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Functional and Structural Genomics Studies for Plant Breeding

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: 30 July 2024 | Viewed by 998

Special Issue Editors


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Guest Editor
Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
Interests: plant genomics; genome sequencing; plant breeding; repetitive DNA; transposons
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
Interests: plant genetics; plant genomics; genome-wide association study; plant gene editing; plant transcriptomics

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Guest Editor
Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
Interests: plant transcriptomics; plant breeding; plant-fungi interactions; abiotic stresses; plant gene editing

Special Issue Information

Dear Colleagues,

In recent years, many techniques have been developed to carry out both structural and functional genomic studies, allowing the discovery of the genetic basis of many useful traits. In fact, genomics studies can help better understand the evolution, development, and functional biology of plants, through the analysis of gene families, genetic variability, gene-environment interactions, and gene regulatory networks. Plant genomics and transcriptomics have many practical applications for agriculture, conservation, health, and industry. It can help identify and transfer desirable genes and alleles into crops, to increase their yield, their resistance to environmental stresses and diseases, and their nutritional quality. Moreover, structural and functional genomics data can be conveniently used to produce molecules of biotechnological interest, such as drugs, vaccines, biofuels, and materials, using plants as factories or sources of raw materials.

This Special Issue aims to gather information about new genomic data potentially useful for crop breeding, in order to obtaining, in a sustainable way, plants more adapted to consumers' and farmers' needs, with special, but not exclusive, reference to minor crops, for which genomic studies are still at an early stage.

Prof. Dr. Andrea Cavallini
Dr. Tommaso Giordani
Dr. Alberto Vangelisti
Guest Editors

Manuscript Submission Information

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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 transcriptomics
  • genome sequencing
  • plant gene function
  • molecular plant breeding
  • structural genomics
 

Published Papers (1 paper)

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Research

20 pages, 5985 KiB  
Article
Transcriptomic Analyses Reveal Insights into the Shared Regulatory Network of Phenolic Compounds and Steviol Glycosides in Stevia rebaudiana
by Samuel Simoni, Alberto Vangelisti, Clarissa Clemente, Gabriele Usai, Marco Santin, Maria Ventimiglia, Flavia Mascagni, Lucia Natali, Luciana G. Angelini, Andrea Cavallini, Silvia Tavarini and Tommaso Giordani
Int. J. Mol. Sci. 2024, 25(4), 2136; https://doi.org/10.3390/ijms25042136 - 10 Feb 2024
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Abstract
Stevia rebaudiana (Bertoni) is a highly valuable crop for the steviol glycoside content in its leaves, which are no-calorie sweeteners hundreds of times more potent than sucrose. The presence of health-promoting phenolic compounds, particularly flavonoids, in the leaf of S. rebaudiana adds further [...] Read more.
Stevia rebaudiana (Bertoni) is a highly valuable crop for the steviol glycoside content in its leaves, which are no-calorie sweeteners hundreds of times more potent than sucrose. The presence of health-promoting phenolic compounds, particularly flavonoids, in the leaf of S. rebaudiana adds further nutritional value to this crop. Although all these secondary metabolites are highly desirable in S. rebaudiana leaves, the genes regulating the biosynthesis of phenolic compounds and the shared gene network between the regulation of biosynthesis of steviol glycosides and phenolic compounds still need to be investigated in this species. To identify putative candidate genes involved in the synergistic regulation of steviol glycosides and phenolic compounds, four genotypes with different contents of these compounds were selected for a pairwise comparison RNA-seq analysis, yielding 1136 differentially expressed genes. Genes that highly correlate with both steviol glycosides and phenolic compound accumulation in the four genotypes of S. rebaudiana were identified using the weighted gene co-expression network analysis. The presence of UDP-glycosyltransferases 76G1, 76H1, 85C1, and 91A1, and several genes associated with the phenylpropanoid pathway, including peroxidase, caffeoyl-CoA O-methyltransferase, and malonyl-coenzyme A:anthocyanin 3-O-glucoside-6″-O-malonyltransferase, along with 21 transcription factors like SCL3, WRK11, and MYB111, implied an extensive and synergistic regulatory network involved in enhancing the production of such compounds in S. rebaudiana leaves. In conclusion, this work identified a variety of putative candidate genes involved in the biosynthesis and regulation of particular steviol glycosides and phenolic compounds that will be useful in gene editing strategies for increasing and steering the production of such compounds in S. rebaudiana as well as in other species. Full article
(This article belongs to the Special Issue Functional and Structural Genomics Studies for Plant Breeding)
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