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Root Development and Architecture in Relation to Environmental Conditions
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Root Development and Architecture in Relation to Environmental Conditions

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 May 2021) | Viewed by 44904

Special Issue Editors

Dr. Viola Willemsen

E-Mail Website
Guest Editor
Lab. of Plant Developmental Biology, Wageningen University, Wageningen, The Netherlands
Interests: stem cells; lateral roots; adventitious roots; root development; root architecture
Dr. Wouter Kohlen

E-Mail Website
Guest Editor
Lab. of Molecular Biology, Wageningen University, Wageningen, The Netherlands
Interests: plant hormones; root nodule initiation; meristems; develomental physiology

Special Issue Information

Dear Colleagues,

Plant roots are dynamic, and their growth is strongly affected by the environmental conditions found in the soil. These effects include alterations in the activation of primary root growth and the initiation of additional lateral organs such as lateral roots and, for legumes, root nodules. Cumulatively, these growth alterations and lateral organ initiations lead to changes in the root system architecture. Such architectural changes are regulated by both internal and external cues. Nutrient levels, soil composition, and microbes are some examples of potent external environmental cues, whereas plant hormones are among the internal cues affecting root development. This Special Issue of Genes on “Root Development and Architecture in Relation to Environmental Conditions” will address the mechanisms through which root development and architecture can respond and adapt to environmental conditions, providing an overview of recent developments in specialized research topics and critical perspectives on upcoming challenges.

Dr. Viola Willemsen
Dr. Wouter Kohlen
Guest Editors

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Keywords

  • Plant roots
  • Lateral root organs
  • Plant hormones
  • Root development
  • Environment adaptation
  • Root architecture
  • Plant microbe interactions
  • Plant stem cells
  • Abiotic factors
  • Plant soil feedback

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Published Papers (7 papers)

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Research

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11 pages, 1309 KiB  
Article
Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling
by Yinwei Zeng, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste and Danny Geelen
Genes 2021, 12(8), 1141; https://doi.org/10.3390/genes12081141 - 27 Jul 2021
Cited by 16 | Viewed by 3448
Abstract
Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated [...] Read more.
Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition. Full article
(This article belongs to the Special Issue Root Development and Architecture in Relation to Environmental Conditions)
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14 pages, 3464 KiB  
Article
Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments
by Merijn Kerstens, Vera Hesen, Kavya Yalamanchili, Andrea Bimbo, Stephen Grigg, Davy Opdenacker, Tom Beeckman , Renze Heidstra and Viola Willemsen
Genes 2021, 12(7), 1028; https://doi.org/10.3390/genes12071028 - 1 Jul 2021
Cited by 8 | Viewed by 4795
Abstract
Root development is crucial for plant growth and therefore a key factor in plant performance and food production. Arabidopsis thaliana is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but [...] Read more.
Root development is crucial for plant growth and therefore a key factor in plant performance and food production. Arabidopsis thaliana is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but this approach poorly reflects the natural situation, which fact in recent years has led to a dramatic shift toward studying RSA in soil. Here, we directly compare RSA responses to agar-based medium (plates) and potting soil (rhizotrons) for a set of redundant loss-of-function plethora (plt) CRISPR mutants with variable degrees of secondary root defects. We demonstrate that plt3plt7 and plt3plt5plt7 plants, which produce only a handful of emerged secondary roots, can be distinguished from other genotypes based on both RSA shape and individual traits on plates and rhizotrons. However, in rhizotrons the secondary root density and the total contribution of the side root system to the RSA is increased in these two mutants, effectively rendering their phenotypes less distinct compared to WT. On the other hand, plt3, plt3plt5, and plt5plt7 mutants showed an opposite effect by having reduced secondary root density in rhizotrons. This leads us to believe that plate versus rhizotron responses are genotype dependent, and these differential responses were also observed in unrelated mutants short-root and scarecrow. Our study demonstrates that the type of growth system affects the RSA differently across genotypes, hence the optimal choice of growth conditions to analyze RSA phenotype is not predetermined. Full article
(This article belongs to the Special Issue Root Development and Architecture in Relation to Environmental Conditions)
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14 pages, 2318 KiB  
Article
The Effect of Exogenous Nitrate on LCO Signalling, Cytokinin Accumulation, and Nodule Initiation in Medicago truncatula
by Kerstin Gühl, Rens Holmer, Ting Ting Xiao, Defeng Shen, Titis A. K. Wardhani, René Geurts, Arjan van Zeijl and Wouter Kohlen
Genes 2021, 12(7), 988; https://doi.org/10.3390/genes12070988 - 28 Jun 2021
Cited by 13 | Viewed by 2889
Abstract
Nitrogen fixation by rhizobia is a highly energy-demanding process. Therefore, nodule initiation in legumes is tightly regulated. Environmental nitrate is a potent inhibitor of nodulation. However, the precise mechanism by which this agent (co)regulates the inhibition of nodulation is not fully understood. Here, [...] Read more.
Nitrogen fixation by rhizobia is a highly energy-demanding process. Therefore, nodule initiation in legumes is tightly regulated. Environmental nitrate is a potent inhibitor of nodulation. However, the precise mechanism by which this agent (co)regulates the inhibition of nodulation is not fully understood. Here, we demonstrate that in Medicago truncatula the lipo-chitooligosaccharide-induced accumulation of cytokinins is reduced in response to the application of exogenous nitrate. Under permissive nitrate conditions, perception of rhizobia-secreted signalling molecules leads to an increase in the level of four cytokinins (i.e., iP, iPR, tZ, and tZR). However, under high-nitrate conditions, this increase in cytokinins is reduced. The ethylene-insensitive mutant Mtein2/sickle, as well as wild-type plants grown in the presence of the ethylene biosynthesis inhibitor 2-aminoethoxyvinyl glycine (AVG), is resistant to the inhibition of nodulation by nitrate. This demonstrates that ethylene biosynthesis and perception are required to inhibit nodule organogenesis under high-nitrate conditions. Full article
(This article belongs to the Special Issue Root Development and Architecture in Relation to Environmental Conditions)
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12 pages, 3173 KiB  
Article
Nitrate Modulates Lateral Root Formation by Regulating the Auxin Response and Transport in Rice
by Bobo Wang, Xiuli Zhu, Xiaoli Guo, Xuejiao Qi, Fan Feng, Yali Zhang, Quanzhi Zhao, Dan Han and Huwei Sun
Genes 2021, 12(6), 850; https://doi.org/10.3390/genes12060850 - 1 Jun 2021
Cited by 8 | Viewed by 3120
Abstract
Nitrate (NO3-) plays a pivotal role in stimulating lateral root (LR) formation and growth in plants. However, the role of NO3- in modulating rice LR formation and the signalling pathways involved in this process remain unclear. Phenotypic [...] Read more.
Nitrate (NO3-) plays a pivotal role in stimulating lateral root (LR) formation and growth in plants. However, the role of NO3- in modulating rice LR formation and the signalling pathways involved in this process remain unclear. Phenotypic and genetic analyses of rice were used to explore the role of strigolactones (SLs) and auxin in NO3--modulated LR formation in rice. Compared with ammonium (NH4+), NO3- stimulated LR initiation due to higher short-term root IAA levels. However, this stimulation vanished after 7 d, and the LR density was reduced, in parallel with the auxin levels. Application of the exogenous auxin α-naphthylacetic acid to NH4+-treated rice plants promoted LR initiation to levels similar to those under NO3- at 7 d; conversely, the application of the SL analogue GR24 to NH4+-treated rice inhibited LR initiation to levels similar to those under NO3- supply by reducing the root auxin levels at 10 d. D10 and D14 mutations caused loss of sensitivity of the LR formation response to NO3-. The application of NO3- and GR24 downregulated the transcription of PIN-FORMED 2(PIN2), an auxin efflux carrier in roots. LR number and density in pin2 mutant lines were insensitive to NO3- treatment. These results indicate that NO3- modulates LR formation by affecting the auxin response and transport in rice, with the involvement of SLs. Full article
(This article belongs to the Special Issue Root Development and Architecture in Relation to Environmental Conditions)
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18 pages, 3070 KiB  
Article
Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions
by Li Song, Zhenzhi Pan, Lin Chen, Yi Dai, Jinrong Wan, Heng Ye, Henry T. Nguyen, Guozheng Zhang and Huatao Chen
Genes 2020, 11(12), 1520; https://doi.org/10.3390/genes11121520 - 19 Dec 2020
Cited by 22 | Viewed by 3987
Abstract
Alternative splicing (AS) is a common post-transcriptional regulatory mechanism that modulates gene expression to increase proteome diversity. Increasing evidence indicates that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate [...] Read more.
Alternative splicing (AS) is a common post-transcriptional regulatory mechanism that modulates gene expression to increase proteome diversity. Increasing evidence indicates that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate drought responses in soybean remains poorly understood. In this study, we performed a genome-wide analysis of AS events in soybean (Glycine max) roots grown under various drought conditions using the high-throughput RNA-sequencing method, identifying 385, 989, 1429, and 465 AS events that were significantly differentially spliced under very mild drought stress, mild drought stress, severe drought stress, and recovery after severe drought conditions, respectively. Among them, alternative 3′ splice sites and skipped exons were the major types of AS. Overall, 2120 genes that experienced significant AS regulation were identified from these drought-treated root samples. Gene Ontology term analysis indicated that the AS regulation of binding activity has vital roles in the drought response of soybean root. Notably, the genes encoding splicing regulatory factors in the spliceosome pathway and mRNA surveillance pathway were enriched according to the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Splicing regulatory factor-related genes in soybean root also responded to drought stress and were alternatively spliced under drought conditions. Taken together, our data suggest that drought-responsive AS acts as a direct or indirect mode to regulate drought response of soybean roots. With further in-depth research of the function and mechanism of AS in the process of abiotic stress, these results will provide a new strategy for enhancing stress tolerance of plants. Full article
(This article belongs to the Special Issue Root Development and Architecture in Relation to Environmental Conditions)
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Review

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14 pages, 1484 KiB  
Review
Lateral Root Initiation and the Analysis of Gene Function Using Genome Editing with CRISPR in Arabidopsis
by Nick Vangheluwe and Tom Beeckman
Genes 2021, 12(6), 884; https://doi.org/10.3390/genes12060884 - 8 Jun 2021
Cited by 15 | Viewed by 6116
Abstract
Lateral root initiation is a post-embryonic process that requires the specification of a subset of pericycle cells adjacent to the xylem pole in the primary root into lateral root founder cells. The first visible event of lateral root initiation in Arabidopsis is the [...] Read more.
Lateral root initiation is a post-embryonic process that requires the specification of a subset of pericycle cells adjacent to the xylem pole in the primary root into lateral root founder cells. The first visible event of lateral root initiation in Arabidopsis is the simultaneous migration of nuclei in neighbouring founder cells. Coinciding cell cycle activation is essential for founder cells in the pericycle to undergo formative divisions, resulting in the development of a lateral root primordium (LRP). The plant signalling molecule, auxin, is a major regulator of lateral root development; the understanding of the molecular mechanisms controlling lateral root initiation has progressed tremendously by the use of the Arabidopsis model and a continual improvement of molecular methodologies. Here, we provide an overview of the visible events, cell cycle regulators, and auxin signalling cascades related to the initiation of a new LRP. Furthermore, we highlight the potential of genome editing technology to analyse gene function in lateral root initiation, which provides an excellent model to answer fundamental developmental questions such as coordinated cell division, growth axis establishment as well as the specification of cell fate and cell polarity. Full article
(This article belongs to the Special Issue Root Development and Architecture in Relation to Environmental Conditions)
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12 pages, 6384 KiB  
Review
Rooting in the Desert: A Developmental Overview on Desert Plants
by Gwendolyn K. Kirschner, Ting Ting Xiao and Ikram Blilou
Genes 2021, 12(5), 709; https://doi.org/10.3390/genes12050709 - 10 May 2021
Cited by 31 | Viewed by 19510
Abstract
Plants, as sessile organisms, have evolved a remarkable developmental plasticity to cope with their changing environment. When growing in hostile desert conditions, plants have to grow and thrive in heat and drought. This review discusses how desert plants have adapted their root system [...] Read more.
Plants, as sessile organisms, have evolved a remarkable developmental plasticity to cope with their changing environment. When growing in hostile desert conditions, plants have to grow and thrive in heat and drought. This review discusses how desert plants have adapted their root system architecture (RSA) to cope with scarce water availability and poor nutrient availability in the desert soil. First, we describe how some species can survive by developing deep tap roots to access the groundwater while others produce shallow roots to exploit the short rain seasons and unpredictable rainfalls. Then, we discuss how desert plants have evolved unique developmental programs like having determinate meristems in the case of cacti while forming a branched and compact root system that allows efficient water uptake during wet periods. The remote germination mechanism in date palms is another example of developmental adaptation to survive in the dry and hot desert surface. Date palms have also designed non-gravitropic secondary roots, termed pneumatophores, to maximize water and nutrient uptake. Next, we highlight the distinct anatomical features developed by desert species in response to drought like narrow vessels, high tissue suberization, and air spaces within the root cortex tissue. Finally, we discuss the beneficial impact of the microbiome in promoting root growth in desert conditions and how these characteristics can be exploited to engineer resilient crops with a greater ability to deal with salinity induced by irrigation and with the increasing drought caused by global warming. Full article
(This article belongs to the Special Issue Root Development and Architecture in Relation to Environmental Conditions)
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