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Omics in Horticultural Crops
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Omics in Horticultural Crops

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 October 2025 | Viewed by 1246

Special Issue Editors

Dr. Octavio Martínez

E-Mail Website
Guest Editor
Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
Interests: computational biology; transcriptomics; Capsicum; modeling of gene and metabolite expression; domestication
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Neftalí Ochoa-Alejo

E-Mail Website
Guest Editor
Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36824, Guanajuato, Mexico
Interests: Capsicum; chili pepper; tissue culture; biochemistry; molecular biology; secondary compounds; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticulture is the science and art of growing fruits, vegetables, flowers, and ornamental plants, or, alternatively, horticulture is the branch of plant agriculture dealing with garden crops, generally fruits, vegetables, and ornamental plants. Horticultural crops include important species such as Solanum lycopersicum (tomato), Solanum tuberosum (potato), Solanum melongena (eggplant), Capsicum spp. (chili peppers), Nicotiana tabacum (tobacco), and Petunia, all of them belonging to the Solanaceae family, which comprises approximately 100 genera and 2500 species. The Cucurbitaceae family consists of 101 genera and 965 species, of which Cucumis melo (melon), Cucumis sativus (cucumber), Cucurbita pepo (squash), and Citrullus lanatus (watermelon) are maybe the most relevant. The Brassicaceae family includes 372 genera and 4060 species, with Brassica oleracea (cabbage, cauliflower, and broccoli), Brassica napus (rapeseed), Raphanus sativus (common radish), and the model plant Arabidopsis thaliana as representatives.

Some other horticultural families of importance are Umbelliferae (carrots, celery, and parsley), Amaryllidaceae (garlic, onion, shallots, and asparagus), Rosaceae (strawberry, cherry, raspberry, blackberry, pear, apple, and plum), Asteraceae or Compositae (lettuce, artichoke, chicory, and chamomile), Chenopodiaceae (spinach, and beets), Fabaceae (bean, pea, lentil, soybean, fava bean, and peanut), Liliaceae (important for its many garden ornamentals and houseplants), among others. In addition to their economic value, members of all these families have been model systems in plant biology research to study plant development, fruit development, and defense responses to different environmental stresses.

Omics represent powerful tools to investigate fundamental aspects of plant biology to reveal diverse molecular biology mechanisms involving not only the genomes, the expression of genes, or the encoded proteins, but also the ultimate metabolite products. All omics approaches are currently applied to horticultural crop breeding and improvement as well as strategies to investigate different plant aspects, such as changes in gene expression during growth, development, ripening, and senescence, and to study responses of plants to environmental stresses, changes in the quality of tubers, roots, bulbs, flowers, or fruits after harvesting, and even under storage conditions (postharvest).

This Special Issue of Plants aims to contribute to a comprehensive understanding of the diverse molecular biology aspects of horticultural crops through integrative omics advances

Dr. Octavio Martínez
Prof. Dr. Neftalí Ochoa-Alejo
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 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. 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

  • horticultural crops
  • vegetables
  • fruits
  • flowers
  • ornamentals
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics

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Published Papers (3 papers)

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Research

14 pages, 1487 KiB  
Article
Genome-Wide Association Analysis of Sweet Pepper (Capsicum annuum) Based on Agronomic Traits Using PepperSNP50K
by Yaolong Wang, Entong Li, Jiawei Lu, Jing Wang, Qiaolu Zang, Yanping Liang, Ruxia Tian, Changwei Zhang, Fangling Jiang and Yan Cheng
Plants 2025, 14(10), 1506; https://doi.org/10.3390/plants14101506 - 17 May 2025
Viewed by 251
Abstract
As one of the most important vegetables globally, peppers have garnered significant attention from breeders due to their diverse agronomic traits, including plant type, leaf shape, and maturity. Understanding the genetic mechanisms underlying these traits is crucial for systematic advancements in sweet pepper [...] Read more.
As one of the most important vegetables globally, peppers have garnered significant attention from breeders due to their diverse agronomic traits, including plant type, leaf shape, and maturity. Understanding the genetic mechanisms underlying these traits is crucial for systematic advancements in sweet pepper breeding. In this study, leveraging the PepperSNP50K liquid breeding chip, we conducted a comprehensive analysis of horticultural traits and genetic diversity using sweet pepper germplasm samples. Initially, the sweet pepper populations were analyzed using SNP-based liquid chip technology. Subsequently, phenotypic surveys were performed on 217 sweet pepper samples, and the collected phenotypic data were integrated with SNP markers to conduct a genome-wide association study (GWAS) of key agronomic traits. Among the 25 horticultural traits evaluated, 11 exhibited significant associations with 54 SNP polymerization regions and 193 candidate genes. These findings provide a robust foundation for the utilization of sweet pepper germplasm resources and the development of new, improved varieties. Furthermore, in this study, we identified Caz06g05770 (Lycopene beta-cyclase) as a candidate gene responsible for the color of mature ripe fruits. This research not only enhances our understanding of the genetic basis of sweet pepper traits but also offers a practical roadmap for advancing breeding programs and boosting agricultural productivity. By bridging the gap between genetic research and practical breeding applications, this study paves the way for the development of high-yield, high-quality sweet pepper varieties tailored to meet the growing demands of global agriculture. Full article
(This article belongs to the Special Issue Omics in Horticultural Crops)
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16 pages, 3991 KiB  
Article
Non-Target Metabolomics Reveals Changes in Metabolite Profiles in Distant Hybrid Incompatibility Between Paeonia sect. Moutan and P. lactiflora
by Wenqing Jia, Yingyue Yu, Zhaorong Mi, Yan Zhang, Guodong Zhao, Yingzi Guo, Zheng Wang, Erqiang Wang and Songlin He
Plants 2025, 14(9), 1381; https://doi.org/10.3390/plants14091381 - 3 May 2025
Viewed by 257
Abstract
Peonies are globally renowned ornamental plants, and distant hybridization is a key method for breeding new varieties, though it often faces cross-incompatibility challenges. The metabolic mechanisms underlying the crossing barrier between tree peony (Paeonia sect. Moutan) and herbaceous peony ( [...] Read more.
Peonies are globally renowned ornamental plants, and distant hybridization is a key method for breeding new varieties, though it often faces cross-incompatibility challenges. The metabolic mechanisms underlying the crossing barrier between tree peony (Paeonia sect. Moutan) and herbaceous peony (P. lactiflora) remain unclear. To identify key metabolites involved in cross-incompatibility, we performed a cross between P. ostii ‘Fengdanbai’ (female parent) and P. lactiflora ‘Red Sara’ (male parent) and analyzed metabolites in the stigma 12 h after pollination using UPLC-MS. We identified 1242 differential metabolites, with 433 up-regulated and 809 down-regulated, including sugars, nucleotides, amino acids, lipids, organic acids, benzenoids, flavonoids, and alkaloids. Most differential metabolites were down-regulated in hybrid stigmas, potentially affecting pollen germination and pollen tube growth. Cross-pollinated stigma exhibited lower levels of high-energy nutrients (such as amino acids, nucleotides, and tricarboxylic acid cycle metabolites) compared to self-pollinated stigma, which suggests that energy deficiency is a contributing factor to the crossing barrier. Additionally, cross-pollination significantly impacted KEGG pathways such as nucleotide metabolism, purine metabolism, and vitamin B6 metabolism, with most metabolites in these pathways being down-regulated. These findings provide new insights into the metabolic basis of cross-incompatibility between tree and herbaceous peonies, offering a foundation for overcoming hybridization barriers in peony breeding. Full article
(This article belongs to the Special Issue Omics in Horticultural Crops)
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15 pages, 3935 KiB  
Article
Identification of the UGT Family and Functional Validation of MwUGT2 in Meconopsis wilsonii
by Lin Zhou, Xiaojuan Chen, Wenkun Su, Zhi Ou and Yan Qu
Plants 2025, 14(6), 944; https://doi.org/10.3390/plants14060944 - 17 Mar 2025
Viewed by 349
Abstract
Flower color is one of the most ornamental values of Meconopsis wilsonii, but very limited studies have been reported on its flower color formation. The UDP-glycosyltransferase (UGT) gene family plays a crucial role in plant flower color formation. In this study, the [...] Read more.
Flower color is one of the most ornamental values of Meconopsis wilsonii, but very limited studies have been reported on its flower color formation. The UDP-glycosyltransferase (UGT) gene family plays a crucial role in plant flower color formation. In this study, the full-length transcriptome data of M. wilsonii was used to identify MwUGTs, focusing on protein physicochemical properties’ subcellular localization, and phylogenetic relationships. In addition, sequence analysis, expression pattern analysis, subcellular localization, and functional validation of MwUGT2 were also performed. A total of 26 MwUGTs were identified in full-length transcriptome and clustered into eight subgroups. Phylogenetic analysis and KEGG database annotation showed that MwUGT2 is associated with anthocyanin synthesis and accumulation. Subsequently, based on the expression of MwUGT2 during flower development and in different tissues, it was preliminarily determined that MwUGT2 plays a role in the flower bud stage. Subcellular localization assays suggested that MwUGT2 is present in the nucleus and cytoplasm. Overexpression in Nicotiana tabacum showed that MwUGT2 significantly increased the content of Cyanidin-3-O-glucoside and resulted in dark pink flowers in transgenic plants. In summary, our findings suggest that MwUGT2 plays a crucial role in the biosynthesis of anthocyanin and will also contribute to understanding the mechanisms of flower color formation in M. wilsonii. Full article
(This article belongs to the Special Issue Omics in Horticultural Crops)
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