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Horticultural Plants Research from an Omics Perspective
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Horticultural Plants Research from an Omics Perspective

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 December 2024) | Viewed by 2531

Special Issue Editor

Dr. Linfang Huang

E-Mail Website
Guest Editor
The Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100193, China
Interests: transcriptomics, proteomics and metabolomics of medicinal plants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural plants generally include vegetables, fruit trees, tea trees, ornamental plants and medicinal plants. They are indispensable in people's daily lives.

Multi-omics techniques (such as chloroplast genomics, mitochondrial genomics, microbiomics, transcriptomics, genomics, proteomics, metabolomics and phenomics) play an increasingly important role in addressing fundamental issues related to the conservation and utilization of horticultural plants.

The chloroplast and mitochondrial genomes have become important tools for studying the evolution, species identification and genetic variation in horticultural plants. By analyzing the sequence and structural changes in the chloroplast and mitochondrial genomes, we can gain in-depth insights into the phylogenetic relationships among horticultural plant species, trace their origins and evolutionary processes, and provide valuable information for the genetic improvement and conservation of horticultural plant genetic resources.

The comprehensive analysis of genomics, proteomics, metabolomics and microbiomics data provides comprehensive biological information, helping us understand the genetic characteristics of horticultural plants, and the synthesis and regulatory mechanisms of bioactive compounds.

This Special Issue of Genes focuses on horticultural plant research from an omics perspective, and welcomes articles and reviews on the study of horticultural plants through multi-omics methods. The topics include, but are not limited to, the following: 1) identifying candidate stress resistance loci/genes in horticultural crops through omics data mining and other methods; 2) investigation of gene families related to horticultural plants, regulation of gene expression and validation of gene function using mutants and overexpression; and 3) analyzing the evolutionary process of horticultural plants through genomic data.

Dr. Linfang Huang
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

  • chloroplast genome and mitochondrial genomes
  • transcriptomics, proteomics and metabolomics
  • vegetables
  • fruits
  • medicinal plants
  • ornamental plants
  • gene cloning
  • gene family

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Published Papers (3 papers)

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Research

12 pages, 3167 KiB  
Article
The GA2ox Gene Family in Solanum pennellii: Genome-Wide Identification and Expression Analysis Under Salinity Stresses
by Xianjue Ruan, Min Zhang, Tingting Ling, Xiaoyan Hei and Jie Zhang
Genes 2025, 16(2), 158; https://doi.org/10.3390/genes16020158 - 26 Jan 2025
Viewed by 477
Abstract
Background: GA 2-oxidases (GA2oxs), a class of enzymes, inhibit the biosynthesis of bioactive gibberellins (GAs) in plants. The GA2 oxidase gene is crucial for regulating the passivation process of active GA and is widely involved in hormone signaling and abiotic stress processes. Objective/Methods: [...] Read more.
Background: GA 2-oxidases (GA2oxs), a class of enzymes, inhibit the biosynthesis of bioactive gibberellins (GAs) in plants. The GA2 oxidase gene is crucial for regulating the passivation process of active GA and is widely involved in hormone signaling and abiotic stress processes. Objective/Methods: To examine the potential effects of the GA2 oxidase gene on Solanum pennellii, one of the important stress-tolerance wild species of tomato, a systematic analysis was performed to study the structure, phylogenetic tree, genomic locus, and upstream cis-regulatory elements of SpGA2ox genes. The expression patterns of the SpGA2ox family in various tissues were analyzed on the basis of published RNA-seq data, and the changes in SpGA2ox expression in the leaves of seedlings were detected under salinity stress and GA treatment by real-time fluorescence quantitative PCR. Results: We identified nine SpGA2ox genes in S. pennellii. They were located on chromosomes 1, 2, 4, 7, 8, and 10. The SpGA2ox family was clearly divided into three groups through phylogenetic relationship analysis, namely, five in C19-GA2ox class I, one in C19-GA2ox class II, and three in C20-GA2ox class. And cis-element analysis provided the basis for understanding the function of growth, development, hormones, and abiotic stress of GA2ox genes in S. pennellii. The expression patterns of the SpGA2ox family were different in three classes, and SpGA2ox1 exhibited higher expression levels in the stem compared to other tissues. The expression levels of all SpGA2ox genes increased significantly under salt stress and decreased by treatment with GA3. With the largest changes in relative expression levels, SpGA2ox3 and SpGA2ox8 might exert key effects on the regulation of GA synthesis and the response to salt stress. Conclusions: The present study may be instrumental for further investigation into the impact of SpGA2oxs on responses to abiotic stress and provide potential targets for the genetic improvement of S. pennellii. Full article
(This article belongs to the Special Issue Horticultural Plants Research from an Omics Perspective)
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14 pages, 12339 KiB  
Article
Transcriptomic Profiling Highlights Metabolic and Biosynthetic Pathways Involved in In Vitro Flowering in Anoectochilus roxburghii (Wall.) Lindl.
by Shuisheng Yu, Julian Liu, Chenchen Cai, Yi Zhang, Shuangbin Fu, Yanping Yang, Zhuang Zhou and Zhen Ying
Genes 2025, 16(2), 132; https://doi.org/10.3390/genes16020132 - 24 Jan 2025
Viewed by 609
Abstract
Background: Tissue culture is one of the most important methods for propagating orchids. Notably, many orchid seedlings exhibit autonomous flowering during the cultivation process. To explore the underlying mechanism, Anoectochilus roxburghii (Wall.) Lindl., an orchid that spontaneously forms in vitro flowers, was analyzed [...] Read more.
Background: Tissue culture is one of the most important methods for propagating orchids. Notably, many orchid seedlings exhibit autonomous flowering during the cultivation process. To explore the underlying mechanism, Anoectochilus roxburghii (Wall.) Lindl., an orchid that spontaneously forms in vitro flowers, was analyzed in this study. Methods: Bud samples at the early, middle, and fully open stages were collected for transcriptome sequencing, followed by differential expression, trend, enrichment and protein–protein interaction (PPI) network analyses. Results: Differential gene expression analysis identified 2364, 4137, and 6522 differentially expressed genes (DEGs) in the early vs. middle, middle vs. open, and early vs. open comparisons, respectively. These DEGs were significantly enriched in various metabolic and biosynthetic pathways, particularly in ko01100 (metabolic pathways). PPI network analysis further identified hub genes, including MCM3, MCM4, and MCM7, which are associated with DNA replication, and CURL3, which is linked to plant hormone signal transduction pathways. Conclusion: Our findings provide novel insights into the molecular mechanisms driving in vitro flowering in A. roxburghii, highlighting the importance of metabolic and biosynthetic process signaling in this unique developmental transition. These results provide valuable resources for future studies on orchid propagation and floral development. Full article
(This article belongs to the Special Issue Horticultural Plants Research from an Omics Perspective)
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16 pages, 4759 KiB  
Article
Genetic Evidence of SpGH9A3 in Leaf Morphology Variation of Spathiphyllum ‘Mojo’
by Songlin Yang, Minghua Hu, Runxin Wu, Zhiwen Hou, Huan Zhang, Wenying He, Lili Gao and Feixiong Liao
Genes 2024, 15(9), 1132; https://doi.org/10.3390/genes15091132 - 28 Aug 2024
Viewed by 1090
Abstract
Leaves play a crucial role as ornamental organs in Spathiphyllum, exhibiting distinct differences across various Spathiphyllum varieties. Leaf development is intricately linked to processes of cell proliferation and expansion, with cell morphology often regulated by plant cell walls, primarily composed of cellulose. [...] Read more.
Leaves play a crucial role as ornamental organs in Spathiphyllum, exhibiting distinct differences across various Spathiphyllum varieties. Leaf development is intricately linked to processes of cell proliferation and expansion, with cell morphology often regulated by plant cell walls, primarily composed of cellulose. Alterations in cellulose content can impact cell morphology, subsequently influencing the overall shape of plant organs. Although cellulases have been shown to affect cellulose levels in plant cells, genetic evidence linking them to the regulation of leaf shape remains limited. This study took the leaves of Spathiphyllum ‘Mojo’ and its somatic variants as the research objects. We screened four cellulase gene family members from the transcriptome and then measured the leaf cellulose content, cellulase activity, and expression levels of cellulase-related genes. Correlation analysis pinpointed the gene SpGH9A3 as closely associated with leaf shape variations in the mutant. Green fluorescent fusion protein assays revealed that the SpGH9A3 protein was localized to the cell membrane. Notably, the expression of the SpGH9A3 gene in mutant leaves peaked during the early spread stage, resulting in smaller overall leaf size and reduced cellulose content upon overexpression in Arabidopsis. Full article
(This article belongs to the Special Issue Horticultural Plants Research from an Omics Perspective)
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