Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

Plant Molecular Biology, Journal Year: 2021, Volume and Issue: 105(6), P. 655 - 684

Published: Feb. 11, 2021

Abstract Key message This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence rice, providing possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during senescence. LncRNAs have been reported to play crucial roles diverse biological processes. However, no lncRNAs associated with plants has studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice leaves developing from normal A total 3953 38757 mRNAs were identified, which 343 9412 differentially expressed. Through weighted gene co-expression network (WGCNA), 22 continuously down-expressed targeting 812 co-expressed 48 up-expressed 1209 considered be significantly Gene Ontology results suggested that senescence-associated targeted many processes, including transcription, hormone response, oxidation–reduction process substance metabolism. Additionally, 43 predicted target 111 transcription factors. Interestingly, 8 29 found separately 12 20 well-studied genes (SAGs). Furthermore, on competing endogenous RNA (CeRNA) revealed 6 possibly regulated 51 through 15 miRNAs, 14 117 21 miRNAs. Importantly, by expression validation, conserved miR164-NAC pathway involved senescence, where lncRNA MSTRG.62092.1 may serve as binding miR164a miR164e regulate three And two key MSTRG.31014.21 MSTRG.31014.36 also could abscisic-acid biosynthetic BGIOSGA025169 ( OsNCED4 ) BGIOSGA016313 (NAC family) osa-miR5809. The regulation discussed, several candidate recommended for prior transgenic analysis. These findings will extend understanding lay foundation functional research lncRNAs.

Language: Английский

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The Roles of microRNA-Long Non-coding RNA-mRNA Networks in the Regulation of Leaf and Flower Development in Liriodendron chinense

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Jan. 27, 2022

The leaf and the flower are vital plant organs owing to their roles in photosynthesis reproduction. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs), transcription factors (TFs) very important development of these organs. Liriodendron chinense is a common ornamental tree species southern China with an unusual shape tulip-like flowers. genetic mechanisms underlying L. miRNA-lncRNA-TF regulatory networks poorly studied. Through integration analysis different types sequencing data, we identified that were related development. These contained 105 miRNAs, 258 lncRNAs, 393 TFs, 22 endogenous target mimics. Notably, lch-lnc7374-miR156h-SPL3 lch-lnc7374-miR156j-SPL9 potential regulators stamen pistil chinense, respectively. miRNA-lncRNA-mRNA shown impact anther development, male female fertility, petal color by regulating biosynthesis phenylpropanoid metabolites. Phenylpropanoid metabolite genes TFs targeted miRNAs lncRNAs differentially expressed flower. Moreover, RT-qPCR confirmed among which most them showed obvious or specificity; miR157a-SPL miR160a-ARF module verified using RLM-RACE, two modules findings provide insight into organ function will facilitate further investigation chinense.

Language: Английский

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Gypsy retrotransposon‐derived maize lncRNA GARR2 modulates gibberellin response

The Plant Journal, Journal Year: 2022, Volume and Issue: 110(5), P. 1433 - 1446

Published: April 3, 2022

Long non-coding RNAs (lncRNAs) mediate diverse biological events mainly through the modulation of transcriptional hierarchy. The phytohormone gibberellin (GA) is essential for various aspects plant growth and development. However, roles lncRNAs in regulation GA response remain largely unknown. Through sequencing multiple strand-specific ribosomal-depleted RNA libraries, we delineated landscape maize (Zea mays). Out identified lncRNAs, 445 GIBBERELLIN-RESPONSIVE (GARRs) were differentially expressed upon application. By intersection GARRs from normal-height dwarf plants an advanced backcross population, four shared (GARR1 to GARR4) identified. these GARRs, GARR2 was derived a Gypsy LTR retrotransposon. GA-responsive element P-boxes upstream GARR2. GARR2-edited lines exhibited GA-induced phenotype. Editing resulted changes abundance pathway components endogenous contents. Besides GA, affected primary auxin response. An pull-down assay revealed HECT ubiquitin-protein ligase family member ZmUPL1 as potential interaction target influenced Our study uncovers lncRNA players involved guides development height ideotype driven by knowledge GA.

Language: Английский

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Rice EIL1 interacts with OsIAAs to regulate auxin biosynthesis mediated by the tryptophan aminotransferase MHZ10/OsTAR2 during root ethylene responses

The Plant Cell, Journal Year: 2022, Volume and Issue: 34(11), P. 4366 - 4387

Published: Aug. 16, 2022

Abstract Ethylene plays essential roles in adaptive growth of rice (Oryza sativa). Understanding the crosstalk between ethylene and auxin (Aux) is limited rice. Here, from an analysis root-specific ethylene-insensitive mutant mao hu zi 10 (mhz10), we identified tryptophan aminotransferase (TAR) MHZ10/OsTAR2, which catalyzes key step indole-3-pyruvic acid-dependent Aux biosynthesis. Genetically, OsTAR2 acts downstream signaling root responses. ETHYLENE INSENSITIVE3 like1 (OsEIL1) directly activated expression. Surprisingly, induction expression still required pathway. We also show that Os indole-3-acetic acid (IAA)1/9 OsIAA21/31 physically interact with OsEIL1 promotive repressive effects on OsEIL1-activated promoter activity, respectively. These likely depend their EAR motif-mediated histone acetylation/deacetylation modification. The special promoting activity OsIAA1/9 may require both motifs flanking sequences for recruitment acetyltransferase. repressors exhibit earlier degradation upon treatment than activators a TIR1/AFB-dependent manner, allowing activation by signal amplification. This study reveals positive feedback regulation biosynthesis highlights pathways at previously underappreciated level

Language: Английский

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IbMYB308, a Sweet Potato R2R3-MYB Gene, Improves Salt Stress Tolerance in Transgenic Tobacco

Genes, Journal Year: 2022, Volume and Issue: 13(8), P. 1476 - 1476

Published: Aug. 18, 2022

The MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factor family plays an important role in plant growth, development, and response to biotic abiotic stresses. However, the gene functions of factors sweet potato (Ipomoea batatas (L.) Lam) have not been elucidated. In this study, gene, IbMYB308, was identified isolated from potato. Multiple sequence alignment showed that IbMYB308 is a typical R2R3-MYB factor. Further, quantitative real-time PCR (qRT-PCR) analysis revealed expressed root, stem, and, especially, leaf tissues. Moreover, it had tissue-specific profile. experiment also expression induced by different stresses (20% PEG-6000, 200 mM NaCl, 20% H2O2). After NaCl treatment, several stress-related genes (SOD, POD, APX, P5CS) upregulation transgenic plants, CAT activity, POD proline content, protein content tobacco increased, while MDA decreased. conclusion, study demonstrated could improve salt stress tolerance tobacco. These findings lay foundation for future studies on suggest potentially be used as positive breeding plants.

Language: Английский

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