The devastating yield losses caused by rice blast can be mitigated by breeding resistant cultivars with QTLs enriched with resistance (R-gene) and defence related genes. These genes are the arsenal of the plant’s immune system against pathogen invasion. qBFR4 and qLBL5, are two stable QTLs known to contribute moderate level of resistance against blast disease. In this study we aim to characterize and understand the interconnectivity between the genes within these QTLs by producing a defence model based on the interplay of defence and resistance genes found within these QTLs. To achieve this end we identified defence and R-genes in qBFR4 and qLBL5 into functional groups and classes of R-genes, and classified their roles in mounting a defence against pathogens. Blast2GO analysis retrieved the description, gene ontology annotations and domains for 361 genes in qBFR4 and 617 genes in qLBL5. With this, it is concluded that qBFR4 (2.38 Mbps) has 27 R-genes (7.33%) and 14 (0.04%) defence- genes whereas qLBL5 (4.1 Mbps) has 25 R-genes (3.88%) and 17 defence genes (0.03%). R-genes and defence genes were classified into domains and functional groups respectively and directed acyclic graphs (DAG) were constructed for both QTLs explaining the role of these QTLs in quantitative resistance against rice blast. In conclusion, qBRF4 is was found to be more beneficial than qLBL5 based on the defence and resistance gene composition where SA/JA mediated signalling plays a crucial role in signal tranduction between R genes and the defence system. Apart from QTL pyramiding using the QTLs in this study, the major R-genes found within these QTLs can be subjected to cloning to develop resistant cultivars.