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 .