From germplasm to genomics: integrated breeding and omics approaches for enhancing rice root knot nematode resistance in Direct-Seeded Rice systems.

Rice (Oryza sativa L.) is a major cereal crop critical for global food security, particularly in Asia, where it is predominantly cultivated. Although conventional puddled transplanting is widely practiced, it is resource-intensive and presents challenges for sustainable production. As a result, Direct-Seeded Rice (DSR) systems are gaining popularity due to their lower water and labour requirements. However, DSR faces significant agronomic challenges, particularly heavy weed infestations and severe damage from the Rice Root Knot Nematode (RRKN). In DSR, the absence of flooded conditions creates a favourable environment for RRKN proliferation and leads to substantial yield losses. RRKN is a major threat to rice production, necessitating the development of effective management strategies to mitigate its agronomic and economic impact. This review focuses on advanced breeding methodologies aimed at enhancing RRKN resistance in rice. It examines molecular host-pathogen interactions, the identification and molecular characterisation of resistant accessions or Quantitative trait loci (QTLs), and the application of marker-assisted selection. To date, several QTLs have been identified for RRKN resistance, and the MG1 gene has been successfully cloned. Furthermore, the integration of multi-omics technologies, including transcriptomics, metabolomics, proteomics, phenomics, and genome editing with traditional breeding approaches, is discussed. These integrated strategies not only accelerate the development of RRKN-resistant rice cultivars but also pave the way for deploying resilient genotypes across diverse agroecologies, thereby reinforcing food and livelihood security.