Transcriptome-wide analysis of chromium-stress responsive microRNAs to explore miRNA-mediated regulatory networks in radish (Raphanus sativus L.)

Liu, Wei; Xu, Liang; Wang, Yan; Shen, Hong; Zhu, Xiaoming; Zhang, Keyun; Chen, Yinglong; Yu, Rugang; Limera, Cecilia; Liu, Liwang

doi:10.1038/srep14024

Cited by 56 publications

(37 citation statements)

References 58 publications

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“…To further obtain an overview of these biological processes altered during H. glycines infection, the core DEGs were assigned to KEGG pathways, as previously described 19 . In total, eight and six KEGG pathways were over-represented for up- and down-regulated DEGs, respectively (Table S6 ).…”

Section: Resultsmentioning

confidence: 99%

Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja)

Zhang

Kjemtrup-Lovelace

et al. 2017

Sci Rep

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Soybean cyst nematode (SCN) is the most damaging pest of soybean worldwide. The molecular mechanism of SCN resistance remains largely unknown. We conducted a global RNA-seq comparison between a resistant genotype (S54) and a susceptible genotype (S67) of Glycine soja, the wild progenitor of soybean, to understand its regulatory network in SCN defense. The number of differentially expressed genes (DEGs) in S54 (2,290) was much larger than that in S67 (555). A number of defense-related genes/pathways were significantly induced only in S54, while photosynthesis and several metabolic pathways were affected in both genotypes with SCN infection. These defense-associated DEGs were involved in pathogen recognition, calcium/calmodulin-mediated defense signaling, jasmonic acid (JA)/ethylene (ET) and sialic acid (SA)-involved signaling, the MAPK signaling cascade, and WRKY-involved transcriptional regulation. Our results revealed a comprehensive regulatory network involved in SCN resistance and provided insights into the complex molecular mechanisms of SCN resistance in wild soybean.

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Section: Resultsmentioning

confidence: 99%

Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja)

Zhang

Kjemtrup-Lovelace

et al. 2017

Sci Rep

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“…Microarray analysis in Glycine max led to the identification of 26 Cd-responsive miRNAs (Fang et al, 2013). Solexa sequencing in radish (Raphanus sativus) identified 54 known and 16 novel miRNAs that were differentially expressed under Cr stress (Liu et al, 2015). Deep sequencing in the Cd hyperaccumulator Sedum alfredii identified 356 miRNAs, of which 79 miRNAs were differentially expressed under Cd stress (Han et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

MicroRNA166 Modulates Cadmium Tolerance and Accumulation in Rice

et al. 2018

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MicroRNAs (miRNAs) are 20- to 24-nucleotide small noncoding RNAs that regulate gene expression in eukaryotic organisms. Several plant miRNAs, such as miR166, have vital roles in plant growth, development and responses to environmental stresses. One such environmental stress encountered by crop plants is exposure to cadmium (Cd), an element highly toxic to most organisms, including humans and plants. In this study, we analyzed the role of miR166 in Cd accumulation and tolerance in rice (). The expression levels of miR166 in both root and leaf tissues were significantly higher in the reproductive stage than in the seedling stage in rice. The expression of miR166 in the roots of rice seedlings was reduced after Cd treatment. Overexpression of miR166 in rice improved Cd tolerance, a result associated with the reduction of Cd-induced oxidative stress in transgenic rice plants. Furthermore, overexpression of miR166 reduced both Cd translocation from roots to shoots and Cd accumulation in the grains. miR166 targets genes encoding the class-III homeodomain-Leu zipper (HD-Zip) family proteins in plants. In rice, () gene (Os03g43930), which encodes an HD-Zip protein, was up-regulated by Cd treatment but down-regulated by overexpression of miR166 in transgenic rice plants. Overexpression of increased Cd sensitivity and Cd accumulation in the leaves and grains of transgenic rice plants. By contrast, silencing by RNA interference enhanced Cd tolerance in transgenic rice plants. These results indicate a critical role for miR166 in Cd accumulation and tolerance through regulation of its target gene, , in rice.

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“…Increasing evidences have revealed that proteomic studies are playing important roles in the post-genomic era for characterizing the molecular mechanisms underlying plant responses to HM stresses (Fukao et al, 2011; Wang et al, 2013, 2014; Sebastiani et al, 2014). Radish is an important root vegetables worldwide, which has been considered as one of the most significant root species for dissecting the molecular regulatory network of HM stress in Brassicaceae crops (Xu et al, 2012; Wang et al, 2014, 2015a; Liu et al, 2015; Xie et al, 2015). In the current study, comparative proteomics analysis by iTRAQ together with other-omics techniques reveals complex regulatory network and provides insights into the response of radish root under Pb exposure.…”

Section: Discussionmentioning

confidence: 99%

Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure

Wang

Tang

et al. 2016

Front. Plant Sci.

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Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO3)2 at 500 mg L−1(Pb500) and 1000 mg L−1(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification). A total of 3898 protein species were successfully detected and 2141 were quantified. Among them, a subset of 721 protein species were differentially accumulated upon at least one Pb treatment, and 135 ones showed significantly abundance changes under both two Pb-stressed conditions. Many critical protein species related to protein translation, processing, and degradation, reactive oxygen species (ROS) scavenging, photosynthesis, and respiration and carbon metabolism were successfully identified. Gene Ontology (GO) and pathway enrichment analysis of the 135 differential abundance protein species (DAPS) revealed that the overrepresented GO terms included “cell wall,” “apoplast,” “response to metal ion,” “vacuole,” and “peroxidase activity,” and the critical enriched pathways were involved in “citric acid (TCA) cycle and respiratory electron transport,” “pyruvate metabolism,” “phenylalanine metabolism,” “phenylpropanoid biosynthesis,” and “carbon metabolism.” Furthermore, the integrative analysis of transcriptomic, miRNA, degradome, metabolomics and proteomic data provided a strengthened understanding of radish response to Pb stress at multiple levels. Under Pb stress, many key enzymes (i.e., ATP citrate lyase, Isocitrate dehydrogenase, fumarate hydratase and malate dehydrogenase) involved in the glycolysis and TCA cycle were severely affected, which ultimately cause alteration of some metabolites including glucose, citrate and malate. Meanwhile, a series of other defense responses including ascorbate (ASA)–glutathione (GSH) cycle for ROS scavenging and Pb-defense protein species (glutaredoxin, aldose 1-epimerase malate dehydrogenase and thioredoxin), were triggered to cope with Pb-induced injuries. These results would be helpful for further dissecting molecular mechanism underlying plant response to HM stresses, and facilitate effective management of HM contamination in vegetable crops by genetic manipulation.

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Transcriptome-wide analysis of chromium-stress responsive microRNAs to explore miRNA-mediated regulatory networks in radish (Raphanus sativus L.)

Cited by 56 publications

References 58 publications

Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja)

Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja)

MicroRNA166 Modulates Cadmium Tolerance and Accumulation in Rice

Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure

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