ARCHIPELAGO: A Dedicated Resource for Exploiting Past, Present, and Future Genomic Data on Disease Resistance Regulation in Rice

Large amounts of expression data dealing with biotic stresses in rice have been produced in the past 5 years. Here, we extensively review approximately 70 publications and gather together information on more than 2,500 genes of the rice defense arsenal. This information was integrated into the OryGenesDB database. Several genes (e.g., metallothioneins and PBZ1) appear to be hallmarks of rice–pathogen interactions. Cross-referencing this information with the rice kinome highlighted some defense genes and kinases as possible central nodes of regulation. Cross referencing defense gene expression and quantitative trait loci (QTL) information identified some candidate genes for QTL. Overall, pathogenesis-related genes and disease regulators were found to be statistically associated with disease QTL. At the genomic level, we observed that some regions are richer than others and that some chromosomes (e.g., 11 and 12), which contain a lot of resistance gene analogs, have a low content of defense genes. Finally, we show that classical defense genes and defense-related genes such as resistance genes are preferentially organized in clusters. These clusters are not always coregulated and individual paralogs can show specific expression patterns. Thus, the rice defense arsenal has an ARCHIPELAGO-like genome structure at the macro and micro level. This resource opens new possibilities for marker-assisted selection and QTL cloning.

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Cytokinins Act Synergistically with Salicylic Acid to Activate Defense Gene Expression in Rice

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-06-12-0152-r ◽

2013 ◽

Vol 26 (3) ◽

pp. 287-296 ◽

Cited By ~ 88

Author(s):

Chang-Jie Jiang ◽

Masaki Shimono ◽

Shoji Sugano ◽

Mikiko Kojima ◽

Xinqiong Liu ◽

...

Keyword(s):

Salicylic Acid ◽

Histochemical Staining ◽

Rice Seedlings ◽

Defense Gene Expression ◽

Defense Gene ◽

Glucuronidase Activity ◽

Blast Fungus ◽

Pathogenesis Related ◽

Isopentenyl Adenine ◽

Plant Pathogen Interactions

Hormone crosstalk is pivotal in plant–pathogen interactions. Here, we report on the accumulation of cytokinins (CK) in rice seedlings after infection of blast fungus Magnaporthe oryzae and its potential significance in rice–M. oryzae interaction. Blast infection to rice seedlings increased levels of N6-(Δ2-isopentenyl) adenine (iP), iP riboside (iPR), and iPR 5′-phosphates (iPRP) in leaf blades. Consistent with this, CK signaling was activated around the infection sites, as shown by histochemical staining for β-glucuronidase activity driven by a CK-responsive OsRR6 promoter. Diverse CK species were also detected in the hyphae (mycelium), conidia, and culture filtrates of blast fungus, indicating that M. oryzae is capable of production as well as hyphal secretion of CK. Co-treatment of leaf blades with CK and salicylic acid (SA), but not with either one alone, markedly induced pathogenesis-related genes OsPR1b and probenazole-induced protein 1 (PBZ1). These effects were diminished by RNAi-knockdown of OsNPR1 or WRKY45, the key regulators of the SA signaling pathway in rice, indicating that the effects of CK depend on these two regulators. Taken together, our data imply a coevolutionary rice–M. oryzae interaction, wherein M. oryzae probably elevates rice CK levels for its own benefits such as nutrient translocation. Rice plants, on the other hand, sense it as an infection signal and activate defense reactions through the synergistic action with SA.

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Impact of IL-1 signalling on experimental uveitis and arthritis

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2011-200556 ◽

2012 ◽

Vol 71 (5) ◽

pp. 753-760 ◽

Cited By ~ 23

Author(s):

Stephen R Planck ◽

April Woods ◽

Jenna S Clowers ◽

Martin J Nicklin ◽

James T Rosenbaum ◽

...

Keyword(s):

Expression Patterns ◽

Eye Disease ◽

Negative Regulators ◽

Specific Expression ◽

Local Responses ◽

Intraocular Injection ◽

Inflammatory Eye Disease ◽

Pathogenesis Related ◽

Organ Specific ◽

Organ Specific Expression

BackgroundUveitis, or inflammatory eye disease, is a common extra-articular manifestation of many systemic autoinflammatory diseases involving the joints. Anakinra (recombinant interleukin (IL)-1 receptor antagonist (Ra)) is an effective therapy in several arthritic diseases; yet, few studies have investigated the extent to which IL-1 signalling or IL-1Ra influences the onset and/or severity of uveitis.ObjectiveTo seek possible links between arthritis and uveitis pathogenesis related to IL-1 signalling.MethodsThe eyes of IL-1Ra-deficient BALB/c mice were monitored histologically and by intravital videomicroscopy to determine if uveitis developed along with the expected spontaneous arthritis in ankles and knees. Expression levels of IL-1R and its negative regulators (IL-1Ra, IL-1RII, IL-1RAcP and single Ig IL-1R-related molecule) in eye and joint tissues were compared. Differences in uveitis induced by intraocular injection of lipopolysaccharide (LPS) in mice lacking IL-1R or IL-1Ra were assessed.ResultsDeficiency in IL-1Ra predisposes to spontaneous arthritis, which is exacerbated by previous systemic LPS exposure. The eye, however, does not develop inflammatory disease despite the progressive arthritis or LPS exposure. Organ-specific expression patterns for IL-1Ra and negative regulators of IL-1 activity were observed that appear to predict predisposition to inflammation in each location in IL-1Ra knockout mice. The eye is extremely sensitive to locally administered LPS, and IL-1Ra deficiency markedly exacerbates the resulting uveitis.ConclusionThis study demonstrates that IL-1Ra plays an important role in suppressing local responses in eyes injected with LPS and that there is discordance between murine eyes and joints in the extent to which IL-1Ra protects against spontaneous inflammation.

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Genome-Wide Prediction, Functional Divergence, and Characterization of Stress-Responsive BZR Transcription Factors in B. napus

Frontiers in Plant Science ◽

10.3389/fpls.2021.790655 ◽

2022 ◽

Vol 12 ◽

Author(s):

Rehman Sarwar ◽

Rui Geng ◽

Lei Li ◽

Yue Shan ◽

Ke-Ming Zhu ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Functional Divergence ◽

Expression Patterns ◽

Future Research ◽

Plant Tolerance ◽

Specific Expression ◽

Biotic Stresses ◽

Organ Specific ◽

Duplication Events

BRASSINAZOLE RESISTANT (BZR) are transcriptional factors that bind to the DNA of targeted genes to regulate several plant growth and physiological processes in response to abiotic and biotic stresses. However, information on such genes in Brassica napus is minimal. Furthermore, the new reference Brassica napus genome offers an excellent opportunity to systematically characterize this gene family in B. napus. In our study, 21 BnaBZR genes were distributed across 19 chromosomes of B. napus and clustered into four subgroups based on Arabidopsis thaliana orthologs. Functional divergence analysis among these groups evident the shifting of evolutionary rate after the duplication events. In terms of structural analysis, the BnaBZR genes within each subgroup are highly conserved but are distinctive within groups. Organ-specific expression analyses of BnaBZR genes using RNA-seq data and quantitative real-time polymerase chain reaction (qRT-PCR) revealed complex expression patterns in plant tissues during stress conditions. In which genes belonging to subgroups III and IV were identified to play central roles in plant tolerance to salt, drought, and Sclerotinia sclerotiorum stress. The insights from this study enrich our understanding of the B. napus BZR gene family and lay a foundation for future research in improving rape seed environmental adaptability.

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Defense gene expression patterns of three SAR-induced tomato cultivars in the field

Physiological and Molecular Plant Pathology ◽

10.1016/j.pmpp.2008.02.002 ◽

2007 ◽

Vol 71 (4-6) ◽

pp. 192-200 ◽

Cited By ~ 31

Author(s):

M.A.B. Herman ◽

S. Restrepo ◽

C.D. Smart

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Defense Gene Expression ◽

Defense Gene ◽

Tomato Cultivars

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Arabidopsis flower specific defense gene expression patterns affect resistance to pathogens

Frontiers in Plant Science ◽

10.3389/fpls.2015.00079 ◽

2015 ◽

Vol 6 ◽

Cited By ~ 9

Author(s):

Luisa Ederli ◽

Adam Dawe ◽

Stefania Pasqualini ◽

Mara Quaglia ◽

Liming Xiong ◽

...

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Defense Gene Expression ◽

Defense Gene

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The MicroRNA miR773 Is Involved in the Arabidopsis Immune Response to Fungal Pathogens

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-05-17-0108-r ◽

2018 ◽

Vol 31 (2) ◽

pp. 249-259 ◽

Cited By ~ 16

Author(s):

Raquel Salvador-Guirao ◽

Patricia Baldrich ◽

Detlef Weigel ◽

Ignacio Rubio-Somoza ◽

Blanca San Segundo

Keyword(s):

Fungal Pathogens ◽

Adaptive Responses ◽

Defense Gene Expression ◽

Pathogen Infection ◽

Defense Gene ◽

Biotic Stresses ◽

Molecular Pattern ◽

Pathogen Challenge ◽

Wide Range ◽

Resistance To Infection

MicroRNAs (miRNAs) are 21- to 24-nucleotide short noncoding RNAs that trigger gene silencing in eukaryotes. In plants, miRNAs play a crucial role in a wide range of developmental processes and adaptive responses to abiotic and biotic stresses. In this work, we investigated the role of miR773 in modulating resistance to infection by fungal pathogens in Arabidopsis thaliana. Interference with miR773 activity by target mimics (in MIM773 plants) and concomitant upregulation of the miR773 target gene METHYLTRANSFERASE 2 (MET2) increased resistance to infection by necrotrophic (Plectosphaerrella cucumerina) and hemibiotrophic (Fusarium oxysporum, Colletototrichum higginianum) fungal pathogens. By contrast, both MIR773 overexpression and MET2 silencing enhanced susceptibility to pathogen infection. Upon pathogen challenge, MIM773 plants accumulated higher levels of callose and reactive oxygen species than wild-type plants. Stronger induction of defense-gene expression was also observed in MIM773 plants in response to fungal infection. Expression analysis revealed an important reduction in miR773 accumulation in rosette leaves of plants upon elicitor perception and pathogen infection. Taken together, our results show not only that miR773 mediates pathogen-associated molecular pattern-triggered immunity but also demonstrate that suppression of miR773 activity is an effective approach to improve disease resistance in Arabidopsis plants.

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Defense gene expression in root galls induced by Nacobbus aberrans in CM334 chilli plants

Helminthologia ◽

10.1515/helmin-2015-0014 ◽

2015 ◽

Vol 52 (1) ◽

pp. 77-82

Author(s):

E. Villar-Luna ◽

J. A. García-Espinoza ◽

O. Goméz-Rodriguez ◽

R. I. Rojas-martínez ◽

E. Zavaleta-Mejía

Keyword(s):

Incompatible Interaction ◽

Successful Completion ◽

Defense Gene Expression ◽

Defense Gene ◽

Over Expression ◽

Pathogenesis Related Protein ◽

Pathogenesis Related ◽

Transcriptional Alterations ◽

Nacobbus Aberrans ◽

Related Proteins

Summary Capsicum annuum L. CM334 is susceptible to Nacobbus aberrans but highly resistant to Phy-tophthora capsici. Resistance to P. capsici is associated with the over-expression of various defense genes such as those encoding pathogenesis-related proteins. The transcriptional alterations of defense-related genes were determined in galls induced by N. aberrans (Na) in CM334 chili roots. Transcripts accumulation of WRKY-a, WRKY1, POX (peroxidase), PR-1 (pathogenesis-related protein 1), and EAS (5-epiaristolochene synthase) was estimated by qRT-PCR, and they were compared with those recorded in the incompatible CM334- P. capsici (Pc) interaction. The levels of all studied genes were significantly (P s 0.05) lower (WRKY1, POX and PR-1) or down-regulated (WRKY-a and EAS) in the presence of N. aberrans; in contrast, in the incompatible interaction, all genes were significantly up-regulated. The alterations induced by N. aberrans could be necessary to ensure the successful completion of its life cycle in CM334 chili roots.

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Defense Gene Expression Associated with Biotrophic Phase of Mycosphaerella fijiensis M. Morelet Infection in Banana

Plant Disease ◽

10.1094/pdis-08-15-0950-re ◽

2016 ◽

Vol 100 (6) ◽

pp. 1170-1175 ◽

Cited By ~ 9

Author(s):

Hector A. Rodriguez ◽

Esperanza Rodriguez-Arango ◽

Juan G. Morales ◽

Gert Kema ◽

Rafael E. Arango

Keyword(s):

Reference Genes ◽

Ribosomal Subunit ◽

Defense Responses ◽

Mycosphaerella Fijiensis ◽

Defense Gene Expression ◽

Resistance Response ◽

Defense Gene ◽

Pathogenesis Related ◽

Host Defense Response ◽

Black Leaf Streak

Banana black leaf streak, caused by Mycosphaerella fijiensis M. Morelet, is a primary phytosanitary concern in export of this fruit around the world. To develop improved cultivars resistant to this disease, an understanding of host response to infection is necessary. In this study, we obtained expression data on 14,872 genes by microarray analysis in the resistant genotype Musa acuminata subsp. burmannicoides ‘Calcutta 4’ after inoculation with Mycosphaerella fijiensis. From these data, 16 genes were analyzed as potential reference genes and 12 genes were identified as potential early indicators of the onset of the host defense response. Subsequently, these genes were analyzed by quantitative reverse-transcription polymerase chain reaction in susceptible ‘Williams’ and resistant Calcutta 4. The 18S and 26S ribosomal subunit genes in both cultivars showed the best characteristics as reference genes. In all, 5 of the 12 defense genes expressed shortly after infection (peroxidase, pathogenesis-related [PR]-4, PR-10, phenylalanine ammonia-liase, and disease resistance response 1) showed overexpression in Calcutta 4 between 6 and 24 h after inoculation as opposed to Williams, which did not show overexpression after 144 h. Early induction of defense-related genes could be a key component of the resistance of the Calcutta 4 genotype against M. fijiensis. In addition, these five genes could be used as indicators of the activation of defense responses in the interaction between banana and M. fijiensis.

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In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses

PeerJ ◽

10.7717/peerj.8539 ◽

2020 ◽

Vol 8 ◽

pp. e8539 ◽

Cited By ~ 2

Author(s):

Kang Zhang ◽

Lu Yu ◽

Xi Pang ◽

Hongzhe Cao ◽

Helong Si ◽

...

Keyword(s):

Gene Expression ◽

Heat Stress ◽

Gene Family ◽

Histone Deacetylases ◽

Expression Patterns ◽

In Silico Analysis ◽

Hormone Treatment ◽

Specific Expression ◽

Systematic Analysis ◽

Biotic Stresses

Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. However, systematic analysis of HDAC gene family and gene expression in response to abiotic and biotic stresses has not yet been reported. In this study, a systematic analysis of the HDAC gene family in maize was performed and 18 ZmHDACs distributed on nine chromosomes were identified. Phylogenetic analysis of ZmHDACs showed that this gene family could be divided into RPD3/HDA1, SIR2, and HD2 groups. Tissue-specific expression results revealed that ZmHDACs exhibited diverse expression patterns in different tissues, indicating that these genes might have diversified functions in growth and development. Expression pattern of ZmHDACs in hormone treatment and inoculation experiment suggested that several ZmHDACs might be involved in jasmonic acid or salicylic acid signaling pathway and defense response. Interestingly, HDAC genes were downregulated under heat stress, and immunoblotting results demonstrated that histones H3K9ac and H4K5ac levels were increased under heat stress. These results provide insights into ZmHDACs, which could help to reveal their functions in controlling maize development and responses to abiotic or biotic stresses.

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