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. 2024 Oct 3;25(19):10655.
doi: 10.3390/ijms251910655.

Transcriptomic Analysis of the CNL Gene Family in the Resistant Rice Cultivar IR28 in Response to Ustilaginoidea virens Infection

Zuo-Qian Wang  1   2 , Yu-Fu Wang  3 , Ting Xu  1   2 , Xin-Yi Li  1   2 , Shu Zhang  1   2 , Xiang-Qian Chang  1   2 , Xiao-Lin Yang  1   2 , Shuai Meng  4 , Liang Lv  1   2
Affiliations

Transcriptomic Analysis of the CNL Gene Family in the Resistant Rice Cultivar IR28 in Response to Ustilaginoidea virens Infection

Zuo-Qian Wang et al. Int J Mol Sci. .

Abstract

Rice false smut, caused by Ustilaginoidea virens, threatens rice production by reducing yields and contaminating grains with harmful ustiloxins. However, studies on resistance genes are scarce. In this study, the resistance level of IR28 (resistant cultivar) to U. virens was validated through artificial inoculation. Notably, a reactivation of resistance genes after transient down-regulation during the first 3 to 5 dpi was observed in IR28 compared to WX98 (susceptible cultivar). Cluster results of a principal component analysis and hierarchical cluster analysis of differentially expressed genes (DEGs) in the transcriptome exhibited longer expression patterns in the early infection phase of IR28, consistent with its sustained resistance response. Results of GO and KEGG enrichment analyses highlighted the suppression of immune pathways when the hyphae first invade stamen filaments at 5 dpi, but sustained up-regulated DEGs were linked to the 'Plant-pathogen interaction' (osa04626) pathway, notably disease-resistant protein RPM1 (K13457, CNLs, coil-coiled NLR). An analysis of CNLs identified 245 proteins containing Rx-CC and NB-ARC domains in the Oryza sativa Indica genome. Partial candidate CNLs were shown to exhibit up-regulation at both 1 and 5 dpi in IR28. This study provides insights into CNLs' responses to U. virens in IR28, potentially informing resistance mechanisms and genetic breeding targets.

Keywords: CNLs; NLR immune receptor; Ustilaginoidea virens; transcriptome analysis.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Cultivar IR28 was more resistant to rice false smut than cultivar WX98, and resistance-related genes were induced in IR28 panicles. (A,B): Three panicles infected by U. virens and their corresponding false smut balls on IR28 and WX98, respectively. (C): Number of smut balls and infected flower ratio. (D): Relative expression level of resistance-related genes OsBETV1 and OsPR10b in IR28 and WX98 under U. virens inoculation at 0, 1, 3, 5, and 7 dpi. Panicles were collected after artificial inoculation with U. virens HWD-2. Their RNAs were extracted using liquid nitrogen and reverse-transcribed into cDNA. Ubiquitin10 was set as reference gene. (E): Relative expression levels of OsBETV1 and OsPR10b in panicles, leaves, and stems at 3 and 5 dpi. *, **, and *** indicate significant difference between samples (p < 0.05, p < 0.01 and p < 0.001).
Figure 2
Figure 2
Principal component analysis (PCA) and hierarchical cluster analysis (HCA) revealed two phases of immune response during U. virens infection. (A): PCA of gene expression dynamics in resistant cultivar IR28 and the susceptible cultivar WX98 under U. virens infection. Four groups included samples from IR28 at 1, 5, and 9 dpi, IR28 at 13 dpi, WX98 at 1 and 5 dpi, and WX98 at 9 and 13 dpi, respectively. (B): HCA of gene expression dynamics in IR28 and WX98. Five subgroups included samples IR28 at 13 dpi, WX98 at 9 and 13 dpi, WX98 at 1 and 5 dpi, IR28 at 1 dpi, and IR28 at 5 and 9 dpi, respectively. Group I and II were clustered into late phase of infection. Group III, IV and V were clustered into early phase of infection.
Figure 3
Figure 3
Differential gene expression analysis in IR28 compared to WX98. (A): Volcano plots display the DEGs identified in IR28 compared to WX98 during U. virens infection at 1, 5, 9, and 13 dpi. (B): Number of DEGs in IR28 at different dpi. (C): Venn diagram of the 2585 DEGs enriched at 1, 5, 9, and 13 dpi. (D): GO enrichment of DEGs in IR28 vs. WX98 at 1, 5, 9, and 13 dpi. (E–H): Ten most enriched GO terms of up-regulated DEGs in IR28 at 1 dpi, 5 dpi, 9 dpi, and 13 dpi, respectively.
Figure 4
Figure 4
KEGG pathway enrichment analysis of DEGs in plant–pathogen interactions. (A): KEGG pathway enrichment analysis of a total of 2404 DEGs significantly up-regulated in IR28 compared to WX98 at both 1 and 5 dpi (adjusted p-value < 0.05). (B): Heatmap of DEGs enriched in the plant–pathogen interaction pathway. (C): Expression profile of DEGs enriched in nodes of plant–pathogen interaction pathway.
Figure 5
Figure 5
CNL identification in Oryza sativa Indica genome and expression profile. (A): Venn diagram exhibiting the number of proteins containing Rx-CC and NB-ARC domains. (B): CNL distribution in chromosomes and results of duplication analysis. (C): Hierarchically clustered heatmap of CNLs in IR28 and WX98 at 1 dpi and 5 dpi.
Figure 6
Figure 6
qRT-PCR validation of candidate CNL expression in IR28 and WX98 at 0, 1, 3, 5, and 7 dpi. *, **, and *** indicate significant difference between samples (p < 0.05, p < 0.01 and p < 0.001).
Figure 7
Figure 7
qRT-PCR validation of candidate CNL expression in IR28 during U. virens infection in panicle, leaves, and stems at 3 and 5 dpi. *, **, and *** indicate significant difference between samples (p < 0.05, p < 0.01 and p < 0.001).
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References

    1. Song J.H., Wei W., Lv B., Lin Y., Yin W.X., Peng Y.L., Schnabel G., Huang J.B., Jiang D.H., Luo C.X. Rice false smut fungus hijacks the rice nutrients supply by blocking and mimicking the fertilization of rice ovary. Environ. Microbiol. 2016;18:3840–3849. doi: 10.1111/1462-2920.13343. - DOI - PubMed
    1. Wen Ming W., Jing F., John Martin Jerome J. Rice false smut: An increasing threat to grain yield and quality. In: Yulin J., editor. Protecting Rice Grains in the Post-Genomic Era. IntechOpen; Rijeka, Croatia: 2019. p. Ch.7.
    1. Sun Q., Liu H., Zhang Y., Yi X.E., Kong R., Cheng S., Man J., Zheng L., Huang J., Su G., et al. Global distribution of ustiloxins in rice and their male-biased hepatotoxicity. Environ. Pollut. 2022;301:118992. doi: 10.1016/j.envpol.2022.118992. - DOI - PubMed
    1. Zhang Y., Xu Q., Sun Q., Kong R., Liu H., Yi X.e., Liang Z., Letcher R.J., Liu C. Ustiloxin a inhibits proliferation of renal tubular epithelial cells in vitro and induces renal injury in mice by disrupting structure and respiratory function of mitochondria. J. Hazard. Mater. 2023;448:130791. doi: 10.1016/j.jhazmat.2023.130791. - DOI - PubMed
    1. Fan J., Yang J., Wang Y.Q., Li G.B., Li Y., Huang F., Wang W.M. Current understanding on villosiclava virens, a unique flower-infecting fungus causing rice false smut disease. Mol. Plant Pathol. 2016;17:1321–1330. doi: 10.1111/mpp.12362. - DOI - PMC - PubMed

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