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Agronomy
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Enhancing Crop Production: Unveiling the Vital Role of Plant Roots...
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Enhancing Crop Production: Unveiling the Vital Role of Plant Roots and Their Dynamic Interplay with Soil and the Environment

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Plant-Crop Biology and Biochemistry".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 2516

Special Issue Editors

Dr. Márcia Carvalho

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Guest Editor
Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-food Production (Inov4Agro), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
Interests: root phenotyping; molecular biology; genetic diversity; abiotic stress; gene expression
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Valdemar Pedrosa Carnide

E-Mail Website
Guest Editor
Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-food Production (Inov4Agro), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
Interests: morphological characterization; genetic diversity; root phenotyping

Special Issue Information

Dear Colleagues,

Roots are an important vegetative organ that have the function of supporting the plant, absorbing water and nutrients, synthesizing and storing organic matter, and stablishing interactions with soil. These functions are fundamental for plant growth, stress adaptation, and crop yield. Root system architecture (RSA) is an underexplored trait, but a highly promising trait to better understand the crops’ ecophysiology and abiotic stress tolerances. This Special Issue focuses on providing valuable insights in root system studies that contribute to a more sustainable agriculture, including anatomy, cytology, biochemistry, physiology, modern methods of molecular biology, genomics, metabolomics, and proteomics studies. Also, other important topics need to be explored, such as root’s role in plant nutrition, the interactions between root, symbiosis and agronomic views using field trials and hydroponic experiments, and root development and pattern formation in diverse species. New approaches of root phenotyping, including 2D, 3D, and hyperspectral root imaging techniques, rhizotrons, and next-generation sequencing methods, will be a valuable contribute for this Special Issue.

This Special Issue on ‘Enhancing Crop Production: Unveiling the Vital Role of Plant Roots and Their Dynamic Interplay with Soil and the Environment’ welcomes the submission of original research papers, opinions, reviews, short communications, and methods that focus on root system architecture and functions, plant phenotyping systems, soil structure and fertility, environmental stress adaptation, innovative agriculture practises, root–microbiome interactions, genetic and molecular bases, etc.

Dr. Márcia Carvalho
Prof. Dr. Valdemar Pedrosa Carnide
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • root system architecture
  • sustainable agriculture
  • root–soil–microbiome
  • soil health
  • environmental impact
  • roots diversity

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Published Papers (3 papers)

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Research

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22 pages, 13145 KiB  
Article
Comparative Transcriptomic Profiling Reveals Divergent Drought-Response Mechanisms Between Resistant and Susceptible Apple Genotype Roots
by Jinjiao Yan, Shicong Wang, Dan Xiao, Mengyao Yang, Bingjie Miao, Bolin Niu, Jiangbo Wang, Jie Wei, Fengwang Ma and Jidi Xu
Agronomy 2025, 15(3), 748; https://doi.org/10.3390/agronomy15030748 - 20 Mar 2025
Viewed by 345
Abstract
Drought stress caused a significant threat to apple growth and production. Although there is an increasing studies concerning the molecular mechanism in apple response to drought, most of these studies focus on the leaves. However, the roots is the first organism to sense [...] Read more.
Drought stress caused a significant threat to apple growth and production. Although there is an increasing studies concerning the molecular mechanism in apple response to drought, most of these studies focus on the leaves. However, the roots is the first organism to sense the drought signal and play important role in drought response. The molecular mechanisms underlying the apple roots in response to drought needs to be further explored. In this study, we conducted a comparative transcriptomic analysis of roots from drought-resistant (Malus prunifolia) and drought-susceptible (Malus hupehensis) apple genotypes under different soil water contents with 60% (control), 30% (mild drought), 10% (moderate drought), and 5% (severe drought). The further Mapman pathways analysis showed that Malus prunifolia exhibited more rapid activation of abscisic acid (ABA) biosynthesis (NCED, PYL) and signaling pathway, as well as the induction of transcription factors (NAC, WRKY, MYB) compare to Malus prunifolia under mild and moderate drought treatments. This might be one of the reasons why Malus prunifolia exhibits greater drought resistance. Furthermore, weighted gene co-expression network analysis (WGCNA) was adopted for the identification of core drought-responsive genes. Notably, three hub genes, ubiquitin-conjugating enzyme 32 (UBC32), basic leucine-zipper 4 (bZIP4), and highly ABA-induced PP2C gene 2 (HAI2), were selected from the different modules, suggesting their vital roles in drought response. Taken together, our results gain insights into the global expression alterations in drought-resistance and susceptible germplasms under different drought conditions and identify some key genes involved in drought response, which is helpful for drought-resistant apple breeding in future. Full article
(This article belongs to the Special Issue Enhancing Crop Production: Unveiling the Vital Role of Plant Roots and Their Dynamic Interplay with Soil and the Environment)
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18 pages, 2778 KiB  
Article
Characterization of Neopestalotiopsis Species Associated with Strawberry Crown Rot in Italy
by Greta Dardani, Ilaria Martino, Francesco Aloi, Cristiano Carli, Roberto Giordano, Davide Spadaro and Vladimiro Guarnaccia
Agronomy 2025, 15(2), 422; https://doi.org/10.3390/agronomy15020422 - 7 Feb 2025
Cited by 1 | Viewed by 1230
Abstract
Different Pestalotiopsis-like species have been reported in strawberry worldwide, as agents of leaf spot, root rot, and crown rot. The identification of Pestalotiopsis-like fungi is based on both molecular and morphological analyses to discriminate between species and clarify phylogenetic relationships. Recent [...] Read more.
Different Pestalotiopsis-like species have been reported in strawberry worldwide, as agents of leaf spot, root rot, and crown rot. The identification of Pestalotiopsis-like fungi is based on both molecular and morphological analyses to discriminate between species and clarify phylogenetic relationships. Recent studies have provided robust multi-locus analyses, which reclassified most Pestalotiopsis-like isolates associated with strawberry root and crown rot diseases as Neopestalotiopsis spp. Numerous disease outbreaks have been observed in strawberry fields in Italy in recent years, showing that Neopestalotiopsis is an emerging pathogen. A survey was conducted in Northern Italy during 2022–2023 to investigate the diversity and distribution of Neopestalotiopsis species. Morphological and phylogenetic characterization, based on ITS, tef1 and tub2, led to the identification of four species: Neopestalotiopsis rosae, N. iranensis, N. hispanica (syn. vaccinii) and N. scalabiensis. Based on our results from multi-locus phylogenetic analysis, N. hispanica and N. vaccinii were grouped in the same cluster; thus, they were confirmed to be the same species. Pathogenicity tests with representative isolates of each species were conducted on strawberry ‘Portola’ transplants. All isolates were shown to be wound pathogens in strawberry, causing crown rot, and were successfully re-isolated. Neopestalotiopsis rosae was confirmed to be the most dominant and virulent species associated with these symptoms, as well as the most dominant among the obtained isolates. To the best of our knowledge, this work represents the first report of N. scalabiensis being associated with the crown rot of strawberry in Italy and the first report of N. iranensis in association with the crown rot of strawberry worldwide. Full article
(This article belongs to the Special Issue Enhancing Crop Production: Unveiling the Vital Role of Plant Roots and Their Dynamic Interplay with Soil and the Environment)
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Review

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15 pages, 1180 KiB  
Review
Root Phenotyping: A Contribution to Understanding Drought Stress Resilience in Grain Legumes
by Patrícia Afonso, Isaura Castro, Pedro Couto, Fernanda Leal, Valdemar Carnide, Eduardo Rosa and Márcia Carvalho
Agronomy 2025, 15(4), 798; https://doi.org/10.3390/agronomy15040798 - 24 Mar 2025
Viewed by 599
Abstract
Global climate change predictions point to an increase in the frequency of droughts and floods, which are a huge challenge to food production. During crop evolution, different mechanisms for drought resilience have emerged, and studies suggest that roots can be an important key [...] Read more.
Global climate change predictions point to an increase in the frequency of droughts and floods, which are a huge challenge to food production. During crop evolution, different mechanisms for drought resilience have emerged, and studies suggest that roots can be an important key in understanding these mechanisms. However, knowledge is still scarce, being fundamental to its exploitation. Plant-based protein, especially grain legume crops, will be crucial in meeting the demand for affordable and healthy food due to their high protein content. In addition, grain legumes have the unique ability for biological nitrogen fixation (BNF) through symbiosis with bacteria, which contributes to sustainable agriculture. The exploitation of root phenotyping techniques in grain legumes is an important step toward understanding their drought resilience mechanisms and selecting more resilient genotypes. Different methodologies are available for root phenotyping, including the paper pouch approach, rhizotrons and the semi-hydroponic system. Additionally, different imaging techniques have been employed to assess root traits. This review provides an overview of the root system architecture (RSA) of grain legumes, its role in drought stress resilience and the phenotyping approaches useful for the identification of accessions resilient to water stress. Consequently, this knowledge will be important in mitigating the effects of climate change and improving grain legume production. Full article
(This article belongs to the Special Issue Enhancing Crop Production: Unveiling the Vital Role of Plant Roots and Their Dynamic Interplay with Soil and the Environment)
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