Effect of Leptosphaeria maculans Infection on Promoter DNA Methylation of Defence Genes in Brassica napus

Tirnaz, Soodeh; Merce, Clementine; Bayer, Philipp E.; Severn‐Ellis, Anita A.; Edwards, David; Batley, Jacqueline

doi:10.3390/agronomy10081072

Cited by 12 publications

(7 citation statements)

References 45 publications

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“…However, as shown in Figure 4C, the overall expression of RGA genes was higher in G20 than in Y61 at 48 h after C. brevisporum infection, suggesting that RGA expression level may contribute to the greater resistance of G20. These overall RGA expression levels may be influenced by several factors, such as the regulation of methylation and transcription factors (Liu et al, 2015;Tirnaz et al, 2020). Many transcription factors identified in this study were potential regulators of RGAs.…”

Section: Discussionmentioning

confidence: 79%

Comparative transcriptomics and genomic analyses reveal differential gene expression related to Colletotrichum brevisporum resistance in papaya (Carica papaya L.)

et al. 2022

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Colletotrichum brevisporum is an important causal pathogen of anthracnose that seriously affects the fruit quality and yield of papaya (Carica papaya L.). Although many genes and biological processes involved in anthracnose resistance have been reported in other species, the molecular mechanisms involved in the response or resistance to anthracnose in post-harvest papaya fruits remain unclear. In this study, we compared transcriptome changes in the post-harvest fruits of the anthracnose-susceptible papaya cultivar Y61 and the anthracnose-resistant cultivar G20 following C. brevisporum inoculation. More differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElnRNAs) were identified in G20 than in Y61, especially at 24 h post-inoculation (hpi), suggesting a prompt activation of defense responses in G20 in the first 24 h after C. brevisporum inoculation. These DEGs were mainly enriched in plant-pathogen interaction, phenylpropanoid biosynthesis/metabolism, and peroxisome and flavonoid biosynthesis pathways in both cultivars. However, in the first 24 hpi, the number of DEGs related to anthracnose resistance was greater in G20 than in Y61, and changes in their expression levels were faster in G20 than in Y61. We also identified a candidate anthracnose-resistant gene cluster, which consisted of 12 genes, 11 in G20 and Y61, in response to C. brevisporum inoculation. Moreover, 529 resistance gene analogs were identified in papaya genome, most of which responded to C. brevisporum inoculation and were genetically different between papaya cultivars and wild-type populations. The total expression dose of the resistance gene analogs may help papaya resist C. brevisporum infection. This study revealed the mechanisms underlying different anthracnose resistance between the anthracnose-resistant and anthracnose-susceptible cultivars based on gene expression, and identified some potential anthracnose resistance-related candidate genes/major regulatory factors. Our findings provided potential targets for developing novel genetic strategies to overcome anthracnose in papaya.

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Section: Discussionmentioning

confidence: 79%

Comparative transcriptomics and genomic analyses reveal differential gene expression related to Colletotrichum brevisporum resistance in papaya (Carica papaya L.)

et al. 2022

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“…In B. napus in response to blackleg disease in a resistant cultivar (“Sturt”), more promoters of resistance genes (23.66%) were differentially methylated in comparison to the susceptible cultivar “Westar” (14.42%) (Tirnaz et al, 2020b ). In this study, similar numbers of DMRs were observed in the susceptible cultivar (“Misugi”) and the resistant cultivar (“Nanane”), and no overlapped DMRs were found between the two cultivars, indicating that DMRs by A. candida infection are cultivar specific.…”

Section: Discussionmentioning

confidence: 99%

“…The higher number of CHG and CHH DMRs indicates that CHG and CHH sites are the most affected loci during A. candida infection, which may be due to the difference in robustness of DNA methylation between CG and non-CG methylation. Similarly, methylation at CHH sites has been reported to be the mainly affected in wheat against powdery mildew disease (Geng et al, 2019 ), in Citrullus lanatus against cucumber green mottle mosaic virus (CGMMV) (Sun et al, 2019 ), and in B. napus against blackleg disease (Tirnaz et al, 2020b ). There were differences in the ratios between the number of DMRs of hyper- and hypo-methylation by A. candida infection between cultivars.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome DNA Methylation Analysis in Brassica rapa subsp. perviridis in Response to Albugo candida Infection

Tirnaz

Miyaji²,

Takuno³

et al. 2022

Front. Plant Sci.

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DNA methylation is an epigenetic mark associated with several mechanisms in plants including immunity mechanisms. However, little is known about the regulatory role of DNA methylation in the resistance response of Brassica species against fungal diseases. White rust, caused by the fungus Albugo candida, is one of the most widespread and destructive diseases of all the cultivated Brassica species, particularly Brassica rapa L. and Brassica juncea (L.) Czern and Coss. Here, we investigate whole-genome DNA methylation modifications of B. rapa subsp. perviridis in response to white rust. As a result, 233 and 275 differentially methylated regions (DMRs) in the susceptible cultivar “Misugi” and the resistant cultivar “Nanane” were identified, respectively. In both cultivars, more than half of the DMRs were associated with genes (DMR-genes). Gene expression analysis showed that 13 of these genes were also differentially expressed between control and infected samples. Gene ontology enrichment analysis of DMR genes revealed their involvement in various biological processes including defense mechanisms. DMRs were unevenly distributed around genes in susceptible and resistant cultivars. In “Misugi,” DMRs tended to be located within genes, while in “Nanane,” DMRs tended to be located up and downstream of the genes. However, CG DMRs were predominantly located within genes in both cultivars. Transposable elements also showed association with all three sequence contexts of DMRs but predominantly with CHG and CHH DMRs in both cultivars. Our findings indicate the occurrence of DNA methylation modifications in B. rapa in response to white rust infection and suggest a potential regulatory role of DNA methylation modification in defense mechanisms which could be exploited to improve disease resistance.

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“…to reveal the plant’s immunity against pathogens. A recent study by Tirnaz et al [ 170 ] has shown that DNA methylation regulates the promoters of defence genes, causing variation in resistance response against black leg infection at the seedling stage of B . napus .…”

Section: Epigenomicsmentioning

confidence: 99%

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L.

Shaw

Shen

et al. 2022

IJMS

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Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.

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Effect of Leptosphaeria maculans Infection on Promoter DNA Methylation of Defence Genes in Brassica napus

Cited by 12 publications

References 45 publications

Comparative transcriptomics and genomic analyses reveal differential gene expression related to Colletotrichum brevisporum resistance in papaya (Carica papaya L.)

Comparative transcriptomics and genomic analyses reveal differential gene expression related to Colletotrichum brevisporum resistance in papaya (Carica papaya L.)

Whole-Genome DNA Methylation Analysis in Brassica rapa subsp. perviridis in Response to Albugo candida Infection

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L.

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