Molecular cloning and functional analysis of Pi65
In our previous work, Pi65(t) was mapped between InDel-1 and SNP-4 on the short arm of chromosome 11 (Zheng et al. 2016); within this interval, Os11g0694500, Os11g0694600, Os11g0694850 and Os11g0695000 were found to contain LRR domains. For Os11g0694500 and Os11g0695000, no sequence difference was observed between the parents. Moreover, these two putative genes showed no difference in expression in GY129 and LX1 and could thus be excluded as candidates for Pi65. In contrast, the other two candidate genes, Os11g0694600 and Os11g0694850, showed sequence polymorphisms between the two parents. Therefore, Os11g0694600-R and Os11g0694850-R were subjected to further functional analysis.
Using a CRISPR/Cas9 gene mutation strategy, we designed two gene-specific sgRNAs to target Os11g0694600-R and Os11g0694850-R (Figs. 1a and S1a). Agrobacterium-mediated transformation was used to generate 12 and 4 T0 transgenic lines with the knockout of Os11g0694600-R or Os11g0694850-R, respectively. Six editing types of Os11g0694600-R (KO-B 1–6) (Fig. 1b) and two editing types of Os11g0694850-R (KO-C 1–2) were obtained (Fig. S1). Homozygous mutants for these two genes in generation T1 were selected for inoculation identification.
Then, we performed rice blast inoculation, and the results showed that in the GY129 background, when Os11g0694850-R was knocked out, the mutants were still resistant to the M. oryzae isolate of QY-13 (Fig. 1b). However, when Os11g0694600-R was knocked out, the mutants became susceptible to QY-13. A comparison of the lesion areas of GY129 and Pi65KO after inoculation showed that the lesion area of GY129 was significantly smaller than that of Pi65KO (Fig. 1b). To further determine the function of Os11g0694600-R, we generated an Os11g0694600-R overexpression vector and transformed it into the susceptible rice variety LX1 and transgenic lines were obtained. The rice blast inoculation results indicated that the transgenic lines were all resistant to QY-13 (Fig. 1c). The above results suggested that Os11g0694600-R was the rice blast resistance gene Pi65.
Sequence structure of Pi65
The full-length cDNA of Pi65 had a single ORF of 3309 bp, containing 2 introns with lengths of 2923 bp and 386 bp, encoding 1102 amino acids. The deduced protein of Pi65 had 15 LRR domains and one serine/threonine protein kinase domain (Fig. 2a and b). The structural annotation results showed that the Pi65 R allele (Os11g0694600-R in GY129) had one more LRR domain than the Pi65 S allele (Os11g0694600-S in LX1) at sites 543–569. This LRR domain difference was due to the nonsynonymous changes caused by the 16 SNPs between Os11g0694600-R and Os11g0694600-S (Fig. 2b). To further detect the potential structural differences between Os11g0694600-R and Os11g0694600-S, we performed protein structure prediction, and the results revealed that clear structural variation in the 420–580 aa region between the S-allele and R-allele of the Pi65 gene (Fig. 2c), implying that the R-allele in this region is essential for the rice blast resistance function of the gene.
Intracellular localization of the Pi65 protein
To investigate the intracellular localization of Pi65, we introduced a green fluorescent protein (GFP) construct fused to the coding sequence of Pi65 into rice yellow tissue protoplast cells and examined its intracellular localization using confocal laser scanning microscopy. The GFP-Pi65 fusion protein was also localized to the nucleus and the plasma membrane (Fig. 3a-d and e-h). When GFP was expressed alone, it localized to the nucleus and the plasma membrane (Fig. 3i-l and m-p). In the subcellular localization analysis, the Pi65 proteins colocalized with a nucleus-specific marker and membrane-specific marker.
Comparative analysis of Pi65 andPigenes
A phylogenetic tree based on sequence similarity was constructed to analyze the structural relationship between Pi65 and other cloned rice R genes. The comparative analysis of Pi65 with 24 rice blast resistance genes revealed that Pi65 appeared to be most closely related to Pid2, indicating high homology (orthologous nature) and a close evolutionary relationship (Fig. S1b). Pi65 was not closely related to other Pi genes, suggesting little or no evolutionary correlation between them.
Distribution of the Pi65 gene in different rice varieties
A previous study indicated that temperate japonica is the most rice blast disease-susceptible rice subpopulation. The analysis of Pi65 alleles and their distribution will help breeders make better use of this rice blast resistance gene. We collected 38 japonica rice varieties from 7 regions of China, including Beijing, Xinjiang, Ningxia, Henan, Heilongjiang, Jilin and Liaoning (Fig. S2, Table S3). Through sequence analysis, we identified three haplotypes of Pi65, Hap1 (GY129, etc.), Hap2 (LX1, etc.) and Hap3 (JingDao2, abbreviated JD2, etc., O. sativa japonica) (Table S4). Hap1 and Hap3 were functional haplotypes (resistant) according to the spray inoculation results. Hap1 was present in 16 varieties that came from Liaoning, Heilongjiang, Henan and Ningxia. Compared with Hap1, Hap3 had a G/A SNP at position 3300, leading to a missense mutation. In addition, 16 SNPs led to missense mutation differences between Hap2 and Hap1, and most rice cultivars carrying Hap2 were susceptible to QY-13, indicating that the SNPs in Hap2 abolished the rice blast resistance function of Pi65.
Spatiotemporal expression profile and constitutive expression of Pi65
To investigate Pi65 expression patterns, we detected the expression of Pi65 in the GY129 seedling stage (root, leaf and stem) and booting stage (leaf, rachilla, panicle, stem and sheath). The strongest expression was found at the booting stage (16 weeks) in leaves, and there was relatively weak expression at the seedling stage (4 weeks) in roots, young leaves and young sheaths, indicating that Pi65 is constitutively expressed at different developmental stages and in different organs examined (Fig. 4a). Furthermore, to determine whether the expression of Pi65 in GY129 could be induced in response to challenge by M. oryzae, we inoculated at the three and half-leaf stage-seedlings (4 weeks) of GY129 (resistant variety) and LX1 (susceptible variety) with QY-13 and performed quantitative (q)RT-PCR at six time points (0, 12, 24, 48, 72 and 96 hpi) (Fig. 4b). Relative to the control, Pi65 expression in GY129 first decreased slightly after inoculation and then increased gradually, reaching a peak at 72 h after inoculation, while in LX1, Pi65 first decreased and then increased significantly at 48 h after inoculation, after which it decreased again and finally reached a peak at 96 h after inoculation. Pi65 expression in GY129 was mostly higher than that in LX1 before and after inoculation; however, Pi65 expression was slightly lower in GY129 than in LX1 only at 48 h after inoculation. It can be concluded that Pi65 is constitutively expressed and that its expression in disease-resistant varieties is mostly higher than in susceptible varieties both before and after inoculation, with the only difference in this pattern occurring 48 h after inoculation.
Analysis of the rice blast resistance mechanism based on transcriptome sequencing regulated by Pi65
To further investigate the regulatory mechanism mediated by Pi65, transcriptome sequencing was performed on samples from GY129 and Pi65KO mutant plants before and 24 h after inoculation with M. oryzae. Genes whose expression levels were increased or decreased by 0.5-fold or more after M. oryzae inoculation compared with mock inoculation were identified as DEGs (Fig. 5a). Only those DEGs found in three independent biological replicates were selected for further analyses. A total of 7852 DEGs (2869 upregulated genes and 4983 genes) and 7316 DEGs (2645 upregulated genes and 4671 downregulated genes) were detected in GY129 and the Pi65KO mutant, respectively. Among all DEGs, 1617 upregulated DEGs and 3431 downregulated DEGs were shared between WT GY129 and the Pi65KO mutant. In addition, 1234 genes and 1525 genes were specifically upregulated and downregulated, respectively, in GY129.
Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the pathways that were most highly enriched in common DEGs in GY129 and Pi65KO were associated with metabolic pathways, biosynthesis of secondary metabolites, fatty acid metabolites, phenylpropanoid biosynthesis and ascorbate and aldarate metabolism (Fig. 5b). Gene Ontology (GO) analysis showed that these DEGs were mainly enriched in the categories of “single-organism process” (GO:0044699), “response to stimulus” (GO:0050896), “response to chemical” (GO:0042221), “response to oxygen-containing compound” (GO:1901700) and “biological regulation” (GO:0065007) (Fig. 5c). The results indicated that both GY129 and Pi65KO mutant rice presented resistance responses after inoculation with M. oryzae.
The analysis of the top 20 GO entries showed that the DEGs that were specifically upregulated in GY129 were mainly involved in the “defense response”, “response to biotic stimulus”, “regulation of response to stress”, “response to other organism”, and “response to external biotic stimulus” (Fig. 6a). Genes related to disease defense accounted for the majority of the DEGs, indicating that many genes related to disease defense were activated in GY129 (with Pi65) relative to Pi65KO after infection by M. oryzae.
The specifically downregulated DEGs in GY129 were mainly involved in “chloroplast”, “photosynthesis” and “single-organism biosynthetic process” pathways, and most of these pathways were associated with amino acid metabolism (three pathways), energy metabolism (one pathways), carbohydrate metabolism (four pathways) and transport and catabolism (two pathways) (Fig. 6b). These results indicated that, relative to Pi65KO, GY129 specifically presented decreases in photosynthesis, carbohydrate metabolism and amino acid metabolism after infection by M. oryzae, which may be closely related to plant resistance to pathogens.