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Plants
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Genomics and Transcriptomics for Plant Development and Improvement
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Genomics and Transcriptomics for Plant Development and Improvement

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 1457

Special Issue Editor

Dr. Parul Gupta

E-Mail Website
Guest Editor
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Interests: plant genomics; transcriptomics; bioinformatics; gene discovery; plant pathway curation; gene regulatory networks; nutritional genomics; secondary plant products; pangenomics; space biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genomics and transcriptomics are fundamental to deciphering the molecular mechanisms of plant development and to advancing crop improvement amid global challenges like climate change and food security. This Special Issue invites authors to submit high-quality research and review articles that apply genomic and transcriptomic approaches to explore plant biology. We encourage submissions that uncover gene regulatory networks, developmental pathways, and stress adaptation mechanisms, with an emphasis on translating these insights into strategies for enhancing agronomic traits. By gathering cutting-edge research, we aim to foster collaboration and accelerate the development of resilient, high-yielding crops. 

We welcome contributions in areas including, but not limited to, the following:

Genomic Basis of Plant Development: Gene function, genome evolution, genetic diversity, and structural variations influencing plant architecture, organ formation, and phase transitions.

Transcriptomic Profiling of Plant Responses: Gene expression studies using RNA-seq and single-cell RNA-seq under stress conditions or during development.

Non-Coding RNAs and Epigenetic Regulation: Roles of miRNAs, siRNAs, lncRNAs, and epigenetic modifications in plant development and adaptation.

Integrative Omics for Trait Discovery: Combining multi-omics data, including single-cell genomics/transcriptomics and pan-genomics, to identify genes and pathways related to yield, quality, nutrient efficiency, and disease resistance.

Applications in Crop Improvement: Use of genomic/transcriptomic data in breeding, gene editing, and variety development.

Dr. Parul Gupta
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 250 words) can be sent to the Editorial Office for assessment.

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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • genetic diversity
  • crop improvement
  • genomics
  • transcriptomics
  • disease resistance
  • genome editing
  • non-coding RNA
  • multi-omics

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Published Papers (3 papers)

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Research

18 pages, 5296 KB  
Article
Identification and Validation of NAC Transcription Factors Enhancing Phenolic Acid Production in Perilla frutescens
by Jiayi Xu, Ping Wang, Junmei Lian, Linqiang Zhang, Xiaobi Zhang, Yan Sui, Jiankang Chen, Heng Wei, Yihan Wang, Rongde Cui, Wanying Li, Nanqi Zhang, Yan Yan, Jian Zhang and Peng Di
Plants 2026, 15(6), 922; https://doi.org/10.3390/plants15060922 - 17 Mar 2026
Viewed by 297
Abstract
Phenolic acids are the major bioactive compounds in Perilla frutescens (L.) Britt; however, the regulatory roles of NAC transcription factors (TFs) in their biosynthesis remain unclear. Here, we performed a genome-wide identification and characterization of the NAC family in P. frutescens and explored [...] Read more.
Phenolic acids are the major bioactive compounds in Perilla frutescens (L.) Britt; however, the regulatory roles of NAC transcription factors (TFs) in their biosynthesis remain unclear. Here, we performed a genome-wide identification and characterization of the NAC family in P. frutescens and explored their involvement in phenolic acid production. A total of 108 PfNAC genes were identified and classified into 17 subfamilies. Expression and promoter analyses suggested potential roles in secondary metabolism. PfNAC29 is located in the plasma membrane and necleus, while PfNAC40 and PfNAC80 are located in the nucleus.Yeast one-hybrid and dual-luciferase assays demonstrated that these TFs bind to the CATGTG motif in the PfC4H promoter and activate its transcription. Overexpression in transgenic hairy roots significantly increased rosmarinic acid, caffeic acid, and ferulic acid accumulation, accompanied by upregulation of key biosynthetic genes. These results indicate that PfNAC29, PfNAC40, and PfNAC80 act as positive regulators of phenolic acid biosynthesis and provide promising targets for metabolic engineering in medicinal plants. Full article
(This article belongs to the Special Issue Genomics and Transcriptomics for Plant Development and Improvement)
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23 pages, 10014 KB  
Article
Identification and Expression Analysis of MADS-Box Gene Family in Pinus koraiensis and Overexpression of PkMADS9 Promoting Early Flowering in Transgenic Arabidopsis
by Xue Luan, Minghui Zhao, Wenjing Gu, Yan Li, Luping Jiang, Shuanglin Song, Haiyang Yu, Yanming Zhang, Xiaona Pei and Xiyang Zhao
Plants 2026, 15(4), 657; https://doi.org/10.3390/plants15040657 - 21 Feb 2026
Viewed by 412
Abstract
Korean pine (Pinus koraiensis) is a vital woody oil tree species native to Northeast Asia, with its pine nuts serving as the primary global source of edible pine nuts globally due to their rich nutritional content. Currently, seed yield from Korean [...] Read more.
Korean pine (Pinus koraiensis) is a vital woody oil tree species native to Northeast Asia, with its pine nuts serving as the primary global source of edible pine nuts globally due to their rich nutritional content. Currently, seed yield from Korean pine is low and unstable, failing to meet the market demand. The limited number of female cones is the primary factor restricting its yield. MADS-box family members are crucial in regulating the initiation, differentiation, and morphogenesis of floral organs. However, systematic identification and characterization of MADS-box proteins in Korean pine have not been reported. This study utilized transcriptome data from reproductive and vegetative buds during the flower bud differentiation stage of Korean pine to comprehensively identify MADS-box family members through bioinformatics analysis and molecular biology approaches. A total of 37 PkMADS-box genes were identified, including 6 type I and 31 type II (MIKC) genes, which were classified into 8 subfamilies. The physicochemical properties, conserved domains, conserved motifs, protein structures, gene expression profiles, and protein–protein interaction networks of these genes were analyzed. Key genes associated with physiological differentiation (flower induction) and sexual organogenesis were identified based on expression patterns during flower bud differentiation and flower organ development. Among these, PkMADS4 and PkMADS26 are likely involved in positively regulating flower induction, while PkMADS9 plays a role in the morphological differentiation of sexual organs in a dose-dependent manner and overexpression of PkMADS9 promoting early flowering in transgenic Arabidopsis. These genes were also identified as key candidates for regulating reproductive phase changes and strobilus development. This study provides a theoretical foundation for further investigation of MADS-box genes in reproduction and offers insights into genetic improvements aimed at enhancing the seed yield of Korean pine. Full article
(This article belongs to the Special Issue Genomics and Transcriptomics for Plant Development and Improvement)
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32 pages, 6380 KB  
Article
Identification and Development of Pathogen- and Pest-Specific Defense–Resistance-Associated SSR Marker Candidates Assisted by Machine Learning and Discovery of Putative QTL Hotspots in Camellia sinensis
by Ayşenur Eminoğlu
Plants 2026, 15(3), 454; https://doi.org/10.3390/plants15030454 - 2 Feb 2026
Viewed by 414
Abstract
In this study, a targeted SSR (Simple Sequence Repeat) marker resource was developed based on genes and protein families associated with pathogen- and pest-related defense–resistance mechanisms in Camellia sinensis. Forty-one genes and protein families reported to show upregulation, increased expression, or functional [...] Read more.
In this study, a targeted SSR (Simple Sequence Repeat) marker resource was developed based on genes and protein families associated with pathogen- and pest-related defense–resistance mechanisms in Camellia sinensis. Forty-one genes and protein families reported to show upregulation, increased expression, or functional validation under disease and pest stress were selected, and the corresponding 195 loci were mapped onto the Camellia sinensis cv. Shuchazao genome. SSR screening within gene bodies and gene-flanking regions (±5 kb) identified 5197 SSR loci. Putative QTL hotspot regions were defined using locus-based sliding-window analysis, Z-score calculations, and permutation tests, yielding 633 SSRs filtered at the 99% and 95% significance thresholds. Proteome-wide scans based on conserved amino acid motifs identified multiple loci within the WRKY, NAC, LRR, PRX, and CHI families, and Random Forest analysis was used to prioritize SSRs within these families. Finally, 386 SSR primer sets were designed and evaluated by in silico PCR across six tea genomes. Of these, 245 primers produced amplicons in more than one genome, and 124 exhibited polymorphic information content values greater than 0.500. Overall, the developed SSR panels represent a biologically contextualized and experimentally transferable marker resource targeting defense–resistance-associated genic and gene-proximal regions. Full article
(This article belongs to the Special Issue Genomics and Transcriptomics for Plant Development and Improvement)
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