Advances in Genetics and Genomics of Plants: 2nd Edition

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 February 2025) | Viewed by 3910

Special Issue Editor


E-Mail Website
Guest Editor
Institute for Advanced Study, Chengdu University, Chengdu 610106, China
Interests: plant genomics; comparative genomic analysis; functional gene analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the recent advances in molecular genetics and high-throughput sequencing technologies, continuous and rapid progress has revealed the complex and varied genomic characteristics and genetics of plants. In the recent past, diverse omics technologies such as genomics, transcriptomics, epigenomics, proteomics, and metabolomics have developed rapidly, providing powerful tools for the comprehensive study of plant nuclear, mitochondrial, and chloroplast genomes and their dynamics. These studies provide valuable insights into the underlying genetic mechanisms driving the complex traits of plants, helping us transform and use plant resources more efficiently. In this Special Issue, we aim to focus on the applications of cutting-edge technologies in the genetic and genomic study of plant species that are related to scientific questions of wide concern. Studies including high-throughput sequencing data analysis and experimental validation analysis on nuclear and organelle genomes are welcome. Both theoretical and empirical contributions will be considered.

Dr. Mingcheng Wang
Guest Editor

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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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 genomics
  • plant genetics
  • high-throughput sequencing
  • genome dynamics
  • organelle genome
  • experimental validation

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

17 pages, 15558 KiB  
Article
Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Dendrobium devonianum Flowers
by Yue Li, Yawen Wu, Ran Pu, Xuejiao Li, Tian Bai, Nengbo Li, Ying Zhou and Jingli Zhang
Genes 2025, 16(3), 264; https://doi.org/10.3390/genes16030264 - 24 Feb 2025
Viewed by 485
Abstract
Background: Dendrobium devonianum is a traditional Chinese medicinal herb with notable ornamental and medicinal value. Methods: In this study, transcriptomic and metabolomic approaches were employed to investigate gene expression and secondary metabolite changes during four developmental stages of D. devonianum flowers. Results: Metabolomic [...] Read more.
Background: Dendrobium devonianum is a traditional Chinese medicinal herb with notable ornamental and medicinal value. Methods: In this study, transcriptomic and metabolomic approaches were employed to investigate gene expression and secondary metabolite changes during four developmental stages of D. devonianum flowers. Results: Metabolomic analysis identified 1186 distinct metabolites, with flavonoid compounds being the most abundant category (213 types). Transcriptomic analysis revealed 31 differentially expressed genes associated with flavonoid biosynthesis and flavonoid and flavonol biosynthesis pathways. Among these, key genes regulating flavonol synthesis, including F3H (Unigene0077194) and FLS (Unigene0062137), exhibited high expression levels in the early developmental stage (S1). Conclusions: Flavonoids serve as the major active components in D. devonianum flowers, exhibiting a wide range of pharmacological properties. This study provides valuable insights into the molecular mechanisms driving flavonoid accumulation in D. devonianum, offering a foundation for further functional studies and applications in ornamental and medicinal plant research. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)
Show Figures

Figure 1

17 pages, 4465 KiB  
Article
Genome-Wide Analyses of the Soybean GmABCB Gene Family in Response to Salt Stress
by Hui Zou, Caiyun Fan, Xiulin Chen, Ruifeng Chen, Zhihui Sun and Xiaorong Wan
Genes 2025, 16(2), 233; https://doi.org/10.3390/genes16020233 - 19 Feb 2025
Viewed by 635
Abstract
Background: Soybean (Glycine max (L.) Merr.) is a significant economic oilseed crop, and saline-alkali soils restrict soybean yield. Identifying salt-tolerant genes is a key strategy for enhancing soybean productivity under saline-alkali conditions. The roles of the GmABCB gene family in growth, [...] Read more.
Background: Soybean (Glycine max (L.) Merr.) is a significant economic oilseed crop, and saline-alkali soils restrict soybean yield. Identifying salt-tolerant genes is a key strategy for enhancing soybean productivity under saline-alkali conditions. The roles of the GmABCB gene family in growth, development, and stress resistance remain incompletely understood. Methods: Bioinformatics approaches were employed to identify and analyze GmABCB genes. A total of 39 GmABCB genes were identified and analyzed in the soybean genome, focusing on their phylogenetic relationships, chromosomal distribution, gene structure, cis-acting elements, evolutionary history, and expression patterns under salt stress. Results: A total of 39 GmABCB genes were identified. These genes are unevenly distributed across the soybean genome, with 21 segmental duplication events identified. Several cis-acting elements associated with abiotic stress responses were identified. Conclusions: The GmABCB gene family likely regulates growth, development, and stress tolerance in soybean. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)
Show Figures

Figure 1

17 pages, 3928 KiB  
Article
Dynamic Chromatin Accessibility and Gene Expression Regulation During Maize Leaf Development
by Yiduo Wang, Shuai Wang, Yufeng Wu, Jiawen Cheng and Haiyan Wang
Genes 2024, 15(12), 1630; https://doi.org/10.3390/genes15121630 - 20 Dec 2024
Viewed by 868
Abstract
Background/Objectives: Chromatin accessibility is closely associated with transcriptional regulation during maize (Zea mays) leaf development. However, its precise role in controlling gene expression at different developmental stages remains poorly understood. This study aimed to investigate the dynamics of chromatin accessibility and [...] Read more.
Background/Objectives: Chromatin accessibility is closely associated with transcriptional regulation during maize (Zea mays) leaf development. However, its precise role in controlling gene expression at different developmental stages remains poorly understood. This study aimed to investigate the dynamics of chromatin accessibility and its influence on genome-wide gene expression during the BBCH_11, BBCH_13, and BBCH_17 stages of maize leaf development. Methods: Maize leaves were collected at the BBCH_11, BBCH_13, and BBCH_17 developmental stages, and chromatin accessibility was assessed using ATAC-seq. RNA-seq was performed to profile gene expression. Integrated analysis of ATAC-seq and RNA-seq data was conducted to elucidate the relationship between chromatin accessibility and transcriptional regulation. Results: A total of 46,808, 38,242, and 41,084 accessible chromatin regions (ACRs) were identified at the BBCH_11, BBCH_13, and BBCH_17 stages, respectively, with 23.4%, 12.2%, and 21.9% of these regions located near transcription start sites (TSSs). Integrated analyses revealed that both the number and intensity of ACRs significantly influence gene expression levels. Motif analysis identified key transcription factors associated with leaf development and potential transcriptional repressors among genes, showing divergent regulation patterns in ATAC-seq and RNA-seq datasets. Conclusions: These findings demonstrate that chromatin accessibility plays a crucial role in regulating the spatial and temporal expression of key genes during maize leaf development by modulating transcription factor binding. This study provides novel insights into the regulatory mechanisms underlying maize leaf development, contributing to a deeper understanding of chromatin-mediated gene expression. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)
Show Figures

Figure 1

Review

Jump to: Research

18 pages, 2505 KiB  
Review
From Species to Varieties: How Modern Sequencing Technologies Are Shaping Medicinal Plant Identification
by Mingcheng Wang, Haifeng Lin, Hongqiang Lin, Panyue Du and Shuqiao Zhang
Genes 2025, 16(1), 16; https://doi.org/10.3390/genes16010016 - 26 Dec 2024
Cited by 6 | Viewed by 1331
Abstract
Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing [...] Read more.
Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing the accuracy and reliability of plant identification. Additionally, the integration of multi-omics approaches is examined to provide a comprehensive understanding of medicinal plant identity. Methods: The literature search for this review was conducted across databases such as Google Scholar, Web of Science, and PubMed, using keywords related to plant taxonomy, genomics, and biotechnology. Inclusion criteria focused on peer-reviewed studies closely related to plant identification methods and techniques that contribute significantly to the field. Results: The review highlights that while sequencing technologies offer substantial improvements, challenges such as high costs, technical expertise, and the lack of standardized protocols remain barriers to widespread adoption. Potential solutions, including AI-driven data analysis and portable sequencers, are discussed. Conclusions: This review provides a comprehensive overview of molecular techniques, their transformative impact, and future perspectives for more accurate and efficient medicinal plant identification. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)
Show Figures

Figure 1

Back to TopTop