Transcriptome analysis revealed hormone signaling response of grapevine buds to strigolactones

Zhuo, Min; Li, Ziyu; Chen, Li; Zhang, Yang; Liu, Min; Xu, Yan; Fang, Yulin

doi:10.1016/j.scienta.2021.109936

Cited by 12 publications

(6 citation statements)

References 54 publications

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“…Strigolactones regulate many aspects of plant physiology and development similar to, and often in concert with, other plant hormones like auxins or cytokinins (Barbier et al, 2019;Brewer et al, 2013;Dun et al, 2023;Waters et al, 2017). Previous studies using whole seedling treatment with various GR24 analogues over periods of time much longer than the time needed to activate degradation SMXL6/7/8 proteins identified a small number of DEGs (Kerr et al, 2020;Lantzouni et al, 2017;Min et al, 2021;Ravazzolo et al, 2021; in comparison with other plant hormones (Lewis et al, 2013;Xie et al, 2018). In this work, we explored the immediate/early gene expression changes in response to rac-GR24 by harnessing the power of leaf-derived protoplasts as an experimental system that enables measurement of early gene expression dynamics in a population of plant cells with synchronised exposure to a signal.…”

Section: Discussionmentioning

confidence: 99%

Strigolactone induces D14‐dependent large‐scale changes in gene expression requiring SWI/SNF chromatin remodellers

Humphreys,

Beveridge,

Tanurdžić

2024

The Plant Journal

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SUMMARYStrigolactones (SL) function as plant hormones in control of multiple aspects of plant development, mostly via the regulation of gene expression. Immediate early‐gene regulation by SL remains unexplored due to difficulty in dissecting early from late gene expression responses to SL. We used synthetic SL, rac‐GR24 treatment of protoplasts and RNA‐seq to explore early SL‐induced changes in gene expression over time (5–180 minutes) and discovered rapid, dynamic and SL receptor D14‐dependent regulation of gene expression in response to rac‐GR24. Importantly, we discovered a significant dependence of SL signalling on chromatin remodelling processes, as the induction of a key SL‐induced transcription factor BRANCHED1 requires the SWI/SNF chromatin remodelling ATPase SPLAYED (SYD) and leads to upregulation of a homologue SWI/SNF ATPase BRAHMA. ATAC‐seq profiling of genome‐wide changes in chromatin accessibility in response to rac‐GR24 identified large‐scale changes, with over 1400 differentially accessible regions. These changes in chromatin accessibility often precede transcriptional changes and are likely to harbour SL cis‐regulatory elements. Importantly, we discovered that this early and extensive modification of the chromatin landscape also requires SYD. This study, therefore, provides evidence that SL signalling requires regulation of chromatin accessibility, and it identifies genomic locations harbouring likely SL cis‐regulatory sequences.

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Section: Discussionmentioning

confidence: 99%

Strigolactone induces D14‐dependent large‐scale changes in gene expression requiring SWI/SNF chromatin remodellers

Humphreys,

Beveridge,

Tanurdžić

2024

The Plant Journal

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“…Strigolactones regulate many aspects of plant physiology and development similar to, and often in concert with other plant hormones like auxins or cytokinins 18,50 . Previous studies using whole seedling treatment with SL over periods of time much longer than the time needed to activate degradation SMXL6/7/8 proteins identified a small number of differentially expressed genes [23][24][25][26]51 in comparison with other plant hormones 52,53 . In this work we explored the immediate/early gene expression changes in response to SL by harnessing the power of leafderived protoplasts as an experimental system that enables measurement of early gene expression dynamics in a synchronized population of plant cells.…”

Section: Discussionmentioning

confidence: 99%

“…Most investigations into transcriptome changes upon SL treatment have been performed following several hours/days of SL application, even though the rice SMXL6/7/8 orthologue D53 is degraded within ten minutes of SL application 21,22 . The complexity of tissues and organs involved in these experiments [23][24][25][26] further complicates inferences in SL-mediated gene expression changes. Protoplasts (plant cells with the cell wall removed 27 ) provide one solution to this confounding problem of sample complexity.…”

Section: Introductionmentioning

confidence: 99%

Strigolactone-dependent gene regulation requires chromatin remodeling

Humphreys

Beveridge

Tanurdžić

2023

Preprint

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Strigolactones (SL) function as plant hormones in control of multiple aspects of plant development. Regulation of gene expression by SL is a critical component of SL function. Immediate early gene regulation by SL remains unexplored due to difficulty in dissecting early from late gene expression responses to SL in whole plants. We used leaf-derived Arabidopsis protoplasts to explore early (5-180 minutes) changes in gene expression induced by SL by employing RNA-seq and ATAC-seq. We discovered over 1500 genes regulated by SL as early as 20 minutes, and up to 3669 genes across the entire time course of the experiment, indicative of rapid, dynamic regulation of gene expression in response to SLs. We identified 1447 regions of changing chromatin accessibility in response to SL that are likely to harbour SL cis-regulatory elements and cognate candidate trans-acting factors regulated early by SL. Importantly, we discovered that this extensive transcriptomic reprogramming requires the SYD-containing SWI/SNF chromatin remodelling complex(es) and regulates other chromatin remodellers. This study therefore provides the first evidence that SL signalling requires regulation of chromatin accessibility, and it identifies previously unknown transcriptional targets of strigolactones.

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“…Since SLs inhibit the growth of lateral buds [291] and increase plant height [286,292,293], SL-induced plant branching control could be very useful for cut flowers and pot plants [294]. High quality cut flowers should produce long and strong flower stalk and stem and one big flower; on the other hand, pot plants require a short plant height with a lot of branches with many flowers.…”

Section: Multidirectional Sl Regulation Of Shoot and Root Architecturementioning

confidence: 99%

Novel Approaches for Sustainable Horticultural Crop Production: Advances and Prospects

Lastochkina

Aliniaeifard

Seifikalhor³

et al. 2022

Horticulturae

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Reduction of plant growth, yield and quality due to diverse environmental constrains along with climate change significantly limit the sustainable production of horticultural crops. In this review, we highlight the prospective impacts that are positive challenges for the application of beneficial microbial endophytes, nanomaterials (NMs), exogenous phytohormones strigolactones (SLs) and new breeding techniques (CRISPR), as well as controlled environment horticulture (CEH) using artificial light in sustainable production of horticultural crops. The benefits of such applications are often evaluated by measuring their impact on the metabolic, morphological and biochemical parameters of a variety of cultures, which typically results in higher yields with efficient use of resources when applied in greenhouse or field conditions. Endophytic microbes that promote plant growth play a key role in the adapting of plants to habitat, thereby improving their yield and prolonging their protection from biotic and abiotic stresses. Focusing on quality control, we considered the effects of the applications of microbial endophytes, a novel class of phytohormones SLs, as well as NMs and CEH using artificial light on horticultural commodities. In addition, the genomic editing of plants using CRISPR, including its role in modulating gene expression/transcription factors in improving crop production and tolerance, was also reviewed.

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Transcriptome analysis revealed hormone signaling response of grapevine buds to strigolactones

Cited by 12 publications

References 54 publications

Strigolactone induces D14‐dependent large‐scale changes in gene expression requiring SWI/SNF chromatin remodellers

Strigolactone induces D14‐dependent large‐scale changes in gene expression requiring SWI/SNF chromatin remodellers

Strigolactone-dependent gene regulation requires chromatin remodeling

Novel Approaches for Sustainable Horticultural Crop Production: Advances and Prospects

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