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Plants
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Omic Sciences in the Fields of Crop Quality and Sustainability
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Omic Sciences in the Fields of Crop Quality and Sustainability

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 19811

Special Issue Editors

Dr. Bhakti Prinsi

E-Mail Website
Guest Editor
Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (DiSAA), Università degli Studi di Milano, 20122 Milano, Italy
Interests: plant proteomics; plant metabolomics; plant physiology; plant biochemistry; plant mineral nutrition; secondary metabolism; plant abiotic stress; nutraceutical properties
Dr. Luigi Lucini

E-Mail Website
Guest Editor
Department for Sustainable Food Processes, Università Cattolica Del Sacro Cuore, 29122 Piacenza, Italy
Interests: food profiling; functional components; food authenticity; traceability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Improvements in agriculture sustainability, food security and crop quality represent key challenges that must be undertaken for the future of society and ecosystems and in response to climate change. These aspects are closely related to plant adaptations to agro-environmental conditions by physiological and biochemical responses that require extensive coordination of metabolic processes and communication among metabolic pathways. Omic sciences, such as genomics, transcriptomics, proteomics and metabolomics, are disciplines intrinsically dedicated to deciphering the complexity and the dynamic plasticity of plant systems in order to discover metabolic networks and to individuate key factors in plant responses to endogenous and environmental stimuli. They gained popularity thanks to their inherent holistic nature, allowing investigating plant metabolism in an untargeted manner. Nonetheless, proteomic and metabolomic profiles represent very informative tools for evaluating quality traits, nutritional values and functional properties of plant-based foods.

In recent years, omics approaches have been increasingly applied to non-model plant species, thus including crops. This Special Issue of Plants aims to gather new knowledge and novel perspectives provided by omic approaches applied in the study of cultivated plant species, including cereals, legumes, horticultural crops and fruit trees. This Special Issue is open to articles (original research papers, perspectives, reviews and methods) related to plant genomics, transcriptomics, proteomics, metabolomics and phenomics, with special interest in biochemistry and physiology of plant mineral nutrition, plant responses to abiotic and biotic factors, root–soil interactions, novel strategies for crop management (including biostimulants), shaping of secondary metabolism, nutraceutical and functional properties, sustainability and plant–environment interactions.

Dr. Bhakti Prinsi
Dr. Luigi Lucini
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • genomics
  • transcriptomics
  • plant proteomics
  • plant metabolomics
  • metabolic networks
  • crop quality
  • sustainability
  • plant mineral nutrition
  • abiotic and biotic stresses
  • environmental stimuli and plant biochemistry
  • novel agricultural practices
  • xenobiotic compounds
  • rhizosphere
  • biostimulants
  • nutraceutical properties
  • secondary metabolism

Published Papers (5 papers)

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Research

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17 pages, 360 KiB  
Article
Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize
by Soumeya Rida, Oula Maafi, Ana López-Malvar, Pedro Revilla, Meriem Riache and Abderahmane Djemel
Plants 2021, 10(9), 1786; https://doi.org/10.3390/plants10091786 - 27 Aug 2021
Cited by 10 | Viewed by 2687
Abstract
Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling [...] Read more.
Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance. Full article
(This article belongs to the Special Issue Omic Sciences in the Fields of Crop Quality and Sustainability)
16 pages, 3722 KiB  
Article
Genome-Wide Identification and Functional Investigation of 1-Aminocyclopropane-1-carboxylic Acid Oxidase (ACO) Genes in Cotton
by Hengling Wei, Yujun Xue, Pengyun Chen, Pengbo Hao, Fei Wei, Lu Sun and Yonglin Yang
Plants 2021, 10(8), 1699; https://doi.org/10.3390/plants10081699 - 18 Aug 2021
Cited by 9 | Viewed by 2514
Abstract
ACO is one of the rate-limiting enzymes in the biosynthesis of ethylene, and it plays a critical role in the regulation of plant growth and development. However, the function of ACO genes in cotton is not well studied. In this study, a total [...] Read more.
ACO is one of the rate-limiting enzymes in the biosynthesis of ethylene, and it plays a critical role in the regulation of plant growth and development. However, the function of ACO genes in cotton is not well studied. In this study, a total of 332 GhACOs, 187 GaACOs, and 181 GrACOs were identified in G. hirsutum, G. arboretum, and G. raimondii, respectively. Gene duplication analysis showed that whole-genome duplication (WGD) and tandem duplication were the major forces driving the generation of cotton ACO genes. In the promoters of GhACOs, there were cis-acting elements responding to stress, phytohormones, light, and circadian factors, indicating the possible involvement of GhACOs in these processes. Expression and co-expression analyses illustrated that most GhACOs were not only widely expressed in various tissues but also coexpressed with other genes in response to salt and drought stress. GhACO106_At overexpression in Arabidopsis promoted flowering and increased salt tolerance. These results provide a comprehensive overview of the ACO genes of cotton and lay the foundation for subsequent functional studies of these genes. Full article
(This article belongs to the Special Issue Omic Sciences in the Fields of Crop Quality and Sustainability)
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17 pages, 1094 KiB  
Article
Biochemical and Proteomic Changes in the Roots of M4 Grapevine Rootstock in Response to Nitrate Availability
by Bhakti Prinsi, Chiara Muratore and Luca Espen
Plants 2021, 10(4), 792; https://doi.org/10.3390/plants10040792 - 17 Apr 2021
Cited by 1 | Viewed by 2021
Abstract
In agricultural soils, nitrate (NO3−) is the major nitrogen (N) nutrient for plants, but few studies have analyzed molecular and biochemical responses involved in its acquisition by grapevine roots. In viticulture, considering grafting, NO3− acquisition is strictly dependent [...] Read more.
In agricultural soils, nitrate (NO3−) is the major nitrogen (N) nutrient for plants, but few studies have analyzed molecular and biochemical responses involved in its acquisition by grapevine roots. In viticulture, considering grafting, NO3− acquisition is strictly dependent on rootstock. To improve the knowledge about N nutrition in grapevine, this study analyzed biochemical and proteomic changes induced by, NO3− availability, in a hydroponic system, in the roots of M4, a recently selected grapevine rootstock. The evaluation of biochemical parameters, such as NO3−, sugar and amino acid contents in roots, and the abundance of nitrate reductase, allowed us to define the time course of the metabolic adaptations to NO3− supply. On the basis of these results, the proteomic analysis was conducted by comparing the root profiles in N-starved plants and after 30 h of NO3− resupply. The analysis quantified 461 proteins, 26% of which differed in abundance between conditions. Overall, this approach highlighted, together with an increased N assimilatory metabolism, a concomitant rise in the oxidative pentose phosphate pathway and glycolysis, needed to fulfill the redox power and carbon skeleton demands, respectively. Moreover, a wide modulation of protein and amino acid metabolisms and changes of proteins involved in root development were observed. Finally, some results open new questions about the importance of redox-related post-translational modifications and of NO3− availability in modulating the dialog between root and rhizosphere. Full article
(This article belongs to the Special Issue Omic Sciences in the Fields of Crop Quality and Sustainability)
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17 pages, 3580 KiB  
Article
Intraspecific Variability Largely Affects the Leaf Metabolomics Response to Isosmotic Macrocation Variations in Two Divergent Lettuce (Lactuca sativa L.) Varieties
by Giandomenico Corrado, Luigi Lucini, Begoña Miras-Moreno, Leilei Zhang, Christophe El-Nakhel, Giuseppe Colla and Youssef Rouphael
Plants 2021, 10(1), 91; https://doi.org/10.3390/plants10010091 - 5 Jan 2021
Cited by 4 | Viewed by 2280
Abstract
Mineral elements are essential for plant growth and development and strongly affect crop yield and quality. To cope with an everchanging environment, plants have developed specific responses to combined nutrient variations. In this work, we investigated the effects of multifactorial treatments with three [...] Read more.
Mineral elements are essential for plant growth and development and strongly affect crop yield and quality. To cope with an everchanging environment, plants have developed specific responses to combined nutrient variations. In this work, we investigated the effects of multifactorial treatments with three macrocations (K, Ca, and Mg) on lettuce (Lactuca sativa L.) varieties that strongly diverge in leaf pigmentation (full red or green). Specifically, we monitored main leaf parameters and metabolomics profiles of hydroponically grown plants fed with isosmotic nutrient solutions that have different proportions of macroelements. The result revealed a high biochemical plasticity of lettuce, significantly affected by the genotype, the nutrient solution, and their interaction. Our work also provided evidence and insights into the different intraspecific responses to multifactorial variation of macrocations, with two varieties having distinct strategies to metabolically respond to nutrient variation. Overall, plant adaptive mechanisms increased the phytochemical diversity between the varieties both among and within the main classes of plant secondary metabolites. Finally, our work also implies that the interaction of a pre-existing phytochemical diversity with the management of multiple mineral elements can offer added health-related benefits to the edible product specific to the variety. Full article
(This article belongs to the Special Issue Omic Sciences in the Fields of Crop Quality and Sustainability)
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Review

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26 pages, 2289 KiB  
Review
Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective
by Chiara Muratore, Luca Espen and Bhakti Prinsi
Plants 2021, 10(4), 681; https://doi.org/10.3390/plants10040681 - 1 Apr 2021
Cited by 40 | Viewed by 9198
Abstract
Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering [...] Read more.
Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H+-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies. Full article
(This article belongs to the Special Issue Omic Sciences in the Fields of Crop Quality and Sustainability)
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