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Horticulturae
Special Issues
Multi-Omics-Driven Breeding for Tropical Horticultural Crops
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Multi-Omics-Driven Breeding for Tropical Horticultural Crops

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 1079

Special Issue Editors

Dr. Zhuang Yang

E-Mail Website
Guest Editor
College of Tropical Crops, Hainan University, Haikou 570228, China
Interests: metabolomics; genomics; phenomics; plant multi-omics database
Dr. Pengfei Wang

E-Mail Website
Guest Editor
Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
Interests: molecular genetics; molecular population genetics; genomics; multiomics
Prof. Dr. Zhiqiang Xia

E-Mail Website
Guest Editor
College of Tropical Crops, Hainan University, Haikou 570228, China
Interests: genomics; multi-omics; big data breeding; artificial intelligence; deep omics

Special Issue Information

Dear Colleagues,

Tropical plants are predominantly found in regions such as Southeast Asia, South Asia, the Amazon River Basin in South America, and the Congo River Basin in Africa, with the total number of species estimated to reach up to 200,000. These plants are characterized by their irreplaceability, high species diversity, and scarcity, making them highly sought after across various countries, which in turn drives robust market demand and a promising industrial outlook.

However, in comparison to plants from other regions, research utilizing multi-omics approaches on tropical plants remains relatively underdeveloped, with many tropical species still lacking corresponding genomic data and comprehensive analyses of key metabolites or traits. To address this gap and promote further research on tropical plants, we have organized a special issue titled "Multi-Omics-Driven Breeding for Tropical Horticultural Crops".

This Research Topic aims to collect various omics data of tropical plants, including the genomes, transcriptomes, metabolomes, and proteomes, as well as the latest research advancements related to relevant databases and omics analysis tools. We also welcome submissions of original research and review articles, including but not limited to studies on the following topics:

Including

  • The deciphering of tropical plant genomes.
  • Tropical plant genome databases and omics analysis tools.
  • Analysis of important traits of tropical plants based on comparative genomics.
  • Transcriptome, metabolome and other multi-omics joint analysis mining tropical plant gene functions.

Dr. Zhuang Yang
Dr. Pengfei Wang
Prof. Dr. Zhiqiang Xia
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. Horticulturae 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 2200 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

  • tropical plant
  • genome
  • multi-omics
  • databases
  • analysis tools

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Published Papers (3 papers)

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Research

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20 pages, 2826 KB  
Article
Integrated Multi-Omics Reveals Anthocyanin Biosynthesis Control During Fruit Peel Color Development in Jaboticaba ‘Essart’
by Zhiheng Lin, Ke Deng, Fei Chen and Long Zhao
Horticulturae 2025, 11(12), 1515; https://doi.org/10.3390/horticulturae11121515 - 15 Dec 2025
Viewed by 186
Abstract
The color change in the peel of Jaboticaba (Myrciaria cauliflora Berg) ‘Essart’ is primarily driven by the spatiotemporal regulation of anthocyanin biosynthesis, but its molecular mechanism remains unclear. This study employed a multi-omics integrated analysis approach, combining targeted metabolomics, transcriptomics, and [...] Read more.
The color change in the peel of Jaboticaba (Myrciaria cauliflora Berg) ‘Essart’ is primarily driven by the spatiotemporal regulation of anthocyanin biosynthesis, but its molecular mechanism remains unclear. This study employed a multi-omics integrated analysis approach, combining targeted metabolomics, transcriptomics, and small RNA sequencing, to systematically elucidate the regulatory mechanism underlying color change during Jaboticaba fruit peel development. The results showed that during the color-turning stage, the content of most anthocyanins tended to decrease, while the content of Cyanidin significantly increased during the fully ripe stage. Weighted Gene Co-expression Network Analysis (WGCNA) identified the brown module as a highly relevant module for anthocyanin accumulation, which includes a co-expression network of 98 transcription factors and 6 structural genes (F3H, CHI, ANS, CHS). Furthermore, small RNA sequencing results discovered a novel regulatory relationship: plant-MIR408-4—McMYB88. This regulatory relationship exhibited precise temporal dynamics: during the green fruit stage, plant-MIR408-4 was highly expressed and McMYB88 was lowly expressed, thereby inhibiting anthocyanin synthesis; however, during the fully ripe stage, plant-MIR408-4 expression decreased and McMYB88 expression increased, promoting anthocyanin accumulation. In summary, this study revealed the molecular regulatory mechanism of color formation in Jaboticaba fruit peel, providing an important theoretical basis for its color improvement and molecular breeding. Full article
(This article belongs to the Special Issue Multi-Omics-Driven Breeding for Tropical Horticultural Crops)
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10 pages, 2427 KB  
Article
A Scheme for Speed Breeding of Tomato Through Modification of the Light Environment
by Youzhi Hu, Xinyang He, Jun Ju, Minggui Zhang, Xiaolong Yang, Jiali Song and Houcheng Liu
Horticulturae 2025, 11(12), 1488; https://doi.org/10.3390/horticulturae11121488 - 9 Dec 2025
Viewed by 233
Abstract
This study aimed to determine optimal light recipes for speed breeding of tomato (Solanum lycopersicum L.) in a plant factory. Two tomato cultivars, Zuanhongmeili and Xiaokeai, were investigated. In Experiment 1, conducted under a 12 h photoperiod, both cultivars showed accelerated [...] Read more.
This study aimed to determine optimal light recipes for speed breeding of tomato (Solanum lycopersicum L.) in a plant factory. Two tomato cultivars, Zuanhongmeili and Xiaokeai, were investigated. In Experiment 1, conducted under a 12 h photoperiod, both cultivars showed accelerated development with increasing light intensity. The optimal light intensity range of 300–400 μmol·m−2·s−1 promoted development and seed maturation. Under these conditions, Zuanhongmeili and Xiaokeai achieved flower bud emergence in the shortest times, at 24.91 ± 0.13 and 24.91 ± 0.12 days after sowing (DAS), respectively. Furthermore, for the two cultivars, anthesis initiation occurred at 39.08 ± 0.62 and 35.78 ± 0.19 DAS, fruit setting at 41.31 ± 0.61 and 38.54 ± 0.24 DAS, and the breaker stage at 83.05 ± 1.05 and 69.78 ± 0.29 DAS, respectively, under these conditions. Critically, germinable seeds were harvested from each cultivar as early as 63 and 60 DAS, projecting a theoretical annual generational turnover of up to six cycles. Based on these results, a baseline irradiance of 350 μmol·m−2·s−1 was selected for Experiment 2, which independently assessed the impact of photoperiod. Zuanhongmeili and Xiaokeai both showed accelerated development with increases in photoperiod. The optimal photoperiod of 20 h promoted development and seed maturation. Under a 20 h photoperiod, Zuanhongmeili and Xiaokeai achieved flower bud emergence in the shortest times, at 25.12 ± 0.09 and 23.76 ± 0.13 DAS, respectively. Furthermore, anthesis initiation occurred at 41.21 ± 0.66 and 37.27 ± 0.34 DAS, fruit setting at 44.51 ± 0.15 and 40.25 ± 0.08 DAS, and the breaker stage at 91.19 ± 0.59 and 77.47 ± 0.36 DAS, respectively, under these conditions. The shortest times to harvest of germinable seeds from the two cultivars in this experiment were 76 and 72 DAS. Overall, this study demonstrates that tailored light environments, particularly the light intensity regime identified in Experiment 1, can dramatically accelerate tomato growth and development, enabling production of six generations per year in a controlled environment. Full article
(This article belongs to the Special Issue Multi-Omics-Driven Breeding for Tropical Horticultural Crops)
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Review

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27 pages, 1696 KB  
Review
Biotechnologies for Promoting Germplasm Resource Utilization and Preservation of the Coconut and Important Palms
by Ke Deng, Shuya Yang, Sisunandar Sisunandar, Binh-Minh Tran, Mridula Kottekate, Nancy Shaftang and Zhihua Mu
Horticulturae 2025, 11(12), 1461; https://doi.org/10.3390/horticulturae11121461 - 3 Dec 2025
Viewed by 448
Abstract
Coconut (Cocos nucifera L.) plays a vital economic and cultural role in many tropical and subtropical regions. A comprehensive review of the existing literature underscores that advanced biotechnologies are pivotal in unlocking the full potential of coconut germplasm exchange, which is crucial [...] Read more.
Coconut (Cocos nucifera L.) plays a vital economic and cultural role in many tropical and subtropical regions. A comprehensive review of the existing literature underscores that advanced biotechnologies are pivotal in unlocking the full potential of coconut germplasm exchange, which is crucial for the future sustainability of this crop. While traditional exchange methods are hampered by phytosanitary risks and logistical burdens, biotechnological interventions such as in vitro conservation and cryopreservation present targeted solutions to overcome these bottlenecks. The exchange, facilitated by these technologies, allows for the efficient introduction of desirable traits. We indicate that diversification and germplasm exchange hold the key to improving coconut quality and yield, developing varieties resistant to pests and diseases, and ensuring long-term conservation of coconut genetic diversity. This review highlights the potential to overcome the challenges faced by regional breeding programs often hindered by restricted genetic resources. Furthermore, by examining past successes and challenges in coconut germplasm identification and exchange, we offer perspectives on optimizing strategies to conserve diversity. This work emphasizes that germplasm exchange paves the way for coconut varieties that can thrive under changing environmental conditions, securing the future of this highly valuable crop. Full article
(This article belongs to the Special Issue Multi-Omics-Driven Breeding for Tropical Horticultural Crops)
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