drought tolerance in rice. By identifying key proteins and their interactions, researchers can pinpoint potential targets for genetic engineering and breeding programs aimed at enhancing drought tolerance. ABA is a premier signal for rice to response to drought, which triggers a variety of physiological processes such as stomatal closure, root system modulation, post-transcriptional gene expression, and metabolic alterations. Under drought stress, recent studies also have highlighted the ABA levels rise and restrict the activity of PP2C (protein phosphatase 2C) by binding the respective promotor Pyrabactin resistance (PYR)/PYR-like (PYL)/ regulatory components of ABA receptors (RCARs) and triggering the activity of SnRK2 (sucrose non-fermenting 1-related protein kinase 2), thus promoting the ABA dependent physiological and molecular response (Dong et al., 2015; Chen et al., 2020). So, the ABA receptors (OsPYL9) have demonstrated potential for improving drought tolerance and grain yield when edited using CRISPR/Cas9 technology (Usman et al., 2020). Furthermore, proteins involved in cell defense, bioenergy, and metabolism, such as malate dehydrogenase and succinyl-CoA, have been identified as pivotal for drought adaptation (Agrawal et al., 2016). These findings indicate that ABA and these proteins are crucial to plant's survive under drought, the CRISPR/Cas9 editing tools also open the new era and extend the research to enhance the yield potential and develop new stress tolerant genotypes. 7.2 Integration of PPI network analysis with other omics data The integration PPI network analysis with genomics and metabolomics omics data, can facilitate a more comprehensive understanding of the drought response in rice. Because the integration PPI data with gene co-expression networks and mitogen-activated protein kinase (MAPK) signaling pathway, calcium signaling pathway can offer a systems-level perspective of intricate drought-responsive processes (Sircar and Parekh, 2018; Aslam et al., 2022). Whole-genome mining and meta-QTL analysis have identified a multitude of candidate genes and molecular markers associated with drought tolerance.These can be further validated and prioritized using PPI networks (Yang et al., 2020; Selamat and Nadarajah, 2021). Proteomic approaches have also revealed significant alterations in protein abundance and post-translational modifications (PTMs) in reponse to drought stress (Liu et al., 2019), providing additional insights that can be integrated with PPI data to identify key regulatory proteins and pathways. This integrative approach can facilitate a deeper comprehension of the molecular mechanisms underlying drought tolerance, thereby enabling the advancement of more resilient rice varieties. 7.3 Implications for sustainable agriculture and water management The insights gained from PPI network analysis and its integration with other omics data have significant implications for sustainable agriculture and water management. The identification and engineering of drought-tolerant rice varieties will facilitate a reduction in the reliance on water-intensive agricultural practices and an improvement in crop yields under water-limited conditions. The development of drought-tolerant rice varieties can contribute to the implementation of more sustainable agricultural practices, as it will result in a reduction of water usage and an increase in the resilience of crops to environmental stressors (Jogaiah et al., 2013).
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