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Vegetable Genetics and Genomics, 3rd Edition
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Vegetable Genetics and Genomics, 3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 July 2025 | Viewed by 4637

Special Issue Editors

Prof. Dr. Yunsong Lai

E-Mail Website
Guest Editor
College of Horticulture, Sichuan Agricultural University, Huimin Rd 211, Wenjiang District, Chengdu 611130, China
Interests: cucumber; capsicum pepper; vegetable germplasm enhancement; vegetable molecular breeding; vegetable genomics; methylation; environmental acclimation; disease resistance; flowering and sex expression
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Xixiang Li

E-Mail Website
Guest Editor
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: vegetable crop evolution and classification; genetic diversity; genetic analysis of target traits; gene mapping; vegetable genomics; transcriptome; flowering and sex expression; resistance to diamond back moth and black rot; radish, cucumber
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue on “Vegetable Genetics and Genomics 2.0”.

Vegetables, as an indispensable non-staple type of food in people’s daily diet, provide a variety of essential vitamins, minerals, and other nutrients, as well as special phytochemicals which are recognized as functional components for human nutritional balance or medicinal purposes. With the increase in population and dramatic climate change all around the world, there is an increasing demand from societies for a higher quantity and quality of major vegetables. In order to improve the production performance and product quality of vegetable crops effectively, it is first necessary to understand the genetic bases of important horticultural traits, quality characteristics, and stress tolerances, and to reveal the crucial genes underlying these traits and their molecular regulation mechanisms for elite trait expression or beneficial component metabolism.

In the past decade, the rapid development of sequencing technologies has promoted great advances in the genetics and genomics of vegetable crops. This Special Issue on “Vegetable Genetics and Genomics” welcomes the submission of review and original research papers or short communications on the following topics: vegetable genome, comparative genome, and variome research; genetic dissections of important horticultural breeding target traits; quality and tolerance to biotic or abiotic stress; and discoveries of new key genes and their molecular regulation mechanisms for valuable traits or metabolic pathways through the advanced technologies of molecular genetics and multiple omics.

Prof. Dr. Yunsong Lai
Prof. Dr. Xixiang Li
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • major vegetable crops
  • genome
  • variome
  • genotyping
  • GWAS
  • QTL mapping
  • functional genome
  • metabolome
  • breeding target characters
  • genetic mechanism
  • functional genes

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Published Papers (4 papers)

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Research

15 pages, 4227 KiB  
Article
Phylogenetic, Structural, and Evolutionary Insights into Pepper NBS-LRR Resistance Genes
by Jia Liu, Yuan Cheng, Meiying Ruan, Qingjing Ye, Rongqing Wang, Zhuping Yao, Guozhi Zhou, Chenxu Liu and Hongjian Wan
Int. J. Mol. Sci. 2025, 26(5), 1828; https://doi.org/10.3390/ijms26051828 - 20 Feb 2025
Cited by 1 | Viewed by 762
Abstract
The comprehensive analysis of NBS-LRR resistance genes in the pepper (Capsicum annuum L.) genome reveals their structural diversity, evolutionary history, and functional importance in plant immunity. A total of 252 NBS-LRR genes were identified, distributed unevenly across all chromosomes, with 54% forming [...] Read more.
The comprehensive analysis of NBS-LRR resistance genes in the pepper (Capsicum annuum L.) genome reveals their structural diversity, evolutionary history, and functional importance in plant immunity. A total of 252 NBS-LRR genes were identified, distributed unevenly across all chromosomes, with 54% forming 47 gene clusters. These clusters, driven by tandem duplications and genomic rearrangements, underscore the dynamic evolution of resistance genes. Phylogenetic analysis demonstrated the dominance of the nTNL subfamily over the TNL subfamily, reflecting lineage-specific adaptations and evolutionary pressures. Structural analyses identified six conserved motifs (P-loop, RNBS-A, kinase-2, RNBS-B, RNBS-C, and GLPL) essential for ATP/GTP binding and resistance signaling. Subfamily-specific differences in motif composition and sequence similarity highlight their functional divergence and specialization. Comparative analyses across species further revealed a greater prevalence of nTNL genes in angiosperms, with significant losses of TNL genes in monocots. This study enhances our understanding of the evolution and diversification of plant-resistance genes and provides a foundation for developing disease-resistant crops through targeted breeding strategies. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics, 3rd Edition)
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25 pages, 5398 KiB  
Article
Integrated Transcriptomics and Metabolomics Analysis Reveals Convergent and Divergent Key Molecular Networks of Dominant Genic Male Sterility and Cytoplasmic Male Sterility in Cabbage
by Nan Zhang, Linqian Kuang, Limei Yang, Yong Wang, Fengqing Han, Yangyong Zhang, Shaohui Wang, Honghao Lv and Jialei Ji
Int. J. Mol. Sci. 2025, 26(3), 1259; https://doi.org/10.3390/ijms26031259 - 31 Jan 2025
Viewed by 908
Abstract
Cytoplasmic male sterility (CMS) and dominant genic male sterility (DGMS) both result in the inability to produce or release functional pollen, making them pivotal systems in the hybridization breeding programs of Brassica crops such as cabbage (B. oleracea var. capitata). However, [...] Read more.
Cytoplasmic male sterility (CMS) and dominant genic male sterility (DGMS) both result in the inability to produce or release functional pollen, making them pivotal systems in the hybridization breeding programs of Brassica crops such as cabbage (B. oleracea var. capitata). However, the underling molecular mechanisms are still largely unexplored. This study integrated transcriptomic and metabolomic analyses of cabbage DGMS line, Ogura CMS line, and the maintainer line to uncover the molecular mechanisms underlying these sterility types. The joint analysis predominantly identified significantly enriched pathways, including carbohydrate metabolism, flavonoid biosynthesis, and phenylpropanoid pathways between the MS lines and the maintainer. Especially, the CMS line exhibited a broader range of metabolic perturbations, with a total of 3556 significantly differentially expressed genes (DEGs) and 439 differentially accumulated metabolites (DAMs) detected, particularly in the vitamin B6 metabolism pathway, which showed significant alterations. Given the differences in the inactivation period of microspores in CMS and DGMS lines, we found that DEGs unique to DGMS and maintainer line, such as BoGRPs and BoLTPs, primarily regulate fertility development before the unicellular stage. The DEGs shared between CMS_vs_maintainer and DGMS_vs_maintainer mainly govern microspore development after release from the tetrad, such as BoHXK1 and BoIDH. Additionally, the DEGs unique to CMS_vs_maintainer may contribute to other damage in floral organs beyond male fertility, potentially leading to severe bud abortion, such as BoPNPO. These findings provide a comprehensive framework for understanding the molecular mechanisms of male sterility and offer valuable insights into future breeding strategies in cruciferous vegetables. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics, 3rd Edition)
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15 pages, 38365 KiB  
Article
Functional Analysis of CsWOX4 Gene Mutation Leading to Maple Leaf Type in Cucumber (Cucumis sativus L.)
by Huizhe Wang, Bo Wang, Yiheng Wang, Qiang Deng, Guoqing Lu, Mingming Cao, Wancong Yu, Haiyan Zhao, Mingjie Lyu and Ruihuan Yang
Int. J. Mol. Sci. 2024, 25(22), 12189; https://doi.org/10.3390/ijms252212189 - 13 Nov 2024
Viewed by 944
Abstract
The leaf morphology is an important agronomic trait in crop production. Our study identified a maple leaf type (mlt) cucumber mutant and located the regulatory gene for leaf shape changes through BSA results. Hybrid F1 and F2 populations were generated by [...] Read more.
The leaf morphology is an important agronomic trait in crop production. Our study identified a maple leaf type (mlt) cucumber mutant and located the regulatory gene for leaf shape changes through BSA results. Hybrid F1 and F2 populations were generated by F1 self-crossing, and the candidate mlt genes were identified within the 2.8 Mb region of chromosome 2 using map cloning. Through the sequencing and expression analysis of genes within the bulk segregant analysis (BSA) region, we identified the target gene for leaf shape regulation as CsWOX4 (CsaV3_2G026510). The change from base C to T in the original sequence led to frameshift mutations and the premature termination of translation, resulting in shortened encoded proteins and conserved WUSCHEL (WUS) box sequence loss. The specific expression analysis of the CsWOX4/Cswox4 genes in the roots, stems, leaves and other tissue types of wild-type (WT) and mutant plants revealed that CsWOX4 was higher in the root, but Cswox4 (mutant gene) was significantly higher in the leaf. Subcellular localization analysis revealed that CsWOX4 was localized in the nucleus. RNA-seq analysis revealed that the differentially expressed genes were mainly enriched in the mitochondrial cell cycle phase transition, nucleosome and microtubule binding pathways. Simultaneously, the quantitative analysis of the expression trends of 25 typical genes regulating the leaf types revealed the significant upregulation of CsPIN3. In our study, we found that the conserved domain of CsWOX4 was missing in the mutant, and the transcriptome data revealed that the expression of some genes, such as CsPIN3, changed simultaneously, thereby jointly regulating changes in the cucumber leaf type. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics, 3rd Edition)
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23 pages, 3188 KiB  
Article
Genome-Wide Association Study of Sweet Potato Storage Root Traits Using GWASpoly, a Gene Dosage-Sensitive Model
by Robert R. Bowers, Tyler J. Slonecki, Bode A. Olukolu, G. Craig Yencho and Phillip A. Wadl
Int. J. Mol. Sci. 2024, 25(21), 11727; https://doi.org/10.3390/ijms252111727 - 31 Oct 2024
Cited by 2 | Viewed by 1653
Abstract
Sweet potato (Ipomoea batatas) is an important food crop that plays a pivotal role in preserving worldwide food security. Due to its polyploid genome, high heterogeneity, and phenotypic plasticity, sweet potato genetic characterization and breeding is challenging. Genome-wide association studies (GWASs) [...] Read more.
Sweet potato (Ipomoea batatas) is an important food crop that plays a pivotal role in preserving worldwide food security. Due to its polyploid genome, high heterogeneity, and phenotypic plasticity, sweet potato genetic characterization and breeding is challenging. Genome-wide association studies (GWASs) can provide important resources for breeders to improve breeding efficiency and effectiveness. GWASpoly was used to identify 28 single nucleotide polymorphisms (SNPs), comprising 21 unique genetic loci, associated with sweet potato storage root traits including dry matter (4 loci), subjective flesh color (5 loci), flesh hue angle (3 loci), and subjective skin color and skin hue angle (9 loci), in 384 accessions from the USDA sweet potato germplasm collection. The I. batatas ‘Beauregard’ and I. trifida reference genomes were utilized to identify candidate genes located within 100 kb from the SNPs that may affect the storage traits of dry matter, flesh color, and skin color. These candidate genes include transcription factors (especially Myb, bHLH, and WRKY family members), metabolite transporters, and metabolic enzymes and associated proteins involved in starch, carotenoid, and anthocyanin synthesis. A greater understanding of the genetic loci underlying sweet potato storage root traits will enable marker-assisted breeding of new varieties with desired traits. This study not only reinforces previous research findings on genes associated with dry matter and β-carotene content but also introduces novel genetic loci linked to these traits as well as other root characteristics. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics, 3rd Edition)
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