RNA sequencing-based exploration of the effects of far-red light on lncRNAs involved in the shade-avoidance response of<i>D. officinale</i>

Li, Hansheng; Ye, Wei; Yaqian, Wang; Chen, Xiaohui; Fang, Yan; Sun, Gang

doi:10.7717/peerj.10769

Cited by 12 publications

(8 citation statements)

References 68 publications

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“…Recently, FR-regulated lncRNAs were identified in Dendrobium officinale , and it was suggested that they might participate in SAS through hormone signal transduction and DNA methylation (Li et al, 2021). However, their potential roles in this pathway remain unknown.…”

Section: Discussionmentioning

confidence: 99%

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controlling shade avoidance syndrome inArabidopsis thaliana

Mammarella

Lucero

Hussain

et al. 2023

Preprint

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The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loop) and modulating local three-dimensional chromatin conformation. Here we show that APOLO is involved in regulating the shade avoidance syndrome (SAS) by dynamically modulating the expression of key factors. In response to far-red (FR) light, the expression of APOLO anticorrelates with its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. APOLO transcriptional accumulation fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves as well as in a late response to FR treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of YUCCA2 (auxin synthesis), PID and WAG2 (auxin efflux).

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Section: Discussionmentioning

confidence: 99%

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controlling shade avoidance syndrome inArabidopsis thaliana

Mammarella

Lucero

Hussain

et al. 2023

Preprint

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show abstract

“…Recently, FR‐regulated lncRNAs were identified in Dendrobium officinale , and it was suggested that they might participate in SAS through hormone signal transduction and DNA methylation (Li et al , 2021). However, their potential roles in this pathway remain unknown.…”

Section: Discussionmentioning

confidence: 99%

Long noncoding RNA‐mediated epigenetic regulation of auxin‐related genes controls shade avoidance syndrome in Arabidopsis

Mammarella,

Lucero,

Hussain

et al. 2023

The EMBO Journal

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The long noncoding RNA (lncRNA) AUXIN‐REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA–DNA hybrids (R‐loops) and modulating local three‐dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far‐red (FR) light, expression of APOLO anti‐correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine‐tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far‐red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far‐red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant–environment interactions may therefore become a new tool for sustainable agriculture.

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“…The soft rot in D. officinale caused by F. oxysporum is one of the main diseases in the productive areas of China. This pathogen harms plants’ roots, causing vascular bundle disease and plant death, which can occur along the entire growth period of D. officinale , resulting in great losses to production [ 39 , 40 , 41 , 42 ]. The seriously damaged crops reported at home and abroad are eggplant, sugarcane, blackberry, cotton, etc.…”

Section: Discussionmentioning

confidence: 99%

Detection and Control of Fusarium oxysporum from Soft Rot in Dendrobium officinale by Loop-Mediated Isothermal Amplification Assays

Xiao

2021

Biology

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Soft rot causing Fusarium oxysporum is one of the most destructive diseases of Dendrobium officinale Kimura et Migo in China that reduces D. officinale yield and quality. A key challenge for an integrated management strategy for this disease is the rapid and accurate detection of F. oxysporum on D. officinale. Therefore, a new loop-mediated isothermal amplification (LAMP) assay was developed for this purpose. In this study, the primers were selected and designed using the translation elongation factor-1α (TEF-1α) gene region as the target DNA sequence in order to screen the best system of reaction of LAMP to detect F. oxysporum through optimizing different conditions of the LAMP reaction, including time, temperature, concentrations of MgSO4, and concentrations of inner and outer primers. The optimized system was able to efficiently amplify the target gene at 62 °C for 60 min with 1.2 μM internal primers, 0.4 μM external primers, 7 mM Mg2+, and 5 fg/µL minimum detection concentration of DNA for F. oxysporum. The amplified products could be detected with the naked eye after completion of the reaction with SYBR green I. We were better able to control the effect of soft rot in D. officinale using fungicides following a positive test result. Additionally, the control effect of synergism combinations against soft rot was higher than 75%. Thus, LAMP assays could detect F. oxysporum in infected tissues of D. officinale and soils in field, allowing for early diagnosis of the disease.

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RNA sequencing-based exploration of the effects of far-red light on lncRNAs involved in the shade-avoidance response ofD. officinale

Cited by 12 publications

References 68 publications

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controlling shade avoidance syndrome inArabidopsis thaliana

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controlling shade avoidance syndrome inArabidopsis thaliana

Long noncoding RNA‐mediated epigenetic regulation of auxin‐related genes controls shade avoidance syndrome in Arabidopsis

Detection and Control of Fusarium oxysporum from Soft Rot in Dendrobium officinale by Loop-Mediated Isothermal Amplification Assays

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