The basal expressions of immune genes in Nipponbare differs from which in Hui1586
As the mock samples of Nipponbare and Hui1586 were clearly separated from each other in the PCA analysis (Fig. 2A), we questioned what genes were differently expressed at the basal level in Hui1586 compared with Nipponbare. There were 5328, 4508, 4215 and 3952 DEGs at 12, 24, 36 and 48 h between the two cultivars with mock treatment (Fig. 3A and Supplemental dataset 2). A Venn diagram analysis identified 1331 overlapped DEGs at all four time points (Fig. 3B and Supplemental dataset 3), indicating that these genes were steadily differentially expressed in the two cultivars. We then functionally analyzed the 1331 DEGs with their Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment to understand the biological relevance underlying these genes. Interestingly, only two pathway terms, “Plant-pathogen interaction” and “Fatty acid elongation”, were significantly enriched in the KEGG pathway analysis (Fig. 3C). Consistently, only defense related GO terms, “defense response”, “response to stress”, “response to stimulus”, “hormone biosynthetic process” and “signal transduction”, were significantly enriched in the GO analysis (Fig. 3D). These results illustrated that defense related genes were differently regulated in the two cultivars, which might be the main driving force for the differential expression of other genes.
The plant immune system mainly relies on receptor-like kinases (RLKs) and NLR receptors to detect pathogen-related molecules and activate defense responses (Cui et al., 2015; Tang et al., 2017; W. Wang et al., 2020). The RLK and NLR receptor genes account for ~1% of the rice genes (Vij, Giri, Dansana, Kapoor, & Tyagi, 2008; T. Zhou et al., 2004). Remarkably, nearly 2.3% and 4.4% of 1331 DEGs encoded RLK and NLR receptors (Fig. 3E and Supplemental dataset 3), respectively, indicating that two types of receptor genes were highly enriched in the 1331 DEGs. Together, these results suggest that the basal expression of many immune receptor genes and defense-related genes are differentially regulated in Nipponbare and Hui1586, which might be one factor contributing their resistant spectrum to M. oryzae .