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Functional and Structural Genomics Studies for Plant Breeding
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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: 20 August 2025 | Viewed by 7295

Special Issue Editors

Prof. Dr. Andrea Cavallini

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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
Dr. Tommaso Giordani

E-Mail Website
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
Dr. Alberto Vangelisti

E-Mail Website
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

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. 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
 

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Published Papers (4 papers)

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Research

14 pages, 9892 KiB  
Article
QTL Mapping of Fiber- and Seed-Related Traits in Chromosome Segment Substitution Lines Derived from Gossypium hirsutum × Gossypium darwinii
by Wenwen Wang, Yan Li, Mingmei Le, Lixia Tian, Xujing Sun, Rui Liu, Xin Guo, Yan Wu, Yibing Li, Jiaoyun Zhao, Dajun Liu and Zhengsheng Zhang
Int. J. Mol. Sci. 2024, 25(17), 9639; https://doi.org/10.3390/ijms25179639 - 5 Sep 2024
Viewed by 1001
Abstract
A narrow genetic basis limits further the improvement of modern Gossypium hirsutum cultivar. The abundant genetic diversity of wild species provides available resources to solve this dilemma. In the present study, a chromosome segment substitution line (CSSL) population including 553 individuals was established [...] Read more.
A narrow genetic basis limits further the improvement of modern Gossypium hirsutum cultivar. The abundant genetic diversity of wild species provides available resources to solve this dilemma. In the present study, a chromosome segment substitution line (CSSL) population including 553 individuals was established using G. darwinii accession 5-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. After constructing a high-density genetic map with the BC1 population, the genotype and phenotype of the CSSL population were investigated. A total of 235 QTLs, including 104 QTLs for fiber-related traits and 132 QTLs for seed-related traits, were identified from four environments. Among these QTLs, twenty-seven QTLs were identified in two or more environments, and twenty-five QTL clusters consisted of 114 QTLs. Moreover, we identified three candidate genes for three stable QTLs, including GH_A01G1096 (ARF5) and GH_A10G0141 (PDF2) for lint percentage, and GH_D01G0047 (KCS4) for seed index or oil content. These results pave way for understanding the molecular regulatory mechanism of fiber and seed development and would provide valuable information for marker-assisted genetic improvement in cotton. Full article
(This article belongs to the Special Issue Functional and Structural Genomics Studies for Plant Breeding)
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16 pages, 6268 KiB  
Article
R2R3 MYB Transcription Factor GhMYB201 Promotes Cotton Fiber Elongation via Cell Wall Loosening and Very-Long-Chain Fatty Acid Synthesis
by Qingwei Suo, Nianjuan Fang, Jianyan Zeng, Fulin Yan, Xi Zhu, Yi Wang, Wanting Yu, Junmin Chen, Aimin Liang, Yaohua Li, Jie Kong and Yuehua Xiao
Int. J. Mol. Sci. 2024, 25(17), 9559; https://doi.org/10.3390/ijms25179559 - 3 Sep 2024
Cited by 1 | Viewed by 1235
Abstract
Cotton fiber is the leading natural textile material, and fiber elongation plays an essential role in the formation of cotton yield and quality. Although a number of components in the molecular network controlling cotton fiber elongation have been reported, a lot of players [...] Read more.
Cotton fiber is the leading natural textile material, and fiber elongation plays an essential role in the formation of cotton yield and quality. Although a number of components in the molecular network controlling cotton fiber elongation have been reported, a lot of players still need to be functionally dissected to understand the regulatory mechanism of fiber elongation comprehensively. In the present study, an R2R3-MYB transcription factor gene, GhMYB201, was characterized and functionally verified via CRISPR/Cas9-mediated gene editing. GhMYB201 was homologous to Arabidopsis AtMYB60, and both coding genes (GhMYB201At and GhMYB201Dt) were preferentially expressed in elongating cotton fibers. Knocking-out of GhMYB201 significantly reduced the rate and duration of fiber elongation, resulting in shorter and coarser mature fibers. It was found that GhMYB201 could bind and activate the transcription of cell wall loosening genes (GhRDLs) and also β-ketoacyl-CoA synthase genes (GhKCSs) to enhance very-long-chain fatty acid (VLCFA) levels in elongating fibers. Taken together, our data demonstrated that the transcription factor GhMYB201s plays an essential role in promoting fiber elongation via activating genes related to cell wall loosening and VLCFA biosynthesis. Full article
(This article belongs to the Special Issue Functional and Structural Genomics Studies for Plant Breeding)
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21 pages, 11935 KiB  
Article
Gene Regulatory Network Controlling Flower Development in Spinach (Spinacia oleracea L.)
by Yaying Ma, Wenhui Fu, Suyan Wan, Yikai Li, Haoming Mao, Ehsan Khalid, Wenping Zhang and Ray Ming
Int. J. Mol. Sci. 2024, 25(11), 6127; https://doi.org/10.3390/ijms25116127 - 1 Jun 2024
Cited by 1 | Viewed by 1881
Abstract
Spinach (Spinacia oleracea L.) is a dioecious, diploid, wind-pollinated crop cultivated worldwide. Sex determination plays an important role in spinach breeding. Hence, this study aimed to understand the differences in sexual differentiation and floral organ development of dioecious flowers, as well as [...] Read more.
Spinach (Spinacia oleracea L.) is a dioecious, diploid, wind-pollinated crop cultivated worldwide. Sex determination plays an important role in spinach breeding. Hence, this study aimed to understand the differences in sexual differentiation and floral organ development of dioecious flowers, as well as the differences in the regulatory mechanisms of floral organ development of dioecious and monoecious flowers. We compared transcriptional-level differences between different genders and identified differentially expressed genes (DEGs) related to spinach floral development, as well as sex-biased genes to investigate the flower development mechanisms in spinach. In this study, 9189 DEGs were identified among the different genders. DEG analysis showed the participation of four main transcription factor families, MIKC_MADS, MYB, NAC, and bHLH, in spinach flower development. In our key findings, abscisic acid (ABA) and gibberellic acid (GA) signal transduction pathways play major roles in male flower development, while auxin regulates both male and female flower development. By constructing a gene regulatory network (GRN) for floral organ development, core transcription factors (TFs) controlling organ initiation and growth were discovered. This analysis of the development of female, male, and monoecious flowers in spinach provides new insights into the molecular mechanisms of floral organ development and sexual differentiation in dioecious and monoecious plants in spinach. Full article
(This article belongs to the Special Issue Functional and Structural Genomics Studies for Plant Breeding)
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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
Viewed by 2152
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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