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Recent Advances in Horticultural Plant Genomics—2nd Edition
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Recent Advances in Horticultural Plant Genomics—2nd Edition

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 December 2026 | Viewed by 883

Special Issue Editors

Prof. Dr. Zhongxiong Lai

E-Mail Website
Guest Editor
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: horticultural crops; genomics; tissue culture; molecular biology; germplasm; somatic embryogenesis
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yuling Lin

E-Mail Website
Guest Editor
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: genomics and biotechnology; plant tissue culture; non-coding RNA; molecular biology; somatic embryogenesis
Special Issues, Collections and Topics in MDPI journals
Dr. Yuqiong Guo

E-Mail Website
Guest Editor
College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: tea processing; tea biotechnology; tea biochemistry; genomics; molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Whole-genome sequencing of plants and animals has developed rapidly over the past 20 years. With the development of sequencing technologies and the reduction in sequencing costs, an increasing number of plant genomes have been sequenced with many results obtained, especially since the advent and application of second- and third-generation sequencing and Hi-C technologies, which have made sequencing a reality in many complex plant genomes. By the end of 2022, more than 400 plant genome sequences have become available, mostly of horticultural plants. Developing and applying sequencing technologies has not only reduced the time needed for and cost of whole-genome sequencing, but has also brought the study and understanding of plants to the whole-genome level, providing a new perspective for understanding gene structure, composition, and function; gene regulation; and species evolution at the molecular level. With advances in high-throughput sequencing technology, multiomics, such as pan-genomics, transcriptomics, and genome-wide non-coding RNAs, have been rapidly developed. Genomic research tools are widely used in horticultural plants such as fruit trees, vegetables, flowers, tea plants, and Chinese herbs for molecular breeding and analyzing growth and development patterns, providing a new perspective on horticultural plant research, which can provide a greater understanding of the evolutionary histories of plant species and genomic resources for molecular studies on the economically important traits of horticultural plants.

Prof. Dr. Zhongxiong Lai
Prof. Dr. Yuling Lin
Dr. Yuqiong Guo
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 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

  • genomics
  • non-coding RNA
  • transcriptomics

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Published Papers (2 papers)

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Research

16 pages, 4892 KB  
Article
Transcriptomics and Gene Family Identification of Cell Wall-Related Differentially Expressed Genes Reveal MaXTH32.5 Involved in Fruit Firmness During Banana Ripening
by Fengjie Yang, Kui Wan, Xiaoli Kang, Wanting Zhong, Jiasi Lv, Yiyao Lin, Jialing Wang, Zhongxiong Lai, Bin Liao and Yuling Lin
Plants 2025, 14(24), 3810; https://doi.org/10.3390/plants14243810 - 14 Dec 2025
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Abstract
Banana (Musa spp.) is a typical climacteric fruit. Xyloglucan endotransglucosylase/hydrolase (XTH) is a key factor regulating plant cell wall dynamic remodeling and participates in fruit ripening. To clarify the core physiological traits of banana ripening, four ripening stages of banana [...] Read more.
Banana (Musa spp.) is a typical climacteric fruit. Xyloglucan endotransglucosylase/hydrolase (XTH) is a key factor regulating plant cell wall dynamic remodeling and participates in fruit ripening. To clarify the core physiological traits of banana ripening, four ripening stages of banana cultivar (Musa AAA ‘Minai No. 1’) fruits in the fully green stage (S1), green-yellow stage (S2), fully yellow stage (S3), and yellow with brown spots stage (S4) were used in this study’s experimental materials, to examine dynamic changes in key physiological–biochemical properties. The results showed that fruit firmness decreased continuously, starch content first increased then decreased, and soluble protein and total soluble solids (TSS) accumulated gradually during the ripening stages of banana fruits. Transcriptome analysis of the four stages found that there were 14,315 differentially expressed genes (DEGs) in S1 versus S4, the GO enrichment pathway is enriched in “protein dephosphorylation”, and the KEGG enrichment pathway is enriched in the “Protein processing in endoplasmic reticulum” and “Ubiquitin mediated proteolysis” pathways. The fruit ripening process involves the processing of numerous proteins. The heatmap revealed that MaXTH32.5 was significantly up-regulated during banana ripening and the result of RT-qPCR is consistent with the transcriptome data. A total of 989 XTH members across 16 Musa varieties of the XTH gene family were further identified. Among them, MaXTH32.5 localized at the chloroplast, and transient overexpression of MaXTH32.5 significantly reduced banana fruit firmness and may be involved in regulating ripening in banana fruits. This study indicated that the differential expression of XTH gene family members may regulate ripening-related processes in banana and MaXTH32.5 as a key candidate, providing insights into banana ripening mechanisms and a foundation for subsequent Musa XTH research. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics—2nd Edition)
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19 pages, 3516 KB  
Article
Multi-Omics Analysis Unravels the Biosynthesis and Regulatory Mechanisms of Floral Scent Across Various Cultivars and Developmental Stages in Phalaenopsis
by Huaiqin Zhong, Yan Chen, Shengyuan Zhong, Jun He, Bing Lin, Jianshe Wu and Ronghui Fan
Plants 2025, 14(23), 3682; https://doi.org/10.3390/plants14233682 - 3 Dec 2025
Viewed by 454
Abstract
Phalaenopsis is one of the most economically valuable genera in the Orchidaceae family. However, the common varieties of Phalaenopsis in the market rarely have fragrance, greatly limiting the sustainable development of the Phalaenopsis industry. Here, an integrated investigation was conducted on the patterns [...] Read more.
Phalaenopsis is one of the most economically valuable genera in the Orchidaceae family. However, the common varieties of Phalaenopsis in the market rarely have fragrance, greatly limiting the sustainable development of the Phalaenopsis industry. Here, an integrated investigation was conducted on the patterns and determinants of aroma release in Phalaenopsis. GC-MS/MS analysis revealed that the primary volatile organic compounds (VOCs) in 10 fragrant Phalaenopsis cultivars are consistent. Terpenoids, alcohols, ketones, and esters collectively accounted for an average of 66.59% of the total VOCs across these 10 varieties. By performing metabolomic and transcriptomic analyses, we investigated the variation in 1532 VOCs in four different developmental stages of Phalaenopsis Formosa Sweet Memory. Metabolite analysis revealed that the levels of total volatiles, terpenoids, esters, and heterocyclic compounds were significantly upregulated during the flowering stages, and Linalool, β-Ocimene, and Methyl Benzoate were selected as key metabolites. While analyzing the correlation network between aroma components synthesis and differentially expressed genes, 33 key structural genes were detected and regulated by transcription factors. PAXXG356500_TPS, PAXXG333030_4CL, and PAXXG061420_SAM were key genes in the terpenoids and esters’ biosynthetic pathway, and they were co-expressed with aroma release. In summary, this study characterized the key metabolic pathways involved in aroma formation in Phalaenopsis and constructed the corresponding transcriptional regulatory network. These results laid a theoretical foundation for the subsequent research on aroma of Phalaenopsis and genetic engineering technology breeding. Full article
(This article belongs to the Special Issue Recent Advances in Horticultural Plant Genomics—2nd Edition)
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