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Special Issue "Molecular Analysis of Crop Diversity"

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: 31 December 2021.

Special Issue Editors

Prof. Dr. Roberto Papa
E-Mail Website
Guest Editor
Dipartimento di Scienze Agrarie, Alimentari e Ambientali—D3A, Università Politecnica delle Marche, 60131 Ancona, Italy
Interests: plant breeding; evolutionary genetics; genomics; domestication and crop evolution; agrobiodiversity and plant genetic resources conservation; adaptation; food legumes; cereal
Special Issues and Collections in MDPI journals
Prof. Dr. Emidio Albertini
E-Mail Website
Guest Editor
Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
Interests: plant reproduction; epigenetics; apomixis; stresses; tomato; grape
Special Issues and Collections in MDPI journals
Dr. Valerio Di Vittori
E-Mail Website
Guest Editor
Division of Central Metabolism, Max Planck Institute of Molecular Plant Physiology , Am Muehlenberg 1, 14476 Potsdam - Golm, Germany
Interests: Plant Breeding; Crop domestication; GWAS and QTL mapping; Population Genetics; Molecular Phenotyping

Special Issue Information

Dear Colleagues,

In the last decade, the development of high-throughput phenotyping and genotyping methods tremendously boosted the study of crop diversity. These advances allowed addressing topics of both fundamental and applied interest. The possibility to explore the phenotypic space (i.e., the pattern of phenotypic expression or reaction norm) of one or several genotypes at the molecular level using transcriptomics, epigenomics, and metabolomics as well as other phenomics approaches, can be combined with the most appropriate approach for the analysis of complex datasets, to shed light on the molecular basis of complex traits and on genetic variation in response to environmental variation. In parallel, the same studies could be successfully used for the identification of genotypes enriched for specific compounds with a relevant nutritional value for crop breeding. This Special Issue will positively consider, but will not be limited to, manuscripts focusing on recent progress in the understanding of crop diversity at least at one -omic level (e.g., genomics, transcriptomics, metabolomics, and epigenomics) in order to identify the genetic and molecular basis of the adaptation of plants in response to biotic and abiotic factors, as well as manuscripts focusing on the nutritional value of crop germplasm and its potential use in plant breeding.

Prof. Dr. Roberto Papa
Prof. Dr. Emidio Albertini
Dr. Valerio Di Vittori
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 papers will be 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • Plant Genetic Resources
  • molecular analysis
  • adaptation
  • phenotypic plasticity
  • plant breeding
  • complex traits
  • nutrition

Published Papers (4 papers)

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Research

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Article
High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata
Int. J. Mol. Sci. 2021, 22(11), 5723; https://doi.org/10.3390/ijms22115723 - 27 May 2021
Viewed by 776
Abstract
A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The [...] Read more.
A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding. Full article
(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)
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Article
Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation
Int. J. Mol. Sci. 2021, 22(9), 4790; https://doi.org/10.3390/ijms22094790 - 30 Apr 2021
Cited by 1 | Viewed by 696
Abstract
Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two [...] Read more.
Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies. Full article
(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)
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Article
Quantitative Proteomics Analysis Reveals the Function of the Putative Ester Cyclase UvEC1 in the Pathogenicity of the Rice False Smut Fungus Ustilaginoidea virens
Int. J. Mol. Sci. 2021, 22(8), 4069; https://doi.org/10.3390/ijms22084069 - 15 Apr 2021
Cited by 1 | Viewed by 556
Abstract
Rice false smut is a fungal disease distributed worldwide and caused by Ustilaginoidea virens. In this study, we identified a putative ester cyclase (named as UvEC1) as being significantly upregulated during U. virens infection. UvEC1 contained a SnoaL-like polyketide cyclase domain, but [...] Read more.
Rice false smut is a fungal disease distributed worldwide and caused by Ustilaginoidea virens. In this study, we identified a putative ester cyclase (named as UvEC1) as being significantly upregulated during U. virens infection. UvEC1 contained a SnoaL-like polyketide cyclase domain, but the functions of ketone cyclases such as SnoaL in plant fungal pathogens remain unclear. Deletion of UvEC1 caused defects in vegetative growth and conidiation. UvEC1 was also required for response to hyperosmotic and oxidative stresses and for maintenance of cell wall integrity. Importantly, ΔUvEC1 mutants exhibited reduced virulence. We performed a tandem mass tag (TMT)-based quantitative proteomic analysis to identify differentially accumulating proteins (DAPs) between the ΔUvEC1-1 mutant and the wild-type isolate HWD-2. Proteomics data revealed that UvEC1 has a variety of effects on metabolism, protein localization, catalytic activity, binding, toxin biosynthesis and the spliceosome. Taken together, our findings suggest that UvEC1 is critical for the development and virulence of U. virens. Full article
(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)
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Review

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Review
Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies
Int. J. Mol. Sci. 2021, 22(18), 9713; https://doi.org/10.3390/ijms22189713 - 08 Sep 2021
Viewed by 232
Abstract
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for [...] Read more.
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family. Full article
(This article belongs to the Special Issue Molecular Analysis of Crop Diversity)
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