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Plants
Special Issues
Root Development and Adaptations
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Root Development and Adaptations

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Physiology and Metabolism".

Deadline for manuscript submissions: closed (31 August 2025) | Viewed by 8665

Special Issue Editor

Dr. Konstantinos E. Vlachonasios

E-Mail Website
Guest Editor
Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
Interests: histone acetylation; plant development; plant molecular genetics; epigenetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants have root systems that not only anchor them to the soil, but also absorb nutrients and water required for their growth. Through evolution, plant root systems have been able to adapt to various environmental cues, such as soil composition, competition with other root systems, and abiotic and biotic stresses, as well as interact with beneficial organisms in the rhizosphere. Root architecture and responses to different environmental conditions are diverse and phenotypically variable. Using Arabidopsis as a model system has improved our understanding of molecular signaling involved in root apical meristem action, pattern formation, root growth rate, and the degree of branching. Given the actual root system diversity and complexity inherent among plant species, new discoveries have enriched our understanding of several aspects of control in root development in diverse species and their role within plant adaptation.

Dr. Konstantinos E. Vlachonasios
Guest Editor

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Keywords

  • root development
  • root apical meristem
  • gravitropism
  • root branching
  • root pattern formation
  • root architecture
  • gene expression
  • molecular mechanisms
  • epigenetic modifications
  • abiotic stress responses
  • rhizosphere
  • biotic stress responses

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Published Papers (4 papers)

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Research

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16 pages, 3799 KB  
Article
Phylogenetic Divergence and Domestication Jointly Shape the Tomato Root Microbiome
by Grigorios Thomaidis, Georgios Boutzikas, Athanasios Alexopoulos and Christos Zamioudis
Plants 2026, 15(1), 163; https://doi.org/10.3390/plants15010163 - 5 Jan 2026
Cited by 1 | Viewed by 924
Abstract
Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and [...] Read more.
Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and crop improvement. Using multi-region 16S rRNA sequencing, we compared the rhizosphere and endosphere bacterial communities of cultivated tomato (Solanum lycopersicum cv. Moneymaker) with six wild relatives (S. pimpinellifolium, S. huaylasense, S. peruvianum, S. chilense, S. habrochaites, and S. pennellii) spanning the main wild lineages within Solanum sect. Lycopersicon. Bacterial community structure in the rhizosphere was broadly conserved across all seven hosts, and diversity remained comparable among genotypes. Despite this overall stability, the rhizosphere microbiomes were ordered along a gradient consistent with host phylogeny, with Moneymaker clustering near S. pimpinellifolium, the four green-fruited Eriopersicon species forming a cohesive block, and S. pennellii occupying the most distinct position. Within this hierarchy, individual hosts showed specific recruitment preferences, including enrichment of Streptomycetaceae in S. pimpinellifolium, Bacillaceae in S. chilense, and contrasting patterns of nitrifiers among Eriopersicon species and S. pennellii. Differential abundance testing in the endosphere revealed consistent reductions in several bacterial families in wild accessions, alongside the enrichment of Streptomycetaceae and Rhodobiaceae in multiple wild species. Overall, our study suggests that domestication exerted a modest effect on tomato root microbiomes, while wild relatives retained microbial association traits that could be harnessed in microbiome-informed breeding to improve resilience in cultivated tomato. Full article
(This article belongs to the Special Issue Root Development and Adaptations)
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17 pages, 3891 KB  
Article
Xylooligosaccharides Enhance Lettuce Root Morphogenesis and Growth Dynamics
by Meng Kong, Jiuxing He, Juan Wang, Min Gong, Qiuyan Huo, Wenbo Bai, Jiqing Song, Jianbin Song, Wei Han and Guohua Lv
Plants 2024, 13(12), 1699; https://doi.org/10.3390/plants13121699 - 19 Jun 2024
Cited by 3 | Viewed by 1980
Abstract
Enhancing root development is pivotal for boosting crop yield and augmenting stress resilience. In this study, we explored the regulatory effects of xylooligosaccharides (XOSs) on lettuce root growth, comparing their impact with that of indole-3-butyric acid potassium salt (IBAP). Treatment with XOS led [...] Read more.
Enhancing root development is pivotal for boosting crop yield and augmenting stress resilience. In this study, we explored the regulatory effects of xylooligosaccharides (XOSs) on lettuce root growth, comparing their impact with that of indole-3-butyric acid potassium salt (IBAP). Treatment with XOS led to a substantial increase in root dry weight (30.77%), total root length (29.40%), volume (21.58%), and surface area (25.44%) compared to the water-treated control. These enhancements were on par with those induced by IBAP. Comprehensive phytohormone profiling disclosed marked increases in indole-3-acetic acid (IAA), zeatin riboside (ZR), methyl jasmonate (JA-ME), and brassinosteroids (BRs) following XOS application. Through RNA sequencing, we identified 3807 differentially expressed genes (DEGs) in the roots of XOS-treated plants, which were significantly enriched in pathways associated with manganese ion homeostasis, microtubule motor activity, and carbohydrate metabolism. Intriguingly, approximately 62.7% of the DEGs responsive to XOS also responded to IBAP, underscoring common regulatory mechanisms. However, XOS uniquely influenced genes related to cutin, suberine, and wax biosynthesis, as well as plant hormone signal transduction, hinting at novel mechanisms of stress tolerance. Prominent up-regulation of genes encoding beta-glucosidase and beta-fructofuranosidase highlights enhanced carbohydrate metabolism as a key driver of XOS-induced root enhancement. Collectively, these results position XOS as a promising, sustainable option for agricultural biostimulation. Full article
(This article belongs to the Special Issue Root Development and Adaptations)
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Review

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18 pages, 656 KB  
Review
Roles of Histone Acetylation and Deacetylation in Root Development
by Christos Tersenidis, Stylianos Poulios, George Komis, Emmanuel Panteris and Konstantinos Vlachonasios
Plants 2024, 13(19), 2760; https://doi.org/10.3390/plants13192760 - 1 Oct 2024
Cited by 2 | Viewed by 3130
Abstract
Roots are usually underground plant organs, responsible for anchoring to the soil, absorbing water and nutrients, and interacting with the rhizosphere. During root development, roots respond to a variety of environmental signals, contributing to plant survival. Histone post-translational modifications play essential roles in [...] Read more.
Roots are usually underground plant organs, responsible for anchoring to the soil, absorbing water and nutrients, and interacting with the rhizosphere. During root development, roots respond to a variety of environmental signals, contributing to plant survival. Histone post-translational modifications play essential roles in gene expression regulation, contributing to plant responses to environmental cues. Histone acetylation is one of the most studied post-translational modifications, regulating numerous genes involved in various biological processes, including development and stress responses. Although the effect of histone acetylation on plant responses to biotic and abiotic stimuli has been extensively reviewed, no recent reviews exist focusing on root development regulation by histone acetylation. Therefore, this review brings together all the knowledge about the impact of histone acetylation on root development in several plant species, mainly focusing on Arabidopsis thaliana. Here, we summarize the role of histone acetylation and deacetylation in numerous aspects of root development, such as stem cell niche maintenance, cell division, expansion and differentiation, and developmental zone determination. We also emphasize the gaps in current knowledge and propose new perspectives for research toward deeply understanding the role of histone acetylation in root development. Full article
(This article belongs to the Special Issue Root Development and Adaptations)
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Other

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8 pages, 1287 KB  
Brief Report
Comparing Results from 2-D and 3-D Phenotyping Systems for Soybean Root System Architecture: A ‘Comparison of Apples and Oranges’?
by François Belzile, Waldiodio Seck, Prabhjot Sanghera, Liwen Han and Pierre Dutilleul
Plants 2024, 13(23), 3369; https://doi.org/10.3390/plants13233369 - 29 Nov 2024
Cited by 1 | Viewed by 1348
Abstract
Typically, root system architecture (RSA) is not visible, and realistically, high-throughput methods for RSA trait phenotyping should capture key features of developing root systems in solid substrates in 3D. In a published 2-D study using thin rhizoboxes, vermiculite as a growing medium, and [...] Read more.
Typically, root system architecture (RSA) is not visible, and realistically, high-throughput methods for RSA trait phenotyping should capture key features of developing root systems in solid substrates in 3D. In a published 2-D study using thin rhizoboxes, vermiculite as a growing medium, and photography for imaging, triplicates of 137 soybean cultivars were phenotyped for their RSA. In the transition to 3-D work using X-ray computed tomography (CT) scanning and mineral soil, two research questions are addressed: (1) how different is the soybean RSA characterization between the two phenotyping systems; and (2) is a direct comparison of the results reliable? Prior to a full-scale study in 3D, we grew, in pots filled with sand, triplicates of the Casino and OAC Woodstock cultivars that had shown the most contrasting RSAs in the 2-D study, and CT scanned them at the V1 vegetative stage of development of the shoots. Differences between soybean cultivars in RSA traits, such as total root length and fractal dimension (FD), observed in 2D, can change in 3D. In particular, in 2D, the mean FD values are 1.48 ± 0.16 (OAC Woodstock) vs. 1.31 ± 0.16 (Casino), whereas in 3D, they are 1.52 ± 0.14 (OAC Woodstock) vs. 1.24 ± 0.13 (Casino), indicating variations in RSA complexity. Full article
(This article belongs to the Special Issue Root Development and Adaptations)
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