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Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era

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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 (30 April 2021) | Viewed by 46483

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Special Issue Editors

Dr. Claudio Pugliesi

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Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
Interests: carotenoid biosynthesis; cell totipotency; development of axillary meristem; disease resistance; flower symmetry; nanotechnology; plant hormones; RNA silencing
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Dr. Marco Fambrini

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Guest Editor

Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
Interests: carotenoid biosynthesis; cell totipotency; plant architecture; disease resistance; flower development; nanotechnology; plant hormones; RNA silencing
Special Issues, Collections and Topics in MDPI journals

Dr. Susanna Pecchia

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Guest Editor

Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
Interests: plant pathology; biology and phylogeny of fungal plant pathogens; molecular diagnostics; sustainable crop protection; nanotechnology; RNA silencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As the increasing food demand and climate changes are the main challenges facing agriculture, there is an urgent need to find new solutions for a sustainable crops development. In this scenario, new molecular approaches and biotechnology tools for better production, improved nutrient content and disease resistance crops are needed. In this context, we wish to point out the importance of two aspects: (1) the key role of developmental biology into crop domestication and production efficiency improvement (2) the crop protection against pathogens with low-impact solutions. As regards the first aspect, genetic improvement will benefit from the isolation and characterization of the genes involved in traits such as the shape and size of the plant organs, the architecture of the plant, the duration of the crop cycle and the increased tolerance to abiotic stresses. For the second topic, it will be essential to identify and characterize target genes involved in the host/pathogen interactions. Furthermore, as demonstrated in various occasions, developmental genetics and the host's response to harmful organisms can be related phenomena.

This Special Issue calls for original research articles, short communications, and review articles in all areas of sustainable management and crop improvement by innovative biotechnological strategies.

Dr. Claudio Pugliesi
Dr. Marco Fambrini
Dr. Susanna Pecchia
Guest Editors

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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.

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Keywords

Crop improvement
Plant architecture
RNA interference
Nanotechnology
Tolerance to abiotic stresses
Disease resistance
Host/pathogen interactions

Published Papers (9 papers)

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Editorial

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6 pages, 208 KiB

Open AccessEditorial

Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-Genomic Era

by Marco Fambrini, Claudio Pugliesi and Susanna Pecchia

Int. J. Mol. Sci. 2022, 23(6), 3273; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23063273 - 18 Mar 2022

Viewed by 1306

Abstract

Safeguarding food supply in a world environment subject to sudden climate change, reducing the use of anthropogenic sources of pollution as much as possible, and using crops that must necessarily be increasingly resilient to biotic and abiotic stresses is a mandatory and ambitious [...] Read more.

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

Research

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16 pages, 2128 KiB

Open AccessArticle

Silencing of the Slt2-Type MAP Kinase Bmp3 in Botrytis cinerea by Application of Exogenous dsRNA Affects Fungal Growth and Virulence on Lactuca sativa

by Maria Spada, Claudio Pugliesi, Marco Fambrini and Susanna Pecchia

Int. J. Mol. Sci. 2021, 22(10), 5362; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22105362 - 19 May 2021

Cited by 16 | Viewed by 3177

Abstract

Botrytis cinerea can attack over 500 genera of vascular plants and is considered the second phytopathogen in the ‘top ten’ for its economic importance. Traditional fungicides can be ineffective and with increasing fungicide resistance, new sustainable technologies are required. Lately, RNA interference-based fungicides are emerging for their potential uses in crop protection. Therefore, we assessed the potential of this innovative approach targeting the MAP kinase Bmp3 in B. cinerea, a gene involved in saprophytic growth, response to low osmolarity, conidiation, surface sensing, host penetration and lesion formation. After performing a prediction analysis of small interfering RNAs, a 427 nucleotides long dsRNA was selected as construct. We tested the effect of topical applications of dsRNA construct both in vitro by a fungal growth assay in microtiter plates and in vivo on detached lettuce leaves artificially inoculated. In both cases, topical applications of dsRNA led to gene knockdown with a delay in conidial germination, an evident growth retardation and a strong reduction of necrotic lesions on leaves. These results correlated with a strongly reduced expression of Bmp3 gene. In accordance to these findings, the Bmp3 gene could be a promising target for the development of an RNAi-based fungicide against B. cinerea. Full article

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

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24 pages, 4492 KiB

Open AccessArticle

Efficient Transformation of Somatic Embryos and Regeneration of Cork Oak Plantlets with a Gene (CsTL1) Encoding a Chestnut Thaumatin-Like Protein

by Vanesa Cano, Mᵃ Teresa Martínez, José Luis Couselo, Elena Varas, Francisco Javier Vieitez and Elena Corredoira

Int. J. Mol. Sci. 2021, 22(4), 1757; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041757 - 10 Feb 2021

Cited by 8 | Viewed by 2031

Abstract

We present a reproducible procedure for transforming somatic embryos of cork oak with the CsTL1 gene that codes for a thaumatin-like protein, in order to confer tolerance to Phytophthora cinnamomi. Different concentrations/combinations of the antibiotics carbenicillin and cefotaxime, as bacteriostatic agents, and kanamycin, as a selective agent, were tested. A lethal dose of 125 mg/L kanamycin was employed to select transgenic somatic embryos, and carbenicillin was used as a bacteriostatic agent at a concentration of 300 mg/L, which does not inhibit somatic embryo proliferation. The transformation efficiency was clearly genotype-dependent and was higher for the TGR3 genotype (17%) than for ALM80 (4.5%) and ALM6 (2%). Insertion of the transgenes in genomic DNA was confirmed by PCR analysis, whereas expression of the CsTL1 gene was evaluated by semi-quantitative real-time PCR (qPCR) analysis. A vitrification treatment successfully cryopreserved the transgenic lines generated. The antifungal activity of the thaumatin-like protein expressed by the gene CsTL1 was evaluated in an in vitro bioassay with the oomycete P. cinnamomi. Of the eight transgenic lines analyzed, seven survived for between one or two times longer than non-transgenic plantlets. Expression of the CsTL1 gene and plantlet survival days were correlated, and survival was generally greater in plantlets that strongly expressed the CsTL1 gene. Full article

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

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19 pages, 3627 KiB

Open AccessArticle

Fast, Precise, and Reliable Multiplex Detection of Potato Viruses by Loop-Mediated Isothermal Amplification

by Güven Edgü, Lena Julie Freund, Stefanie Hartje, Eckhard Tacke, Hans-Reinhard Hofferbert, Richard M. Twyman, Gundula A. Noll, Jost Muth and Dirk Prüfer

Int. J. Mol. Sci. 2020, 21(22), 8741; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21228741 - 19 Nov 2020

Cited by 11 | Viewed by 3629

Abstract

Potato is an important staple food crop in both developed and developing countries. However, potato plants are susceptible to several economically important viruses that reduce yields by up to 50% and affect tuber quality. One of the major threats is corky ringspot, which is a tuber necrosis caused by tobacco rattle virus (TRV). The appearance of corky ringspot symptoms on tubers prior to commercialization results in ≈ 45% of the tubers being downgraded in quality and value, while ≈ 55% are declared unsaleable. To improve current disease management practices, we have developed simple diagnostic methods for the reliable detection of TRV without RNA purification, involving minimalized sample handling (mini), subsequent improved colorimetric loop-mediated isothermal amplification (LAMP), and final verification by lateral-flow dipstick (LFD) analysis. Having optimized the mini-LAMP-LFD approach for the sensitive and specific detection of TRV, we confirmed the reliability and robustness of this approach by the simultaneous detection of TRV and other harmful viruses in duplex LAMP reactions. Therefore, our new approach offers breeders, producers, and farmers an inexpensive and efficient new platform for disease management in potato breeding and cultivation. Full article

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

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29 pages, 8315 KiB

Open AccessArticle

Synergistic Effect of Beauveria bassiana and Trichoderma asperellum to Induce Maize (Zea mays L.) Defense against the Asian Corn Borer, Ostrinia furnacalis (Lepidoptera, Crambidae) and Larval Immune Response

by Raufa Batool, Muhammad Jawad Umer, Yangzhou Wang, Kanglai He, Tiantao Zhang, Shuxiong Bai, Yang Zhi, Jie Chen and Zhenying Wang

Int. J. Mol. Sci. 2020, 21(21), 8215; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21218215 - 03 Nov 2020

Cited by 29 | Viewed by 4480

Abstract

Ostrinia furnacalis, is the major pest of maize causing significant yield losses. So far, many approaches have been used to increase the virulence of entomopathogenic fungal isolates. The current study is an attempt to estimate synergistic effect of Beauveria bassiana and Trichoderma asperellum in order to explore larval immune response through RNA sequencing and differentially expression analysis. In vivo synergism was examined in seven proportions (B. bassiana: T. asperellum = 1:1, 1:2, 1:3, 1:4, 4:1, 3:1, 2:1) and in the in vitro case, two inoculation methods were applied: seed coating and soil drenching. Results revealed significant decrease in plant damage and high larval mortality in fungal treatments. Fungal isolates mediated the plant defense by increasing proline, superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO) and protease activities. Seed coating method was proved to be the most effective in case of maize endophytic colonization. In total, 59 immune-related differentially expressed genes DEGs were identified including, cytochrome P450, heat shock protein, ABC transporter, cadherin, peptidoglycan recognition protein (PGRP), cuticlular protein, etc. Further, transcriptomic response was confirmed by qRT-PCR. Our results concluded that, coculture of B. bassiana and T. asperellum has the synergistic potential to suppress the immune response of O. furnacalis and can be used as sustainable approach to induce plant resistance through activation of defense-related enzymes. Full article

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

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19 pages, 1567 KiB

Open AccessArticle

Mapping Powdery Mildew (Blumeria graminis f. sp. tritici) Resistance in Wild and Cultivated Tetraploid Wheats

by Rosanna Simeone, Luciana Piarulli, Domenica Nigro, Massimo Antonio Signorile, Emanuela Blanco, Giacomo Mangini and Antonio Blanco

Int. J. Mol. Sci. 2020, 21(21), 7910; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21217910 - 24 Oct 2020

Cited by 12 | Viewed by 7204

Abstract

Wheat is the most widely grown crop and represents the staple food for one third of the world’s population. Wheat is attacked by a large variety of pathogens and the use of resistant cultivars is an effective and environmentally safe strategy for controlling diseases and eliminating the use of fungicides. In this study, a collection of wild and cultivated tetraploid wheats (Triticum turgidum) were evaluated for seedling resistance (SR) and adult plant resistance (APR) to powdery mildew (Blumeria graminis) and genotyped with a 90K single nucleotide polymorphism (SNP) array to identify new sources of resistance genes. The genome-wide association mapping detected 18 quantitative trait loci (QTL) for APR and 8 QTL for SR, four of which were identical or at least closely linked to four QTL for APR. Thirteen candidate genes, containing nucleotide binding sites and leucine-rich repeats, were localized in the confidence intervals of the QTL-tagging SNPs. The marker IWB6155, associated to QPm.mgb-1AS, was located within the gene TRITD1Av1G004560 coding for a disease resistance protein. While most of the identified QTL were described previously, five QTL for APR (QPm.mgb-1AS, QPm.mgb-2BS, QPm.mgb-3BL.1, QPm.mgb-4BL, QPm.mgb-7BS.1) and three QTL for SR (QPm.mgb-3BL.3, QPm.mgb-5AL.2, QPm.mgb-7BS.2) were mapped on chromosome regions where no resistance gene was reported before. The novel QTL/genes can contribute to enriching the resistance sources available to breeders. Full article

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

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Review

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14 pages, 314 KiB

Open AccessReview

Frontiers in Dissecting and Managing Brassica Diseases: From Reference-Based RGA Candidate Identification to Building Pan-RGAomes

by Yueqi Zhang, William Thomas, Philipp E. Bayer, David Edwards and Jacqueline Batley

Int. J. Mol. Sci. 2020, 21(23), 8964; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21238964 - 25 Nov 2020

Cited by 12 | Viewed by 3280

Abstract

The Brassica genus contains abundant economically important vegetable and oilseed crops, which are under threat of diseases caused by fungal, bacterial and viral pathogens. Resistance gene analogues (RGAs) are associated with quantitative and qualitative disease resistance and the identification of candidate RGAs associated with disease resistance is crucial for understanding the mechanism and management of diseases through breeding. The availability of Brassica genome assemblies has greatly facilitated reference-based quantitative trait loci (QTL) mapping for disease resistance. In addition, pangenomes, which characterise both core and variable genes, have been constructed for B. rapa, B. oleracea and B. napus. Genome-wide characterisation of RGAs using conserved domains and motifs in reference genomes and pangenomes reveals their clustered arrangements and presence of structural variations. Here, we comprehensively review RGA identification in important Brassica genome and pangenome assemblies. Comparison of the RGAs in QTL between resistant and susceptible individuals allows for efficient identification of candidate disease resistance genes. However, the reference-based QTL mapping and RGA candidate identification approach is restricted by the under-represented RGA diversity characterised in the limited number of Brassica assemblies. The species-wide repertoire of RGAs make up the pan-resistance gene analogue genome (pan-RGAome). Building a pan-RGAome, through either whole genome resequencing or resistance gene enrichment sequencing, would effectively capture RGA diversity, greatly expanding breeding resources that can be utilised for crop improvement. Full article

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

29 pages, 1388 KiB

Open AccessReview

Biotechnological Approaches: Gene Overexpression, Gene Silencing, and Genome Editing to Control Fungal and Oomycete Diseases in Grapevine

by Luca Capriotti, Elena Baraldi, Bruno Mezzetti, Cecilia Limera and Silvia Sabbadini

Int. J. Mol. Sci. 2020, 21(16), 5701; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21165701 - 09 Aug 2020

Cited by 34 | Viewed by 6515

Abstract

Downy mildew, powdery mildew, and grey mold are some of the phytopathological diseases causing economic losses in agricultural crops, including grapevine, worldwide. In the current scenario of increasing global warming, in which the massive use of agrochemicals should be limited, the management of fungal disease has become a challenge. The knowledge acquired on candidate resistant (R) genes having an active role in plant defense mechanisms has allowed numerous breeding programs to integrate these traits into selected cultivars, even though with some limits in the conservation of the proper qualitative characteristics of the original clones. Given their gene-specific mode of action, biotechnological techniques come to the aid of breeders, allowing them to generate simple and fast modifications in the host, without introducing other undesired genes. The availability of efficient gene transfer procedures in grapevine genotypes provide valid tools that support the application of new breeding techniques (NBTs). The expertise built up over the years has allowed the optimization of these techniques to overexpress genes that directly or indirectly limit fungal and oomycetes pathogens growth or silence plant susceptibility genes. Furthermore, the downregulation of pathogen genes which act as virulence effectors by exploiting the RNA interference mechanism, represents another biotechnological tool that increases plant defense. In this review, we summarize the most recent biotechnological strategies optimized and applied on Vitis species, aimed at reducing their susceptibility to the most harmful fungal and oomycetes diseases. The best strategy for combating pathogenic organisms is to exploit a holistic approach that fully integrates all these available tools. Full article

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

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29 pages, 3930 KiB

Open AccessReview

Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives

by Ali Anwar and Ju-Kon Kim

Int. J. Mol. Sci. 2020, 21(8), 2695; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21082695 - 13 Apr 2020

Cited by 87 | Viewed by 13357

Abstract

The recent rapid climate changes and increasing global population have led to an increased incidence of abiotic stress and decreased crop productivity. Environmental stresses, such as temperature, drought, nutrient deficiency, salinity, and heavy metal stresses, are major challenges for agriculture, and they lead to a significant reduction in crop growth and productivity. Abiotic stress is a very complex phenomenon, involving a variety of physiological and biochemical changes in plant cells. Plants exposed to abiotic stress exhibit enhanced levels of ROS (reactive oxygen species), which are highly reactive and toxic and affect the biosynthesis of chlorophyll, photosynthetic capacity, and carbohydrate, protein, lipid, and antioxidant enzyme activities. Transgenic breeding offers a suitable alternative to conventional breeding to achieve plant genetic improvements. Over the last two decades, genetic engineering/transgenic breeding techniques demonstrated remarkable developments in manipulations of the genes for the induction of desired characteristics into transgenic plants. Transgenic approaches provide us with access to identify the candidate genes, miRNAs, and transcription factors (TFs) that are involved in specific plant processes, thus enabling an integrated knowledge of the molecular and physiological mechanisms influencing the plant tolerance and productivity. The accuracy and precision of this phenomenon assures great success in the future of plant improvements. Hence, transgenic breeding has proven to be a promising tool for abiotic stress improvement in crops. This review focuses on the potential and successful applications, recent progress, and future perspectives of transgenic breeding for improving abiotic stress tolerance and productivity in plants. Full article

(This article belongs to the Special Issue Innovative Approaches for Crop Improvement and Sustainable Management of Plant Disease in the Post-genomic Era)

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