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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 March 2023) | Viewed by 22030

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Dr. Silvia Celletti

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Department of Life Sciences, University of Siena, 53100 Siena, Italy
Interests: physiological, biochemical, and molecular responses of plants to abiotic stresses such as deficiencies of natural resources (e.g., nutrients and water) or salinity; analysis of the effects of biofertilizers (i.e., biochar and wood distillate) on the soil–plant system; the use of solid and liquid byproducts of hydrothermal carbonization (HTC) in soilless culture systems; analysis of the impact of bioplastics on plant yield and soil quality
Special Issues, Collections and Topics in MDPI journals

Dr. Stefania Astolfi

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Collection Editor

Department of Agricultural and Forest Sciences (DAFNE), University of Tuscia, Via S. C. de Lellis, 01100 Viterbo, Italy
Interests: plant physiological response to mineral deficiencies (mainly S and Fe); problems related to soil contamination with cadmium; the role of membrane activities in the plant\'s response to stress and variations in nutrient availability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Topical Collection aims to provide a comprehensive overview of recent advances in plant molecular science in Italy by inviting contributions from Italian research institutes/laboratories that consolidate our understanding of this area. Potential topics regarding plants include but are not limited to biophysics, biochemistry, and molecular biology; cell biology; physiology; genomics/epigenomics; proteomics and metabolomics; bioactive phytochemicals; plant–microbe interactions; developmental biology; pests and diseases; synthetic biology; computational biology; and the development of new technologies in plant sciences. In this Topical Collection, we welcome submissions in the form of comprehensive reviews or new research advancements in all the abovementioned areas.

Dr. Silvia Celletti
Dr. Stefania Astolfi
Collection Editors

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Published Papers (7 papers)

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Research

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23 pages, 10468 KiB

Open AccessArticle

Prunus Knotted-like Genes: Genome-Wide Analysis, Transcriptional Response to Cytokinin in Micropropagation, and Rootstock Transformation

by Giulio Testone, Emilia Caboni, Simone D’Angeli, Maria Maddalena Altamura and Donato Giannino

Int. J. Mol. Sci. 2023, 24(3), 3046; https://doi.org/10.3390/ijms24033046 - 3 Feb 2023

Cited by 1 | Viewed by 2124

Abstract

Knotted1-like homeobox (KNOX) transcription factors are involved in plant development, playing complex roles in aerial organs. As Prunus species include important fruit tree crops of Italy, an exhaustive investigation of KNOX genes was performed using genomic and RNA-seq meta-analyses. Micropropagation is an essential technology for rootstock multiplication; hence, we investigated KNOX transcriptional behavior upon increasing 6-benzylaminopurine (BA) doses and the effects on GF677 propagules. Moreover, gene function in Prunus spp. was assessed by Gisela 6 rootstock transformation using fluorescence and peach KNOX transgenes. Based on ten Prunus spp., KNOX proteins fit into I-II-M classes named after Arabidopsis. Gene number, class member distribution, and chromosome positions were maintained, and exceptions supported the diversification of Prunus from Cerasus subgenera, and that of Armeniaca from the other sections within Prunus. Cytokinin (CK) cis-elements occurred in peach and almond KNOX promoters, suggesting a BA regulatory role in GF677 shoot multiplication as confirmed by KNOX expression variation dependent on dose, time, and interaction. The tripled BA concentration exacerbated stress, altered CK perception genes, and modified KNOX transcriptions, which are proposed to concur in in vitro anomalies. Finally, Gisela 6 transformation efficiency varied (2.6–0.6%) with the genetic construct, with 35S:GFP being more stable than 35S:KNOPE1 lines, which showed leaf modification typical of KNOX overexpression. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Italy)

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16 pages, 1512 KiB

Open AccessArticle

CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions

by Giulia Lopatriello, Simone Maestri, Massimiliano Alfano, Roberto Papa, Valerio Di Vittori, Luca De Antoni, Elisa Bellucci, Alice Pieri, Elena Bitocchi, Massimo Delledonne and Marzia Rossato

Int. J. Mol. Sci. 2023, 24(2), 1076; https://doi.org/10.3390/ijms24021076 - 5 Jan 2023

Cited by 2 | Viewed by 3910

Abstract

Complete and accurate identification of genetic variants associated with specific phenotypes can be challenging when there is a high level of genomic divergence between individuals in a study and the corresponding reference genome. We have applied the Cas9-mediated enrichment coupled to nanopore sequencing to perform a targeted de novo assembly and accurately reconstruct a genomic region of interest. This approach was used to reconstruct a 250-kbp target region on chromosome 5 of the common bean genome (Phaseolus vulgaris) associated with the shattering phenotype. Comparing a non-shattering cultivar (Midas) with the reference genome revealed many single-nucleotide variants and structural variants in this region. We cut five 50-kbp tiled sub-regions of Midas genomic DNA using Cas9, followed by sequencing on a MinION device and de novo assembly, generating a single contig spanning the whole 250-kbp region. This assembly increased the number of Illumina reads mapping to genes in the region, improving their genotypability for downstream analysis. The Cas9 tiling approach for target enrichment and sequencing is a valuable alternative to whole-genome sequencing for the assembly of ultra-long regions of interest, improving the accuracy of downstream genotype–phenotype association analysis. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Italy)

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17 pages, 1468 KiB

Open AccessArticle

CRISPR/Cas9-Based Knock-Out of the PMR4 Gene Reduces Susceptibility to Late Blight in Two Tomato Cultivars

by Ruiling Li, Alex Maioli, Zhe Yan, Yuling Bai, Danila Valentino, Anna Maria Milani, Valerio Pompili, Cinzia Comino, Sergio Lanteri, Andrea Moglia and Alberto Acquadro

Int. J. Mol. Sci. 2022, 23(23), 14542; https://doi.org/10.3390/ijms232314542 - 22 Nov 2022

Cited by 8 | Viewed by 3399

Abstract

Phytophthora infestans, the causal agent of late blight (LB) in tomato (Solanum lycopersicum L.), is a devastating disease and a serious concern for plant productivity. The presence of susceptibility (S) genes in plants facilitates pathogen proliferation; thus, disabling these genes may help provide a broad-spectrum and durable type of tolerance/resistance. Previous studies on Arabidopsis and tomato have highlighted that knock-out mutants of the PMR4 susceptibility gene are tolerant to powdery mildew. Moreover, PMR4 knock-down in potato has been shown to confer tolerance to LB. To verify the same effect in tomato in the present study, a CRISPR–Cas9 vector containing four single guide RNAs (sgRNAs: sgRNA1, sgRNA6, sgRNA7, and sgRNA8), targeting as many SlPMR4 regions, was introduced via Agrobacterium-tumefaciens-mediated transformation into two widely grown Italian tomato cultivars: ‘San Marzano’ (SM) and ‘Oxheart’ (OX). Thirty-five plants (twenty-six SM and nine OX) were selected and screened to identify the CRISPR/Cas9-induced mutations. The different sgRNAs caused mutation frequencies ranging from 22.1 to 100% and alternatively precise insertions (sgRNA6) or deletions (sgRNA7, sgRNA1, and sgRNA8). Notably, sgRNA7 induced in seven SM genotypes a −7 bp deletion in the homozygous status, whereas sgRNA8 led to the production of fifteen SM genotypes with a biallelic mutation (−7 bp and −2 bp). Selected edited lines were inoculated with P. infestans, and four of them, fully knocked out at the PMR4 locus, showed reduced disease symptoms (reduction in susceptibility from 55 to 80%) compared to control plants. The four SM lines were sequenced using Illumina whole-genome sequencing for deeper characterization without exhibiting any evidence of mutations in the candidate off-target regions. Our results showed, for the first time, a reduced susceptibility to Phytophtora infestans in pmr4 tomato mutants confirming the role of KO PMR4 in providing broad-spectrum protection against pathogens. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Italy)

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19 pages, 2000 KiB

Open AccessArticle

Intra-Laboratory Evaluation of DNA Extraction Methods and Assessment of a Droplet Digital PCR for the Detection of Xanthomonas citri pv. citri on Different Citrus Species

by Nicoletta Pucci, Valeria Scala, Giuseppe Tatulli, Alessia L’Aurora, Simone Lucchesi, Manuel Salustri and Stefania Loreti

Int. J. Mol. Sci. 2022, 23(9), 4975; https://doi.org/10.3390/ijms23094975 - 29 Apr 2022

Cited by 2 | Viewed by 2250

Abstract

Xanthomonas citri pv. citri (Xcc) and X. citri pv. aurantifolii (Xca), causal agents of citrus bacterial canker, are both regulated by the European Union to prevent their introduction. Xcc is responsible for severe outbreaks of citrus production worldwide, therefore, a prompt and reliable detection is advisable for the early detection of this bacterium either in symptomatic or asymptomatic plant material. The current EPPO (European and Mediterranean Plant Protection Organization) diagnostic protocol, PM 7/44(1), includes several diagnostic tests even if new assays have been developed in the latter years for which validation data are needed. Recently, a test performance study was organized within the Valitest EU Project to validate Xcc diagnostic methods and provide evidence on the most reliable assays; however, the influence of DNA extraction methods (DEM) on the reliability of the detection has never been assessed. In this study we evaluate four different DEM, by following two different approaches: (i) a comparison by real-time PCR standard curves of bacterial DNA versus bacterial DNA added to plant DNA (lemon, leaves and fruit; orange fruit); and (ii) the evaluation of performance criteria of spiked samples (plant extract added with ten-fold diluted bacterial suspensions at known concentrations). Droplet digital PCR is developed and compared with real-time PCR, as the detection method. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Italy)

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22 pages, 3243 KiB

Open AccessArticle

Isoprene Emission Influences the Proteomic Profile of Arabidopsis Plants under Well-Watered and Drought-Stress Conditions

by Ilaria Mancini, Guido Domingo, Marcella Bracale, Francesco Loreto and Susanna Pollastri

Int. J. Mol. Sci. 2022, 23(7), 3836; https://doi.org/10.3390/ijms23073836 - 30 Mar 2022

Cited by 5 | Viewed by 2376

Abstract

Isoprene is a small lipophilic molecule synthesized in plastids and abundantly released into the atmosphere. Isoprene-emitting plants are better protected against abiotic stresses, but the mechanism of action of isoprene is still under debate. In this study, we compared the physiological responses and proteomic profiles of Arabidopsis which express the isoprene synthase (ISPS) gene and emit isoprene with those of non-emitting plants under both drought-stress (DS) and well-watered (WW) conditions. We aimed to investigate whether isoprene-emitting plants displayed a different proteomic profile that is consistent with the metabolic changes already reported. Only ISPS DS plants were able to maintain the same photosynthesis and fresh weight of WW plants. LC–MS/MS-based proteomic analysis revealed changes in protein abundance that were dependent on the capacity for emitting isoprene in addition to those caused by the DS. The majority of the proteins changed in response to the interaction between DS and isoprene emission. These include proteins that are associated with the activation of secondary metabolisms leading to ABA, trehalose, and proline accumulations. Overall, our proteomic data suggest that isoprene exerts its protective mechanism at different levels: under drought stress, isoprene affects the abundance of chloroplast proteins, confirming a strong direct or indirect antioxidant action and also modulates signaling and hormone pathways, especially those controlling ABA synthesis. Unexpectedly, isoprene also alters membrane trafficking. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Italy)

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Review

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30 pages, 1759 KiB

Open AccessReview

The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives

by Luca Nerva, Lorenza Dalla Costa, Angelo Ciacciulli, Silvia Sabbadini, Vera Pavese, Luca Dondini, Elisa Vendramin, Emilia Caboni, Irene Perrone, Andrea Moglia, Sara Zenoni, Vania Michelotti, Sabrina Micali, Stefano La Malfa, Alessandra Gentile, Stefano Tartarini, Bruno Mezzetti, Roberto Botta, Ignazio Verde, Riccardo Velasco, Mickael Arnaud Malnoy and Concetta Licciardello Show full author list Hide full author list

Int. J. Mol. Sci. 2023, 24(2), 977; https://doi.org/10.3390/ijms24020977 - 4 Jan 2023

Cited by 5 | Viewed by 4535

Abstract

Climate change is deeply impacting the food chain production, lowering quality and yield. In this context, the international scientific community has dedicated many efforts to enhancing resilience and sustainability in agriculture. Italy is among the main European producers of several fruit trees; therefore, national research centers and universities undertook several initiatives to maintain the specificity of the ‘Made in Italy’ label. Despite their importance, fruit crops are suffering from difficulties associated with the conventional breeding approaches, especially in terms of financial commitment, land resources availability, and long generation times. The ‘new genomic techniques’ (NGTs), renamed in Italy as ‘technologies for assisted evolution’ (TEAs), reduce the time required to obtain genetically improved cultivars while precisely targeting specific DNA sequences. This review aims to illustrate the role of the Italian scientific community in the use of NGTs, with a specific focus on Citrus, grapevine, apple, pear, chestnut, strawberry, peach, and kiwifruit. For each crop, the key genes and traits on which the scientific community is working, as well as the technological improvements and advancements on the regeneration of local varieties, are presented. Lastly, a focus is placed on the legal aspects in the European and in Italian contexts. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Italy)

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17 pages, 1416 KiB

Open AccessReview

The Italian Research on the Molecular Characterization of Maize Kernel Development

by Gabriella Consonni, Giulia Castorina and Serena Varotto

Int. J. Mol. Sci. 2022, 23(19), 11383; https://doi.org/10.3390/ijms231911383 - 27 Sep 2022

Cited by 2 | Viewed by 2141

Abstract

The study of the genetic control of maize seed development and seed-related pathways has been one of the most important themes approached by the Italian scientific community. Maize has always attracted the interest of the Italian community of agricultural genetics since its beginning, as some of its founders based their research projects on and developed their “schools” by adopting maize as a reference species. Some of them spent periods in the United States, where maize was already becoming a model system, to receive their training. In this manuscript we illustrate the research work carried out in Italy by different groups that studied maize kernels and underline their contributions in elucidating fundamental aspects of caryopsis development through the characterization of maize mutants. Since the 1980s, most of the research projects aimed at the comprehension of the genetic control of seed development and the regulation of storage products’ biosyntheses and accumulation, and have been based on forward genetics approaches. We also document that for some decades, Italian groups, mainly based in Northern Italy, have contributed to improve the knowledge of maize genomics, and were both fundamental for further international studies focused on the correct differentiation and patterning of maize kernel compartments and strongly contributed to recent advances in maize research. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Italy)

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