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Horticulturae
Special Issues
Genomics and Genetic Diversity in Vegetable Crops
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Genomics and Genetic Diversity in Vegetable 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: 20 December 2025 | Viewed by 3285

Special Issue Editors

Dr. Zhoubin Liu

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Guest Editor
Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
Interests: pepper; plant physiology; gene functional analysis; plant biotechnology; genetics and genomics
Dr. Junheng Lv

E-Mail Website
Guest Editor
Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
Interests: agriculture; biotechnology; gene mapping; genetics and genomics
Dr. Zhangsheng Zhu

E-Mail Website
Guest Editor
College of Horticulture, South China Agricultural Unbiersity, Guangzhou 510642, China
Interests: Caspicum; genetics; omics; secondary metabolites
Dr. Zhiqin Liu

E-Mail Website
Guest Editor
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350001, China
Interests: solanaceae vegetables; plant immunity; plant physiology; plant biochemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Vegetable crops are an important source of people’s daily diet and are widely eaten around the world because they are rich in health-promoting vitamins and mineral nutrients. With a growing global population and increasing demand for nutritious food, there is an urgent need to improve vegetable production, quality, and resilience to environmental challenges. At present, genomics and genetic diversity research have become powerful tools to achieve the improvement in vegetable varieties by revealing the genetic basis and improving the important genetic traits.

This Special Issue aims to collect the latest research results in the field of vegetable genomics and genetic diversity. This Special Issue focuses on the research progress of the genetic regulation mechanism of key traits and the development of excellent varieties of vegetables by using modern biotechnology such as genomics in growth and development and resistance to abiotic stress. All kinds of vegetables are welcome, including but not limited to peppers, cabbage, tomatoes, cucumbers, watermelons, melons, broccoli, and carrots.

Dr. Zhoubin Liu
Dr. Junheng Lv
Dr. Zhangsheng Zhu
Dr. Zhiqin Liu
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. 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

  • vegetables
  • genomics
  • genetic diversity
  • growth and development
  • biotic and abiotic stresses
  • molecular mechanism

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Published Papers (5 papers)

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Research

14 pages, 6325 KiB  
Article
Genome-Wide Analysis of Mlo Genes and Functional Characterization of Cm-mlo38 and Cm-mlo44 in Regulating Powdery Mildew Resistance in Melon
by Fangyi Gong, Yanhong Lan, Tian Zhang, Chun Li, Yifan Li, Feng Xia, Xiaojun Liu, Duchen Liu, Genyun Liang, Peng Cai and Chao Fang
Horticulturae 2025, 11(5), 509; https://doi.org/10.3390/horticulturae11050509 - 8 May 2025
Viewed by 267
Abstract
The Mildew Resistance Locus (Mlo) gene family is reported in various species as regulators of powdery mildew (PM) resistance. However, the Mlo genes in cucurbit crops remain limited. In this study, a genome-wide investigation of Mlo genes was conducted in eight Cucurbitaceae species [...] Read more.
The Mildew Resistance Locus (Mlo) gene family is reported in various species as regulators of powdery mildew (PM) resistance. However, the Mlo genes in cucurbit crops remain limited. In this study, a genome-wide investigation of Mlo genes was conducted in eight Cucurbitaceae species and in rice, maize, arabidopsis, and barley, and a total of 202 Mlo genes were identified. The phylogenetic analysis showed that 202 Mlo genes can be classified into six clades, and the Mlo genes from clades I and III are likely pivotal in regulating PM resistance in dicotyledonous and monocotyledonous plants, respectively. The Ka/Ks ratios for these homologous Mlo gene pairs ranged from 0 to 0.6, revealing that they underwent substantial purifying selection during evolution. Among 12 crops, there were the most Mlo genes (22 Cm-mlo) in melon. An expression analysis revealed that six Cm-mlo genes showed expression responses to PM infection in which Cm-mlo38 and Cm-mlo44 were phylogenetically close to Mlo genes that regulated PM resistance. Using the VIGS system for silencing, Cm-mlo38 and Cm-mlo44 enhanced resistance to PM in susceptible material. A protein interaction analysis indicated that Cm-mlo38 might regulate PM resistance through interactions with PR5 and CML proteins. These results provide a comprehensive understanding of the Mlo family in Cucurbitaceae and pave the way for future functional analysis and genetic improvement for improving PM resistance in Cucurbitaceae. Full article
(This article belongs to the Special Issue Genomics and Genetic Diversity in Vegetable Crops)
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19 pages, 16816 KiB  
Article
Genome-Wide Identification and Expression Analysis of UBP Genes in Peppers (Capsicum annuum L.)
by Xuerui Chang, Tiantian Wang, Jiaxin Huang, Jia Xu, Yangyang Ruan, Yanping Liang and Jing Wang
Horticulturae 2025, 11(5), 458; https://doi.org/10.3390/horticulturae11050458 - 25 Apr 2025
Viewed by 350
Abstract
The ubiquitin-specific protease (UBP) family constitutes the largest group within the deubiquitinating enzymes (DUBs) and plays a crucial role in regulating the cell cycle, growth, and developmental processes in living organisms. By utilizing genomic and transcriptomic databases, we employed bioinformatics tools [...] Read more.
The ubiquitin-specific protease (UBP) family constitutes the largest group within the deubiquitinating enzymes (DUBs) and plays a crucial role in regulating the cell cycle, growth, and developmental processes in living organisms. By utilizing genomic and transcriptomic databases, we employed bioinformatics tools to identify UBP family members within pepper genomes and to analyze the expression profiles of CaUBP genes under various abiotic stresses, as well as in different tissues and organs. Our findings revealed the presence of 40 CaUBPs in peppers, exhibiting significant variation in their physicochemical properties. Subcellular localization studies indicated that all CaUBPs are localized in the nucleus. Phylogenetic analysis categorized the 40 CaUBPs into 11 distinct subfamilies (G1–G11), with the largest subfamily comprising seven members. Members within the same subfamily displayed similar domain and motif structures. The promoter regions of CaUBP genes were found to be enriched with elements responsive to light, stress, and hormones. Syntenic analysis revealed that 12 CaUBPs were mapped to the Arabidopsis thaliana genome, suggesting potential functional conservation. Additionally, tandem duplications were observed in the alignment of two sets of genes within the pepper genome. CaUBPs were implicated in the stress response and organ growth, with CaUBP17/34/35 showing significant changes in expression under heat stress. While most genes were not expressed in leaves, the expression of several genes (CaUBP3/17/27/32/35/38) in flowers was significantly altered. This study establishes a foundation for further exploration of the roles of CaUBPs in pepper growth, development, and stress response mechanisms. Full article
(This article belongs to the Special Issue Genomics and Genetic Diversity in Vegetable Crops)
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15 pages, 8706 KiB  
Article
Genome-Wide Identification of the SmHD-zip Genes That Respond to Multiple Ripening-Related Signals in Eggplant Fruit
by Caiqian Jiang, Yunrong Mo, Haoran Zhang, Kaiyun Chen, Ying Zhou, Zushuai Ma, Yuhao Jing, Yu Liu, Yanyan Wang and Kai Zhao
Horticulturae 2025, 11(3), 261; https://doi.org/10.3390/horticulturae11030261 - 28 Feb 2025
Viewed by 385
Abstract
The homeodomain–leucine zipper (HD-zip) gene family plays a crucial role in plant development and stress responses. However, systematic identification studies of this gene family in eggplant are still lacking. In this study, we systematically identified 44 HD-zip [...] Read more.
The homeodomain–leucine zipper (HD-zip) gene family plays a crucial role in plant development and stress responses. However, systematic identification studies of this gene family in eggplant are still lacking. In this study, we systematically identified 44 HD-zip genes in the eggplant genome database using bioinformatics methods and analyzed their expression levels under light and multiple hormones by RT-qPCR. The results show that members of the SmHD-zip gene family were classified into four groups (HD-zip I, II, III, and IV) based on the phylogenetic relationship. Cis-acting elements related to plant development, hormones, and stress were identified in the promoter regions of the SmHD-zip gene family. Furthermore, the expression of the SmHDZ2 gene was upregulated during the fruit development stage, while nine SmHD-zip genes exhibited downregulated expression patterns. Notably, some SmHD-zip genes were identified as key regulators of eggplant responses to light and multiple hormone signals. Overall, these findings not only provide valuable insights into the evolutionary and functional characteristics of eggplant HD-Zips but also suggest that HD-zip genes likely play a significant role in regulating fruit development and ripening by integrating light and multiple hormone signaling pathways. Therefore, this study laid the foundation for further research on eggplant quality. Full article
(This article belongs to the Special Issue Genomics and Genetic Diversity in Vegetable Crops)
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16 pages, 2739 KiB  
Article
Novel Alleles of the Potato Leaf Gene Identified in Italian Traditional Varieties Conferring Potato-like Leaf Shape in Tomato
by Lorenzo Mancini, Barbara Farinon, Ludovica Fumelli, Maurizio Enea Picarella, Andrea Mazzucato and Fabrizio Olivieri
Horticulturae 2025, 11(2), 129; https://doi.org/10.3390/horticulturae11020129 - 25 Jan 2025
Viewed by 833
Abstract
The genetic diversity of tomato in Italy and the growing interest in high-quality food products highlight the importance of establishing varietal distinctiveness through molecular strategies to ensure agrifood product quality and traceability. In this study, four Italian potato-like leaf (PL) landraces were analyzed: [...] Read more.
The genetic diversity of tomato in Italy and the growing interest in high-quality food products highlight the importance of establishing varietal distinctiveness through molecular strategies to ensure agrifood product quality and traceability. In this study, four Italian potato-like leaf (PL) landraces were analyzed: “Spagnoletta di Formia e di Gaeta” (SPA) from southern Lazio, “Giagiù” (GIA) and “Patanara” (PTN) from Campania, and “Pomodoro di Mola” (MOL) from Apulia. These landraces were genotyped for the potato leaf gene (C), with two PL American genotypes and a non-allelic PL mutant line included as outgroups. Nagcarlang served as control. An allelism test confirmed C as determinant gene. The SCAR marker for C revealed that the Italian landraces presented determinants other than the most representative one responsible for PL. Whole-genome sequencing of SPA identified a private novel nonsense SNP variant allele, confirmed through dCAPS marker analysis. Additionally, two novel PL alleles responsible for missense variations were identified in GIA/PTN and MOL. In silico protein analysis suggested that novel C alleles could be functional determinants for the protein activity. Overall, PL mutations identified for the first time could serve as molecular tools for agrifood chain traceability, enabling early differentiation and recognition of genotypically similar varieties. Full article
(This article belongs to the Special Issue Genomics and Genetic Diversity in Vegetable Crops)
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15 pages, 2067 KiB  
Article
Comprehensive Genetic Analysis of Edible-Podded Pea Genotypes: Variability, Heritability, and Multivariate Approach Across Two Agro-Climatic Zones in India
by Saurabh Yadav, Rajinder Kumar Dhall, Hira Singh, Parteek Kumar, Priti Sharma, Pradeep Kumar, Priyanka Kumari and Neha Rana
Horticulturae 2025, 11(1), 22; https://doi.org/10.3390/horticulturae11010022 - 1 Jan 2025
Viewed by 837
Abstract
Evaluating genetically superior genotypes is essential for developing new hybrid varieties. This study aimed to assess the genetic diversity of 28 edible-podded pea genotypes by analyzing phenological traits, vigor, yield, and biochemical traits across two distinct agro-climatic zones in India. Significant variation was [...] Read more.
Evaluating genetically superior genotypes is essential for developing new hybrid varieties. This study aimed to assess the genetic diversity of 28 edible-podded pea genotypes by analyzing phenological traits, vigor, yield, and biochemical traits across two distinct agro-climatic zones in India. Significant variation was observed for most traits, with high genotypic and phenotypic coefficients of variation, heritability, and genetic advance, especially in vigor, yield, and biochemical traits. Phenological traits, except for the node at which the first flower appeared, exhibited minimal variability, indicating a high degree of uniformity. Yield per plant was negatively correlated with plant height but positively correlated with pod length, the number of seeds per pod, the number of pods per plant, and pod weight, indicating the potential for the simultaneous selection of these traits in breeding programs. Principal component analysis (PCA) identified six components explaining over 75% of the total variation, with yield and biochemical traits contributing the most to the observed diversity. These findings provide crucial insights for breeders aiming to improve quantitative traits, supporting the development of high-yielding and climate-resilient edible-podded pea varieties in India. Full article
(This article belongs to the Special Issue Genomics and Genetic Diversity in Vegetable Crops)
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