Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection

Zhang, Jinfeng; Zhao, Wenjuan; Fu, Rong; Fu, Chunyan; Wang, Lingxia; Liu, Huainian; Li, Shuangcheng; Deng, Qi; Wang, Shiquan; Zhu, Jun; Liang, Yueyang; Li, Ping; Zheng, Aiping

doi:10.1007/s10142-018-0607-y

Cited by 18 publications

(15 citation statements)

References 58 publications

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“…RNA sequencing (RNA-seq) analysis is a critical, easy, rapid, and economical approach of transcriptome studies [37]. Different stress responsive genes have been identified by RNA-seq analysis and their expression under salinity stress already been clarified in various plants including Glycine max [38], rice [39], sweet potato [40], and wild barley [41]. RNA-seq generates a bundle of information for a target phenotype or stress; however, resourceful utilization of this data has been a bottleneck.…”

Section: Discussionmentioning

confidence: 99%

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

Zhu

Xie

Wei

et al. 2019

Genes

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Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.

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Section: Discussionmentioning

confidence: 99%

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

Zhu

Xie

Wei

et al. 2019

Genes

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“…The transcription factors including NAC, WRKY, and basic leucine zipper (bZIP) family members differentially regulate the expression of various defense genes and are involved in modulating resistance to R. solani (Olsen et al 2005 ; Zhang et al 2018 ). NAC transcription factors are involved in the regulation of signal transduction pathways mediated by salicylic acid (SA), JA, ethylene and abscisic acid (Zhao et al 2020 ).…”

Section: Countermeasures From the Hostmentioning

confidence: 99%

Strategies to Manage Rice Sheath Blight: Lessons from Interactions between Rice and Rhizoctonia solani

Wei

et al. 2021

Rice

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Rhizoctonia solani is an important phytopathogenic fungus with a wide host range and worldwide distribution. The anastomosis group AG1 IA of R. solani has been identified as the predominant causal agent of rice sheath blight, one of the most devastating diseases of crop plants. As a necrotrophic pathogen, R. solani exhibits many characteristics different from biotrophic and hemi-biotrophic pathogens during co-evolutionary interaction with host plants. Various types of secondary metabolites, carbohydrate-active enzymes, secreted proteins and effectors have been revealed to be essential pathogenicity factors in R. solani. Meanwhile, reactive oxygen species, phytohormone signaling, transcription factors and many other defense-associated genes have been identified to contribute to sheath blight resistance in rice. Here, we summarize the recent advances in studies on molecular interactions between rice and R. solani. Based on knowledge of rice-R. solani interactions and sheath blight resistance QTLs, multiple effective strategies have been developed to generate rice cultivars with enhanced sheath blight resistance.

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“…These results provided new information of the pathogenic process. Zhang et al [17,18] compared the transcriptome changes of leaves between TeQing (a moderately resistant cultivar) and Lemont (a susceptible cultivar) cultivars in response to R. solani infection. The results showed that regulation of photosynthesis, photorespiration, jasmonic acid and phenylpropanoid pathways might contribute to rice resistance to R. solani.…”

Section: Introductionmentioning

confidence: 99%

Comparison of leaf transcriptome in response to Rhizoctonia solani infection between resistant and susceptible rice cultivars

Shi

Zhao

et al. 2020

BMC Genomics

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Background: Sheath blight (SB), caused by Rhizoctonia solani, is a common rice disease worldwide. Currently, rice cultivars with robust resistance to R. solani are still lacking. To provide theoretic basis for molecular breeding of R. solani-resistant rice cultivars, the changes of transcriptome profiles in response to R. solani infection were compared between a moderate resistant cultivar (Yanhui-888, YH) and a susceptible cultivar (Jingang-30, JG). Results: In the present study, 3085 differentially express genes (DEGs) were detected between the infected leaves and the control in JG, with 2853 DEGs in YH. A total of 4091 unigenes were significantly upregulated in YH than in JG before infection, while 3192 were significantly upregulated after infection. Further analysis revealed that YH and JG showed similar molecular responses to R. solani infection, but the responses were earlier in JG than in YH. Expression levels of trans-cinnamate 4-monooxygenase (C4H), ethylene-insensitive protein 2 (EIN2), transcriptome factor WRKY33 and the KEGG pathway plant-pathogen interaction were significantly affected by R. solani infection. More importantly, these components were all over-represented in YH cultivar than in JG cultivar before and/or after infection. Conclusions: These genes possibly contribute to the higher resistance of YH to R. solani than JG and were potential target genes to molecularly breed R. solani-resistant rice cultivar.

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Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection

Cited by 18 publications

References 58 publications

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

Strategies to Manage Rice Sheath Blight: Lessons from Interactions between Rice and Rhizoctonia solani

Comparison of leaf transcriptome in response to Rhizoctonia solani infection between resistant and susceptible rice cultivars

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