Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice

Lavarenne, Jérémy; Gonin, Mathieu; Champion, Antony; Javelle, Marie; Adam, Hélène; Rouster, Jacques; Conéjéro, Geneviève; Lartaud, Marc; Verdeil, Jean‐Luc; Laplaze, Laurent; Sallaud, Christophe; Lucas, Mikaël; Gantet, Pascal

doi:10.1371/journal.pone.0238736

Cited by 8 publications

(3 citation statements)

References 68 publications

(91 reference statements)

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“…Identification of light-induced lncRNAs antisense to ERF99 , B-type response regulator genic region may play a role in its transcriptional regulation. ERF99 is known to modulate root architecture and downregulated in crown root primordia 95 . MADS27 gene targeted by lncRNAs present in both dark and light conditions.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional modulation during photomorphogenesis in rice seedlings

Gupta,

Jaiswal

2023

Preprint

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Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data.

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Section: Discussionmentioning

confidence: 99%

Transcriptional modulation during photomorphogenesis in rice seedlings

Gupta,

Jaiswal

2023

Preprint

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“…Additionally, OsPLT5, in combination with the WUS2 gene, promotes regeneration from tissue culture, suggesting that they function as pluripotency factors in grass species, including O. sativa (Lowe et al, 2016). Expression profiling in rice roots of OsPLT1∼6 revealed that these genes are up-regulated both in the primordia of CRs and in developing CRs (Garg et al, 2020;Lavarenne et al, 2020). Moreover, these euANT/PLT clade A genes are specifically expressed in different sectors of the CR meristem (Li and Xue, 2011;Kitomi et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, euANT/PLT clade B genes including OsPLT8/CRL5 might play a key role during CR initiation without being involved in the later steps of CR primordia differentiation (Garg et al, 2020;Lavarenne et al, 2020). In this sense, OsPLT8/CRL5 was initially demonstrated to be involved in the auxin-dependent de novo pathway of CR initiation in rice, through the repression of cytokinin signaling by positively regulating the type-A RR OsRR1 (Kitomi et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination

et al. 2021

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Grain yield, which is one of the most important traits in rice breeding, is controlled in part by panicle branching patterns. Numerous genes involved in the control of panicle architecture have been identified through mutant and QTL characterization. Previous studies suggested the importance of several AP2/ERF transcription factor-encoding genes in the control of panicle development, including the AINTEGUMENTA/PLETHORA-like (euANT/PLT) genes. The ANT gene was specifically considered to be a key regulator of shoot and floral development in Arabidopsis thaliana. However, the likely importance of paralogous euANT/PLT genes in the regulation of meristem identities and activities during panicle architecture development has not to date been fully addressed in rice. In this study, we observed that the rice euANT/PLT genes displayed divergent temporal expression patterns during the branching stages of early panicle development, with spatial localization of expression in meristems for two of these genes. Moreover, a functional analysis of rice ANT-related genes using genome editing revealed their importance in the control of panicle architecture, through the regulation of axillary meristem (AM) establishment and meristem fate transition. Our study suggests that the paralogous euANT/PLT genes have become partially diversified in their functions, with certain opposing effects, since they arose from ancestral gene duplication events, and that they act in regulating the branching of the rice panicle.

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Lateral Root Formation

Bellande

Laplaze

Guyomarc’h

2022

Encyclopedia of Life Sciences

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The underground development of the plant root system is a complex and plastic process. It enables the plants to mine hydromineral resources while dealing with changes in their environment. Root branching via lateral root formation is considered as an important trait because it greatly influences root system architecture and impacts plant growth and crop performance. In the past few years, major progresses in understanding the mechanisms of root branching have been made. Technical advances lift the veil on multiple molecular and cellular processes that contribute to the robust formation of new lateral roots in plant models and to its response to endogenous and environmental cues. Developing translational approaches should increase in the coming decades to allow a global and integrative vision of root system development and the mechanisms of root branching in various plant species. Moreover, exploring the genetic diversity that modulates this fundamental process opens the way to breeding crops with more efficient root system architectures. Key Concepts Lateral root formation significantly influences root system architecture, a key trait for plant interaction with the soil and especially, plant nutrition. Lateral root primordium initiation, development and emergence from the primary root have been well described in several plant model species. Lateral root formation is highly regulated. Many molecular mechanisms involved in this organogenesis process are known in detail, especially in the plant model Arabidopsis thaliana . Among these, the phytohormone auxin is a key regulatory signal influencing each step of lateral root formation. A complex regulatory network, integrating intercellular signals and mechanical constraints, triggers regularly spaced initiation of lateral root formation, allows robust organ patterning, and controls the lateral root primordium growth through the overlaying primary root tissues. Endogenous and environmental signals modulate lateral root formation kinetics and emergence, yielding plasticity in root system development. Comparison of lateral root development in different plant species reveals specific and conserved pathways. Genetic diversity can be explored and used to breed crops with optimised root branching properties.

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Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice

Cited by 8 publications

References 68 publications

Transcriptional modulation during photomorphogenesis in rice seedlings

Transcriptional modulation during photomorphogenesis in rice seedlings

Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination

Lateral Root Formation

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