Unravelling Updates in Deciphering Plant Defence Mechanisms with Insights from Functional Genomics and Proteomics

Abstract

Functional genomics and proteomics have revolutionized plant defence studies by providing insights into the molecular mechanisms underlying immunity against pathogens. Functional genomics approaches, including genome-wide association studies (GWAS), RNA sequencing (RNA-Seq), and CRISPR/Cas9 genome editing, have identified key resistance (R) genes, susceptibility (S) genes, and transcriptional networks regulating plant defence responses. Proteomics complements genomics by revealing protein-protein interactions, post-translational modifications, and dynamic changes in protein abundance during pathogen attacks. The integration of these approaches has facilitated the development of disease-resistant crop varieties through marker-assisted selection (MAS), transgenic technologies, and biotechnology-based interventions. Despite significant advancements, challenges persist in data integration, the complexity of plant genomes, and the dynamic nature of proteomic responses. Computational tools, artificial intelligence, and systems biology approaches are being employed to address these limitations, enabling precise gene function annotation and predictive modelling of plant immune responses. Additionally, advances in mass spectrometry-based proteomics, single-cell transcriptomics, and data-independent acquisition (DIA) techniques are enhancing our ability to capture molecular changes associated with plant-pathogen interactions. These technological advancements are crucial for improving crop resilience against biotic stressors, contributing to global food security. The future of functional genomics and proteomics in plant defence lies in multi-omics integration, precision agriculture, and gene editing technologies that enable the development of climate-resilient, high-yielding crops with durable resistance. Collaboration among researchers, breeders, and computational biologists will be essential to translate these findings into practical agricultural applications. As we move towards a more data-driven and system-level understanding of plant immunity, functional genomics and proteomics will continue to be indispensable tools in sustainable agriculture, helping to mitigate the impacts of emerging pathogens and environmental stressors on global crop production.