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Horticulturae
Special Issues
Vegetable Genomics and Breeding Research
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Vegetable Genomics and Breeding Research

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: 31 August 2025 | Viewed by 8081

Special Issue Editors

Dr. Xiao Yang

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Guest Editor
Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (IUA-CAAS), Chengdu, China
Interests: horticulture; food science; agricultural plant science
Special Issues, Collections and Topics in MDPI journals
Dr. Feng Yang

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Guest Editor
Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Deyang Branch, Deyang 618099, China
Interests: vegetable breeding; vegetable genomics
Dr. Bin Liu

E-Mail Website
Guest Editor
Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
Interests: vegetable genomics; molecular breeding; gene editing

Special Issue Information

Dear Colleagues,

Vegetables play a crucial role in the human diet, providing essential vitamins, minerals, and dietary fibers necessary for maintaining health. With the global population on the rise and increasing demands for nutritious food, there is a pressing need to enhance vegetable production, quality, and resilience to environmental challenges. Genomics and breeding research have emerged as powerful tools in achieving these objectives by unraveling the genetic basis of important traits and developing improved varieties with desirable characteristics.

This Special Issue aims to compile cutting-edge research in the fields of vegetable genomics and breeding, focusing on advances in understanding the genetic architecture of key traits, genomic-assisted breeding methodologies, and the development of superior vegetable cultivars. Contributions covering a wide range of vegetables, including, but not limited to, tomatoes, peppers, cucumbers, lettuce, carrots, and onions, are welcome. Topics of interest include, but are not limited to, the following:

  1. Genome sequencing and the assembly of important vegetable crops.
  2. The identification and characterization of genes controlling agronomically important traits such as yield, quality, disease resistance, and abiotic stress tolerance.
  3. Functional genomics approaches to decipher gene function and regulatory networks in vegetables, especially associated with plant hormones.
  4. Marker-assisted selection (MAS) and genomic selection (GS) for the accelerated breeding of improved varieties.
  5. Integration of genomic data with traditional breeding methods for trait enhancement.
  6. Genomic resources and tools for vegetable breeding programs.
  7. Applications of genome editing technologies (e.g., CRISPR/Cas9) for targeted trait improvement in vegetables.
  8. Understanding the genetic basis of domestication and evolution in vegetable crops.
  9. Genomic approaches to address challenges related to climate change and sustainable agriculture in vegetable production systems.
  10. Speed breeding technology.

Researchers are invited to submit original research articles, reviews, and short communications related to vegetable genomics and breeding research for consideration in this Special Issue. Manuscripts should be prepared according to the journal's guidelines and submitted online through the journal's submission system. All submissions will undergo rigorous a peer review process to ensure high scientific quality and relevance to the theme of this Special Issue.

Dr. Xiao Yang
Dr. Feng Yang
Dr. Bin 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

  • vegetable genomics
  • plant breeding
  • molecular breeding
  • gene editing
  • genome sequencing

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Published Papers (6 papers)

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Research

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19 pages, 5405 KiB  
Article
Weighted Gene Co-Expression Network Analysis Identifies Hub Genes Governing Resistance to Fusarium oxysporum f. sp. niveum in Watermelon (Citrullus lanatus)
by Chen Zhang, Xufeng Fang, Jing Zhang, Xinying Wang, Zhao Liu, Shusen Liu, Zhengfeng Song, Peng Gao and Feishi Luan
Horticulturae 2025, 11(6), 625; https://doi.org/10.3390/horticulturae11060625 - 3 Jun 2025
Viewed by 363
Abstract
Watermelon (Citrullus lanatus), a vital economic crop, is severely threatened by Fusarium wilt (FW), which is caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. niveum (Fon). To elucidate the molecular mechanisms underlying FW resistance in watermelon, we tracked the [...] Read more.
Watermelon (Citrullus lanatus), a vital economic crop, is severely threatened by Fusarium wilt (FW), which is caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. niveum (Fon). To elucidate the molecular mechanisms underlying FW resistance in watermelon, we tracked the infection process via microscopy, identifying three critical time points (1, 6, and 8 days post-inoculation) corresponding to spore germination, hyphal invasion of the xylem vascular system, and symptom onset, respectively. Transcriptional profiling at these stages revealed six disease-resistance-associated gene modules through differential expression analysis, expression pattern clustering, weighted gene co-expression network analysis, and functional enrichment. These modules exhibited strong correlations with distinct infection phases. Protein–protein interaction networks identified 35 hub genes, including receptor-like kinases; WRKY and ethylene-responsive factor transcription factors; and genes involved in cell wall reinforcement, hormone signaling, defense metabolism/detoxification, programmed cell death regulation, and antimicrobial compound biosynthesis. Differential expressions of these genes across infection stages likely underpin the observed phenotypic disparities. Five hub regulatory genes were identified by quantitative real-time PCR in the SRgreen and SRblack modules, namely, Cla97C01G014990 (WRKY transcription factor 42), Cla97C02G042360 (calcium-transporting ATPase), Cla97C08G155710 (AIG2), Cla97C09G170380 (ethylene-responsive factor 1B-like), and Cla97C06G121810 (receptor kinase, putative). These genes mediate early rapid defense responses via SRgreen and sustain long-term resistance through SRblack. By validating the expression patterns of hub genes, the study elucidated the watermelon resistance response and provided insights into transcriptional regulation during different stages of Fon–watermelon interactions. Additionally, it identified candidate genes that could enhance watermelon resistance to wilt disease. Full article
(This article belongs to the Special Issue Vegetable Genomics and Breeding Research)
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12 pages, 3391 KiB  
Article
The Transcription Factor BrNAC19 Acts as a Positive Regulator of the Heat Stress Response in Chinese Cabbage
by Shuai Yuan, Xiaoping Yong, Yuxin Lu, Yuxin Lei, Weijian Li, Qiuli Shi and Xiuhong Yao
Horticulturae 2024, 10(12), 1236; https://doi.org/10.3390/horticulturae10121236 - 21 Nov 2024
Viewed by 1020
Abstract
The frequent occurrence of excessive heat events driven by global warming poses a great threat to plant growth and food security. To survive in heat stress (HS) environments, plants have evolved sophisticated response mechanisms, and the transcriptional network that controls the expression levels [...] Read more.
The frequent occurrence of excessive heat events driven by global warming poses a great threat to plant growth and food security. To survive in heat stress (HS) environments, plants have evolved sophisticated response mechanisms, and the transcriptional network that controls the expression levels of HS-inducible genes serves as an essential component of this process. NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) play key regulatory roles in the abiotic stress responses of plants. However, the functional roles of NAC TFs in the heat stress response of Chinese cabbage remain elusive. In the present study, we identified the Brassica rapa NAC family transcription factor BrNAC19 as a close homologue of Arabidopsis NAC019 and found that it serves as a positive regulator of the HS response. BrNAC19 displayed inducible gene expression in response to HS, and its subcellular localization showed that it was localized in the nucleus. Heterologous expression of BrNAC19 significantly enhanced the heat tolerance of plants and reduced the accumulation of reactive oxygen species (ROS) under HS conditions. Furthermore, our results demonstrated that BrNAC19 directly targeted and promoted the expression of superoxide dismutase 1 (CSD1) and catalase 2 (CAT2), two antioxidant-enzyme coding genes in Chinese cabbage. Altogether, our results suggest that BrNAC19 enhances heat stress tolerance by positively regulating the expression of genes involved in the HS response and ROS scavenging and exhibits potential as a target gene in Chinese cabbage breeding to increase heat stress tolerance. Full article
(This article belongs to the Special Issue Vegetable Genomics and Breeding Research)
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17 pages, 7053 KiB  
Article
Integrated Phenotypic Physiology and Transcriptome Analysis Revealed the Molecular Genetic Basis of Anthocyanin Accumulation in Purple Pak-Choi
by Qinyu Yang, Tao Huang, Li Zhang, Xiao Yang, Wenqi Zhang, Longzheng Chen, Zange Jing, Yuejian Li, Qichang Yang, Hai Xu and Bo Song
Horticulturae 2024, 10(10), 1018; https://doi.org/10.3390/horticulturae10101018 - 25 Sep 2024
Viewed by 1089
Abstract
Purple Pak-choi is rich in anthocyanins, which have both ornamental and edible health functions, and has been used more and more widely in facility cultivation. In order to further clarify the molecular mechanism of purple Pak-choi, two Pak-choi inbred lines (‘PQC’ and ‘HYYTC’) [...] Read more.
Purple Pak-choi is rich in anthocyanins, which have both ornamental and edible health functions, and has been used more and more widely in facility cultivation. In order to further clarify the molecular mechanism of purple Pak-choi, two Pak-choi inbred lines (‘PQC’ and ‘HYYTC’) were selected for the determination of pigment content and transcriptome analysis, and the key genes controlling the formation of purple character in leaves of Pak-choi were discovered. The results of pigment determination showed that the anthocyanin content of ‘PQC’ was 0.29 mg/g, which was about 100 times than ‘HYYTC’; The chlorophyll content of ‘HYYTC’ was 2.25 mg/g, while ‘PQC’ only contained 1.05 mg/g. A total of 20 structural genes related to anthocyanin biosynthesis and 28 transcriptional regulatory genes were identified by transcriptome analysis. Weighted gene co-expression network analysis (WGCNA) was used to construct the weight network analysis map of 14 genes. The results showed that the cinnamate hydroxylase gene (BraA04002213, BrC4H3), flavanone-3- hydroxylase (BraA09004531, BrF3H1), and chalcone synthetase (BraA10002265, BrCHS1) were the core genes involved in the anthocyanin synthesis pathway of purple Pak-choi. The results identified the key genes controlling the formation of purple leaf traits, which laid a foundation for further analysis of the molecular mechanism of anthocyanin accumulation in purple Pak-choi and provided a theoretical basis for leaf color regulation. Full article
(This article belongs to the Special Issue Vegetable Genomics and Breeding Research)
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16 pages, 3649 KiB  
Article
Pan-Genome Analysis of TRM Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber
by Lili Zhao, Ke Wang, Zimo Wang, Shunpeng Chu, Chunhua Chen, Lina Wang and Zhonghai Ren
Horticulturae 2024, 10(9), 908; https://doi.org/10.3390/horticulturae10090908 - 27 Aug 2024
Cited by 1 | Viewed by 1513
Abstract
Cucumber (Cucumis sativus L.) is a vital economic vegetable crop, and the TONNEAU1 Recruiting Motif (TRM) gene plays a key role in cucumber organ growth. However, the pan-genomic characteristics of the TRM gene family and their expression patterns under different stresses have [...] Read more.
Cucumber (Cucumis sativus L.) is a vital economic vegetable crop, and the TONNEAU1 Recruiting Motif (TRM) gene plays a key role in cucumber organ growth. However, the pan-genomic characteristics of the TRM gene family and their expression patterns under different stresses have not been reported in cucumber. In this study, we identified 29 CsTRMs from the pan-genomes of 13 cucumber accessions, with CsTRM29 existing only in PI183967. Most CsTRM proteins exhibited differences in sequence length, except five CsTRMs having consistent protein sequence lengths among the 13 accessions. All CsTRM proteins showed amino acid variations. An analysis of CsTRM gene expression patterns revealed that six CsTRM genes strongly changed in short-fruited lines compared with long-fruited lines. And four CsTRM genes strongly responded to salt and heat stress, while CsTRM14 showed responses to salt stress, powdery mildew, gray mold, and downy mildew. Some CsTRM genes were induced or suppressed at different treatment timepoints, suggesting that cucumber TRM genes may play different roles in responses to different stresses, with expression patterns varying with stress changes. Remarkably, the expression of CsTRM21 showed considerable change between long and short fruits and in responses to abiotic stresses (salt stress and heat stress), as well as biotic stresses (powdery mildew and gray mold), suggesting a dual role of CsTRM21 in both fruit shape determination and stress resistance. Collectively, this study provided a base for the further functional identification of CsTRM genes in cucumber plant growth and stress resistance. Full article
(This article belongs to the Special Issue Vegetable Genomics and Breeding Research)
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Review

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17 pages, 2132 KiB  
Review
Onion Male Sterility: Genetics, Genomics and Breeding
by Hela Chikh-Rouhou, Saurabh Singh, Srija Priyadarsini and Cristina Mallor
Horticulturae 2025, 11(5), 539; https://doi.org/10.3390/horticulturae11050539 - 16 May 2025
Viewed by 508
Abstract
Onion, belonging to the Allium genus, is an essential and versatile vegetable crop that plays a pivotal role in culinary traditions worldwide. Renowned for its distinctive flavor and nutritional value, onion is an indispensable ingredient in countless dishes. As the global demand for [...] Read more.
Onion, belonging to the Allium genus, is an essential and versatile vegetable crop that plays a pivotal role in culinary traditions worldwide. Renowned for its distinctive flavor and nutritional value, onion is an indispensable ingredient in countless dishes. As the global demand for onion continues to surge, securing a stable supply of high-quality, high-yielding onion varieties becomes ever more pressing. The onion umbel bears numerous tiny flowers that are protandrous in nature. Hybrid breeding is limited in onion due to high inbreeding depression, tedious emasculation and lack of elite inbreds. In this quest for crop improvement, the phenomenon of male sterility stands out as a key tool in modern onion breeding. Male sterility, which is recognized as the incapacity to produce viable pollen grains, inhibition of anther dehiscence and production of non-functional male gametes, has been harnessed as a mechanism to control cross-pollination and escalating hybrid development. The successful utilization of stable male sterile lines in onion holds the promise of producing uniform, high-yielding and disease-resistant hybrids. In recent decades, scientific advances have illuminated the molecular intricacies underlying male sterility systems in onion. Much progress has been made in elucidating the regulation of male sterility systems in the post-genomics era. This review highlights the current status of molecular markers linked with male sterility and provides genetic and molecular insights into its regulation. Additionally, it discusses the role of male sterility as a transformative tool in onion breeding in the genomics era. Full article
(This article belongs to the Special Issue Vegetable Genomics and Breeding Research)
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32 pages, 1226 KiB  
Review
Spontaneous and Chemically Induced Genome Doubling and Polyploidization in Vegetable Crops
by Maria Fomicheva, Yuri Kulakov, Ksenia Alyokhina and Elena Domblides
Horticulturae 2024, 10(6), 551; https://doi.org/10.3390/horticulturae10060551 - 24 May 2024
Cited by 4 | Viewed by 2576
Abstract
Plant ploidy manipulation is often required for breeding purposes. However, there is no comprehensive review covering genome doubling in vegetable crops despite the abundance of data for a large number of vegetable species. Similar to other species, genome doubling is required in vegetable [...] Read more.
Plant ploidy manipulation is often required for breeding purposes. However, there is no comprehensive review covering genome doubling in vegetable crops despite the abundance of data for a large number of vegetable species. Similar to other species, genome doubling is required in vegetable crops to obtain doubled haploids (DHs). It is also utilized for the production of polyploids to overcome interspecific hybrid sterility and improve agricultural traits. Spontaneous haploid genome duplication (SHGD) occurs in many Apiaceae, Brassicaceae, Cucurbitaceae, and Solanaceae crops, allowing for the laborious treatment with antimitotic agents to be bypassed. SHGD mechanisms are not fully understood, but existing data suggest that SHGD can occur via nuclear fusion, endoreduplication, or other mechanisms during microspore or ovule early embryogenic development. Other studies show that SHGD can occur at later developmental stages during extended plant growth in vitro or ex vitro, possibly due to the presence of phytohormones in the medium and/or diploid cell competitive advantage. For unresponsive accessions and species with rare SHGD, such as onion (Allium cepa L.) and beet cultivars (Beta vulgaris subsp. vulgaris L.), antimitotic agent treatment has to be applied. Antimitotic agent application efficiency depends on the treatment conditions, especially the agent concentration and exposure time. Also, plant developmental stage is critical for agent accessibility and plant survival. The existing methods can be used to further improve genome doubling methodology for major vegetable crops and other species. Full article
(This article belongs to the Special Issue Vegetable Genomics and Breeding Research)
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