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Differential expression profiling of the early response to Ustilaginoidea virens between false smut resistant and susceptible rice varieties.

Han Y, Zhang K, Yang J, Zhang N, Fang A, Zhang Y, Liu Y, Chen Z, Hsiang T, Sun W - BMC Genomics (2015)

Bottom Line: Interestingly, the RY repeat motif was significantly more abundant in the 5'-regulatory regions of these differentially regulated PR genes.Furthermore, U. virens genes that are relevant to fungal reproduction and pathogenicity were found to be suppressed in the resistant cultivar.Our results indicate that rice resistance to false smut may be attributable to plant perception of pathogen-associated molecular patterns, activation of resistance signaling pathways, induced production of PR proteins and diterpene phytoalexins, and suppression of pathogenicity genes in U. virens as well.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, China Agricultural University, 2 West Yuanmingyuan Rd., Haidian District, Beijing, 100193, China. yanqinghan125@126.com.

ABSTRACT

Background: Rice false smut caused by Ustilaginoidea virens has recently become one of the most devastating rice diseases worldwide. Breeding and deployment of resistant varieties is considered as the most effective strategy to control this disease. However, little is known about the genes and molecular mechanisms underlying rice resistance against U. virens.

Results: To explore genetic basis of rice resistance to U. virens, differential expression profiles in resistant 'IR28' and susceptible 'LYP9' cultivars during early stages of U. virens infection were compared using RNA-Seq data. The analyses revealed that 748 genes were up-regulated only in the resistant variety and 438 genes showed opposite expression patterns between the two genotypes. The genes encoding receptor-like kinases and cytoplasmic kinases were highly enriched in this pool of oppositely expressed genes. Many pathogenesis-related (PR) and diterpene phytoalexin biosynthetic genes were specifically induced in the resistant variety. Interestingly, the RY repeat motif was significantly more abundant in the 5'-regulatory regions of these differentially regulated PR genes. Several WRKY transcription factors were also differentially regulated in the two genotypes, which is consistent with our finding that the cis-regulatory W-boxes were abundant in the promoter regions of up-regulated genes in IR28. Furthermore, U. virens genes that are relevant to fungal reproduction and pathogenicity were found to be suppressed in the resistant cultivar.

Conclusion: Our results indicate that rice resistance to false smut may be attributable to plant perception of pathogen-associated molecular patterns, activation of resistance signaling pathways, induced production of PR proteins and diterpene phytoalexins, and suppression of pathogenicity genes in U. virens as well.

No MeSH data available.


Related in: MedlinePlus

Venn diagrams of all differentially expressed genes in the resistant variety IR28 and susceptible variety LYP9 in the early stages of U. virens infection. a The expressed genes (expr) and differentially expressed genes (DEGs) in IR28 (R) and LYP9 (S) at 24 hpi and 48 hpi. A total of 205 DEGs were common in IR28 and LYP9 at 24 hpi while 389 DEGs were common at 48 hpi. b Up-regulated and down-regulated genes among common DEGs in IR28 and LYP9 at 24 hpi and 48 hpi. Among common DEGs, more DEGs were up-regulated in IR28 while more DEGs were down-regulated in LYP9
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Fig1: Venn diagrams of all differentially expressed genes in the resistant variety IR28 and susceptible variety LYP9 in the early stages of U. virens infection. a The expressed genes (expr) and differentially expressed genes (DEGs) in IR28 (R) and LYP9 (S) at 24 hpi and 48 hpi. A total of 205 DEGs were common in IR28 and LYP9 at 24 hpi while 389 DEGs were common at 48 hpi. b Up-regulated and down-regulated genes among common DEGs in IR28 and LYP9 at 24 hpi and 48 hpi. Among common DEGs, more DEGs were up-regulated in IR28 while more DEGs were down-regulated in LYP9

Mentions: To uncover the genes that might be involved in RFS resistance, all differentially expressed genes (DEGs) were identified in IR28 and LYP9 at 24 h and 48 h after P1 inoculation as compared with mock-inoculated samples. Venn diagrams were then drawn to show DEGs that were common to both rice genotypes IR28 and LYP9, or specific to either cultivar in response to P1 inoculation (Fig. 1a). A total of 1072 DEGs were identified in IR28 at 24 hpi, among which 94 were IR28-specific, 205 were common to IR28 and LYP9, and 773 were DEGs only in IR28 but were expressed (non-DEG) in LYP9. In contrast, 1590 DEGs were identified in LYP9 including 51 LYP9-specific and 1334 were DEGs only in LYP9 but expressed in IR28. Meanwhile, 1190 and 1790 DEGs were identified in IR28 and LYP9 at 48 hpi, respectively. Among them, 389 were identified as DEGs common to IR28 and LYP9, and 786 were categorized as DEGs only in IR28 but expressed in LYP9; 75 were LYP9-specific, and 1326 were found as DEGs only in LYP9 but expressed in IR28. Among common DEGs shared by both cultivars at 24 hpi, more genes were up-regulated in IR28 (138) than in LYP9 (88) while fewer DEGs (67) in IR28 were down-regulated than those (117) in LYP9. Among 389 common DEGs at 48 hpi, more (335) were up-regulated compared with down-regulated ones (54) in IR28, while many more genes (311) were suppressed than transcriptionally induced genes (78) in LYP9 at this infection stage (Fig. 1b). Interestingly, the majority of common DEGs (438) exhibited opposite expression patterns between the resistant and susceptible varieties after P1 inoculation, suggesting that defense responses are distinctively different between the two varieties in response to U. virens infection. We speculate that the IR28-specific DEGs and common DEGs which were up-regulated in IR28 and down-regulated in LYP9 might be involving in RFS resistance (Additional file 4: Table S2).Fig. 1


Differential expression profiling of the early response to Ustilaginoidea virens between false smut resistant and susceptible rice varieties.

Han Y, Zhang K, Yang J, Zhang N, Fang A, Zhang Y, Liu Y, Chen Z, Hsiang T, Sun W - BMC Genomics (2015)

Venn diagrams of all differentially expressed genes in the resistant variety IR28 and susceptible variety LYP9 in the early stages of U. virens infection. a The expressed genes (expr) and differentially expressed genes (DEGs) in IR28 (R) and LYP9 (S) at 24 hpi and 48 hpi. A total of 205 DEGs were common in IR28 and LYP9 at 24 hpi while 389 DEGs were common at 48 hpi. b Up-regulated and down-regulated genes among common DEGs in IR28 and LYP9 at 24 hpi and 48 hpi. Among common DEGs, more DEGs were up-regulated in IR28 while more DEGs were down-regulated in LYP9
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig1: Venn diagrams of all differentially expressed genes in the resistant variety IR28 and susceptible variety LYP9 in the early stages of U. virens infection. a The expressed genes (expr) and differentially expressed genes (DEGs) in IR28 (R) and LYP9 (S) at 24 hpi and 48 hpi. A total of 205 DEGs were common in IR28 and LYP9 at 24 hpi while 389 DEGs were common at 48 hpi. b Up-regulated and down-regulated genes among common DEGs in IR28 and LYP9 at 24 hpi and 48 hpi. Among common DEGs, more DEGs were up-regulated in IR28 while more DEGs were down-regulated in LYP9
Mentions: To uncover the genes that might be involved in RFS resistance, all differentially expressed genes (DEGs) were identified in IR28 and LYP9 at 24 h and 48 h after P1 inoculation as compared with mock-inoculated samples. Venn diagrams were then drawn to show DEGs that were common to both rice genotypes IR28 and LYP9, or specific to either cultivar in response to P1 inoculation (Fig. 1a). A total of 1072 DEGs were identified in IR28 at 24 hpi, among which 94 were IR28-specific, 205 were common to IR28 and LYP9, and 773 were DEGs only in IR28 but were expressed (non-DEG) in LYP9. In contrast, 1590 DEGs were identified in LYP9 including 51 LYP9-specific and 1334 were DEGs only in LYP9 but expressed in IR28. Meanwhile, 1190 and 1790 DEGs were identified in IR28 and LYP9 at 48 hpi, respectively. Among them, 389 were identified as DEGs common to IR28 and LYP9, and 786 were categorized as DEGs only in IR28 but expressed in LYP9; 75 were LYP9-specific, and 1326 were found as DEGs only in LYP9 but expressed in IR28. Among common DEGs shared by both cultivars at 24 hpi, more genes were up-regulated in IR28 (138) than in LYP9 (88) while fewer DEGs (67) in IR28 were down-regulated than those (117) in LYP9. Among 389 common DEGs at 48 hpi, more (335) were up-regulated compared with down-regulated ones (54) in IR28, while many more genes (311) were suppressed than transcriptionally induced genes (78) in LYP9 at this infection stage (Fig. 1b). Interestingly, the majority of common DEGs (438) exhibited opposite expression patterns between the resistant and susceptible varieties after P1 inoculation, suggesting that defense responses are distinctively different between the two varieties in response to U. virens infection. We speculate that the IR28-specific DEGs and common DEGs which were up-regulated in IR28 and down-regulated in LYP9 might be involving in RFS resistance (Additional file 4: Table S2).Fig. 1

Bottom Line: Interestingly, the RY repeat motif was significantly more abundant in the 5'-regulatory regions of these differentially regulated PR genes.Furthermore, U. virens genes that are relevant to fungal reproduction and pathogenicity were found to be suppressed in the resistant cultivar.Our results indicate that rice resistance to false smut may be attributable to plant perception of pathogen-associated molecular patterns, activation of resistance signaling pathways, induced production of PR proteins and diterpene phytoalexins, and suppression of pathogenicity genes in U. virens as well.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, China Agricultural University, 2 West Yuanmingyuan Rd., Haidian District, Beijing, 100193, China. yanqinghan125@126.com.

ABSTRACT

Background: Rice false smut caused by Ustilaginoidea virens has recently become one of the most devastating rice diseases worldwide. Breeding and deployment of resistant varieties is considered as the most effective strategy to control this disease. However, little is known about the genes and molecular mechanisms underlying rice resistance against U. virens.

Results: To explore genetic basis of rice resistance to U. virens, differential expression profiles in resistant 'IR28' and susceptible 'LYP9' cultivars during early stages of U. virens infection were compared using RNA-Seq data. The analyses revealed that 748 genes were up-regulated only in the resistant variety and 438 genes showed opposite expression patterns between the two genotypes. The genes encoding receptor-like kinases and cytoplasmic kinases were highly enriched in this pool of oppositely expressed genes. Many pathogenesis-related (PR) and diterpene phytoalexin biosynthetic genes were specifically induced in the resistant variety. Interestingly, the RY repeat motif was significantly more abundant in the 5'-regulatory regions of these differentially regulated PR genes. Several WRKY transcription factors were also differentially regulated in the two genotypes, which is consistent with our finding that the cis-regulatory W-boxes were abundant in the promoter regions of up-regulated genes in IR28. Furthermore, U. virens genes that are relevant to fungal reproduction and pathogenicity were found to be suppressed in the resistant cultivar.

Conclusion: Our results indicate that rice resistance to false smut may be attributable to plant perception of pathogen-associated molecular patterns, activation of resistance signaling pathways, induced production of PR proteins and diterpene phytoalexins, and suppression of pathogenicity genes in U. virens as well.

No MeSH data available.


Related in: MedlinePlus