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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

The expression pattern of differentially regulated genes in IR28 and LYP9 during the early stages of U. virens infection. A total of 3847 genes were identified to be differentially regulated in IR28 and LYP9 in response to U. virens at 24 hpi and 48 hpi. Each column represents the Log2 fold change in transcript levels in rice at the indicated times, relative to the levels of mock-inoculated samples. The vertical dimension represents the genes that exhibited changes in transcript level (cutoff: /log2[fold change]/ ≥ 1 and FDR ≤ 0.001). The colour scale indicates transcript abundance relative to the mock-inoculated panicles: red, increase in relative transcript abundance; blue, decrease in relative transcript abundance
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Fig2: The expression pattern of differentially regulated genes in IR28 and LYP9 during the early stages of U. virens infection. A total of 3847 genes were identified to be differentially regulated in IR28 and LYP9 in response to U. virens at 24 hpi and 48 hpi. Each column represents the Log2 fold change in transcript levels in rice at the indicated times, relative to the levels of mock-inoculated samples. The vertical dimension represents the genes that exhibited changes in transcript level (cutoff: /log2[fold change]/ ≥ 1 and FDR ≤ 0.001). The colour scale indicates transcript abundance relative to the mock-inoculated panicles: red, increase in relative transcript abundance; blue, decrease in relative transcript abundance

Mentions: A total of 3847 DEGs in IR28 and in LYP9 were classified through cluster analysis. The heat map generated by cluster analysis showed that the majority of DEGs have similar expression patterns between two different time points in the same cultivar. The analysis also showed that these DEGs can be categorized into four major groups: genes down-regulated in both IR28 and LYP9 (group I); genes up-regulated in IR28 while down-regulated in LYP9 (group II); genes up-regulated in both IR28 and LYP9 (group III); and genes up-regulated in LYP9 while suppressed in IR28 (group IV) (Fig. 2). It was speculated that the genes specifically up-regulated in IR28 may play important roles in RFS resistance.Fig. 2


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)

The expression pattern of differentially regulated genes in IR28 and LYP9 during the early stages of U. virens infection. A total of 3847 genes were identified to be differentially regulated in IR28 and LYP9 in response to U. virens at 24 hpi and 48 hpi. Each column represents the Log2 fold change in transcript levels in rice at the indicated times, relative to the levels of mock-inoculated samples. The vertical dimension represents the genes that exhibited changes in transcript level (cutoff: /log2[fold change]/ ≥ 1 and FDR ≤ 0.001). The colour scale indicates transcript abundance relative to the mock-inoculated panicles: red, increase in relative transcript abundance; blue, decrease in relative transcript abundance
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4647755&req=5

Fig2: The expression pattern of differentially regulated genes in IR28 and LYP9 during the early stages of U. virens infection. A total of 3847 genes were identified to be differentially regulated in IR28 and LYP9 in response to U. virens at 24 hpi and 48 hpi. Each column represents the Log2 fold change in transcript levels in rice at the indicated times, relative to the levels of mock-inoculated samples. The vertical dimension represents the genes that exhibited changes in transcript level (cutoff: /log2[fold change]/ ≥ 1 and FDR ≤ 0.001). The colour scale indicates transcript abundance relative to the mock-inoculated panicles: red, increase in relative transcript abundance; blue, decrease in relative transcript abundance
Mentions: A total of 3847 DEGs in IR28 and in LYP9 were classified through cluster analysis. The heat map generated by cluster analysis showed that the majority of DEGs have similar expression patterns between two different time points in the same cultivar. The analysis also showed that these DEGs can be categorized into four major groups: genes down-regulated in both IR28 and LYP9 (group I); genes up-regulated in IR28 while down-regulated in LYP9 (group II); genes up-regulated in both IR28 and LYP9 (group III); and genes up-regulated in LYP9 while suppressed in IR28 (group IV) (Fig. 2). It was speculated that the genes specifically up-regulated in IR28 may play important roles in RFS resistance.Fig. 2

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