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Special Issue "Root Development in Plants"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 July 2019).

Special Issue Editors

Prof. Dr. Steffen Vanneste

Guest Editor
Universiteit Gent, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
Interests: root development
Prof. Dr. Tom Beeckman
Website
Guest Editor
Universiteit Gent, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent Belgium
Interests: root development; auxin signaling and transport

Special Issue Information

Dear Colleagues,

Roots are fundamental to the success of plants in conquering land. The complexity of a plant’s root system is not a rigorous readout of the predefined body plan as seen in many animals. Instead, it is a highly variable structure that is defined on a plant-per-plant basis in which every individual root tip instructs root architecture elaboration via growth and/or branching based on a specific set of rules in the context of local challenges and limitations. Much of what we know is focused on sub-aspects of factors that control root development, and mainly restricted to Arabidopsis seedlings grown in vitro.

Papers submitted to this Special Issue must report high novelty results and/or plausible and testable models, not restricted to Arabidopsis. The environmental and developmental control over root branching is a reference topic. In addition, studies dealing with root meristem functioning and elongation control are also of interest. Finally, significant advances in tool development to analyze specific aspects of root development are heartily welcomed.

Prof. Dr. Steffen Vanneste
Prof. Dr. Tom Beeckman
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • lateral root
  • adventitious root
  • hormones
  • nutrients
  • evolution
  • signal integration
  • cross-talk

Published Papers (8 papers)

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Research

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Open AccessArticle
A DAO1-Mediated Circuit Controls Auxin and Jasmonate Crosstalk Robustness during Adventitious Root Initiation in Arabidopsis
Int. J. Mol. Sci. 2019, 20(18), 4428; https://doi.org/10.3390/ijms20184428 - 09 Sep 2019
Cited by 1
Abstract
Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious [...] Read more.
Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI. Full article
(This article belongs to the Special Issue Root Development in Plants)
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Open AccessArticle
Physiological and Transcriptomic Changes during the Early Phases of Adventitious Root Formation in Mulberry Stem Hardwood Cuttings
Int. J. Mol. Sci. 2019, 20(15), 3707; https://doi.org/10.3390/ijms20153707 - 29 Jul 2019
Cited by 2
Abstract
The initiation and induction of root primordia are of great importance for adventitious root (AR) formation in cutting propagation of horticultural and forestry crops. However, the underlying mechanisms orchestrating these early phases of AR formation remain largely unexplored. Here, we investigated the physiological [...] Read more.
The initiation and induction of root primordia are of great importance for adventitious root (AR) formation in cutting propagation of horticultural and forestry crops. However, the underlying mechanisms orchestrating these early phases of AR formation remain largely unexplored. Here, we investigated the physiological and transcriptomic changes during the early AR phases in mulberry stem hardwood cuttings. The results showed that the concentrations of soluble proteins increased, whereas concentrations of soluble sugars and starch were decreased. Indole-3-acetic acid (IAA) and zeatin had a rapid transit peak at 6 h after planting (hAP) and declined thereafter. The activities of peroxidase and catalase persistently increased and indole-3-acetic acid oxidase was maintained at a higher stable level from 0 hAP, while the activities of polyphenol oxidase fluctuated with soluble phenolics and IAA levels. The comparative transcriptome identified 4276 common genes that were differentially regulated at −6, 0 and 54 hAP. They were separated into five clusters with distinct biological functions such as defense response and photosynthesis. Considerable common genes were assigned to pathways of sugar metabolism, mitogen-activated protein kinase, and circadian rhythm. The gene co-expression network analysis revealed three major co-expressed modules involved in stress responses, hormone signaling, energy metabolism, starch metabolism, and circadian rhythm. These findings demonstrate the positive effect of auxin on AR induction, and uncovered the crucial roles of stress responses, hormone signaling and circadian rhythm in coordinating the physiological changes during the early phases of AR formation in mulberry stem hardwood cuttings. Full article
(This article belongs to the Special Issue Root Development in Plants)
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Open AccessArticle
An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium ‘Zhongshanshan’
Int. J. Mol. Sci. 2019, 20(5), 1225; https://doi.org/10.3390/ijms20051225 - 11 Mar 2019
Cited by 6
Abstract
Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we [...] Read more.
Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation. Full article
(This article belongs to the Special Issue Root Development in Plants)
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Open AccessArticle
The Involvement of Ethylene in Calcium-Induced Adventitious Root Formation in Cucumber under Salt Stress
Int. J. Mol. Sci. 2019, 20(5), 1047; https://doi.org/10.3390/ijms20051047 - 28 Feb 2019
Cited by 2
Abstract
Calcium and ethylene are essential in plant growth and development. In this study, we investigated the effects of calcium and ethylene on adventitious root formation in cucumber explants under salt stress. The results revealed that 10 μM calcium chloride (CaCl2) or [...] Read more.
Calcium and ethylene are essential in plant growth and development. In this study, we investigated the effects of calcium and ethylene on adventitious root formation in cucumber explants under salt stress. The results revealed that 10 μM calcium chloride (CaCl2) or 0.1 μM ethrel (ethylene donor) treatment have a maximum biological effect on promoting the adventitious rooting in cucumber under salt stress. Meanwhile, we investigated that removal of ethylene suppressed calcium ion (Ca2+)-induced the formation of adventitious root under salt stress indicated that ethylene participates in this process. Moreover, the application of Ca2+ promoted the activities of 1-aminocyclopropane-l-carboxylic acid synthase (ACS) and ACC Oxidase (ACO), as well as the production of 1-aminocyclopropane-l-carboxylic acid (ACC) and ethylene under salt stress. Furthermore, we discovered that Ca2+ greatly up-regulated the expression level of CsACS3, CsACO1 and CsACO2 under salt stress. Meanwhile, Ca2+ significantly down-regulated CsETR1, CsETR2, CsERS, and CsCTR1, but positively up-regulated the expression of CsEIN2 and CsEIN3 under salt stress; however, the application of Ca2+ chelators or channel inhibitors could obviously reverse the effects of Ca2+ on the expression of the above genes. These results indicated that Ca2+ played a vital role in promoting the adventitious root development in cucumber under salt stress through regulating endogenous ethylene synthesis and activating the ethylene signal transduction pathway. Full article
(This article belongs to the Special Issue Root Development in Plants)
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Open AccessArticle
GmZPR3d Interacts with GmHD-ZIP III Proteins and Regulates Soybean Root and Nodule Vascular Development
Int. J. Mol. Sci. 2019, 20(4), 827; https://doi.org/10.3390/ijms20040827 - 14 Feb 2019
Abstract
Fabaceans produce two major classes of symbiotic nodules: the indeterminate type characterized by a persistent meristem, and the determinate type that lacks a persistent meristem. The class III homeodomain leucine zipper (HD-ZIP III) transcription factor family influence development of multiple lateral organs and [...] Read more.
Fabaceans produce two major classes of symbiotic nodules: the indeterminate type characterized by a persistent meristem, and the determinate type that lacks a persistent meristem. The class III homeodomain leucine zipper (HD-ZIP III) transcription factor family influence development of multiple lateral organs and meristem maintenance, but their role in determinate nodule development is not known. HD-ZIP III protein activity is post-translationally regulated by members of the small leucine zipper protein (ZPR) family in arabidopsis. We characterized the ZPR gene family in soybean and evaluated their ability to interact with two key members of GmHD-ZIP III family through yeast two-hybrid assays. GmZPR3d displayed the strongest interaction with GmHD-ZIP III-2 among the different pairs evaluated. GmHD-ZIP III-1, -2, and GmZPR3d showed overlapping expression patterns in the root stele and in nodule parenchyma tissues. Over-expression of GmZPR3d resulted in ectopic root secondary xylem formation, and enhanced expression of vessel-specific master switch genes in soybean. The nodules in ZPR3d over-expressing roots were larger in size, had a relatively larger central zone and displayed increased nodule vascular branching. The results from this study point to a key role for GmZPR3d in soybean root and nodule development. Full article
(This article belongs to the Special Issue Root Development in Plants)
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Open AccessArticle
Morphological Characterization of Root System Architecture in Diverse Tomato Genotypes during Early Growth
Int. J. Mol. Sci. 2018, 19(12), 3888; https://doi.org/10.3390/ijms19123888 - 05 Dec 2018
Cited by 1
Abstract
Plant roots exploit morphological plasticity to adapt and respond to different soil environments. We characterized the root system architecture of nine wild tomato species and four cultivated tomato (Solanum lycopersicum L.) varieties during early growth in a controlled environment. Additionally, the root [...] Read more.
Plant roots exploit morphological plasticity to adapt and respond to different soil environments. We characterized the root system architecture of nine wild tomato species and four cultivated tomato (Solanum lycopersicum L.) varieties during early growth in a controlled environment. Additionally, the root system architecture of six near-isogenic lines from the tomato ‘Micro-Tom’ mutant collection was also studied. These lines were affected in key genes of ethylene, abscisic acid, and anthocyanin pathways. We found extensive differences between the studied lines for a number of meaningful morphological traits, such as lateral root distribution, lateral root length or adventitious root development, which might represent adaptations to local soil conditions during speciation and subsequent domestication. Taken together, our results provide a general quantitative framework for comparing root system architecture in tomato seedlings and other related species. Full article
(This article belongs to the Special Issue Root Development in Plants)
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Review

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Open AccessReview
Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana
Int. J. Mol. Sci. 2020, 21(8), 2880; https://doi.org/10.3390/ijms21082880 - 20 Apr 2020
Abstract
Nitrate (NO3) and auxin are key regulators of root growth and development, modulating the signalling cascades in auxin-induced lateral root formation. Auxin biosynthesis, transport, and transduction are significantly altered by nitrate. A decrease in nitrate (NO3) supply [...] Read more.
Nitrate (NO3) and auxin are key regulators of root growth and development, modulating the signalling cascades in auxin-induced lateral root formation. Auxin biosynthesis, transport, and transduction are significantly altered by nitrate. A decrease in nitrate (NO3) supply tends to promote auxin translocation from shoots to roots and vice-versa. This nitrate mediated auxin biosynthesis regulating lateral roots growth is induced by the nitrate transporters and its downstream transcription factors. Most nitrate responsive genes (short-term and long-term) are involved in signalling overlap between nitrate and auxin, thereby inducing lateral roots initiation, emergence, and development. Moreover, in the auxin signalling pathway, the varying nitrate supply regulates lateral roots development by modulating the auxin accumulation in the roots. Here, we focus on the roles of nitrate responsive genes in mediating auxin biosynthesis in Arabidopsis root, and the mechanism involved in the transport of auxin at different nitrate levels. In addition, this review also provides an insight into the significance of nitrate responsive regulatory module and their downstream transcription factors in root system architecture in the model plant Arabidopsis thaliana. Full article
(This article belongs to the Special Issue Root Development in Plants)
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Open AccessReview
Auxin-Induced Adventitious Root Formation in Nodal Cuttings of Camellia sinensis
Int. J. Mol. Sci. 2019, 20(19), 4817; https://doi.org/10.3390/ijms20194817 - 27 Sep 2019
Abstract
Adventitious root (AR) formation is essential for the successful propagation of Camellia sinensis and auxins play promotive effects on this process. Nowadays, the mechanism of auxin-induced AR formation in tea cuttings is widely studied. However, a lack of global view of the underlying [...] Read more.
Adventitious root (AR) formation is essential for the successful propagation of Camellia sinensis and auxins play promotive effects on this process. Nowadays, the mechanism of auxin-induced AR formation in tea cuttings is widely studied. However, a lack of global view of the underlying mechanism has largely inhibited further studies. In this paper, recent advances including endogenous hormone changes, nitric oxide (NO) and hydrogen peroxide (H2O2) signals, secondary metabolism, cell wall reconstruction, and mechanisms involved in auxin signaling are reviewed. A further time course analysis of transcriptome changes in tea cuttings during AR formation is also suggested to deepen our understanding. The purpose of this paper is to offer an overview on the most recent developments especially on those key aspects affected by auxins and that play important roles in AR formation in tea plants. Full article
(This article belongs to the Special Issue Root Development in Plants)
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