Divergent response associates with the differential amplitudes of immunity against Magnaporthe oryzae by different blast resistance genes

Rice blast disease, caused by <i>Magnaporthe oryzae</i>, poses the most devastating threat to global rice production. The products of most blast resistance (<i>R</i>) genes specifically recognize corresponding a virulence effectors from the pathogen, thereby mediating robust immune responses that are crucial for disease resistance. However, it is unclear why different <i>R</i> genes endow with differential amplitudes of immunity against <i>M</i>. <i>oryzae</i>. Here, we demonstrated that different blast <i>R</i> genes confer differential amplitudes of immunity against <i>M</i>. <i>oryzae</i>, presumably due to divergent reprogramming of transcriptional responses. We detected that three rice restorer lines exhibited differential amplitudes of immune responses, despite all lines displaying resistance to <i>M</i>. <i>oryzae</i>. Consistently, different accessions carrying different single <i>R</i> genes exhibited remarkable differentially expressed genes (DEGs) count, indicating different transcriptional re-programming that leads to different fitness cost. Comparative analysis revealed varying degrees of overlap among DEGs across different accessions. By integrating RNA-seq and RT-qPCR data, we recommended some marker genes that distinguish the differential amplitude of immunity against <i>M</i>. <i>oryzae</i> mediated by different blast <i>R</i> genes. Thus, our study provides valuable insights into the specific and overlapping roles of <i>R</i> gene-mediated immunity. We also propose marker genes that can be used to effectively evaluate the amplitude of immune responses to <i>M</i>. <i>oryzae</i>, thereby facilitating the assessment of <i>R</i> genes with relatively lower amplitude of immunity in order to minimize fitness cost.