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Genes
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Vegetable Genetic Breeding
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Vegetable Genetic Breeding

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 20 February 2025 | Viewed by 8401

Special Issue Editors

Dr. Wei Qian

E-Mail Website
Guest Editor
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: vegetable genetic breeding; molecular marker; QTL; gene mapping; genetic resources
Dr. Jian Wu

E-Mail Website
Guest Editor
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: vegetable genetic breeding; genomics; genetic resources; molecular breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Hongbing She

E-Mail Website
Guest Editor
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: genomics; genetics; gene mapping; resistance breeding

Special Issue Information

Dear Colleagues,

Vegetable crops, such as Chinese cabbage, cabbage, tomato, spinach, carrot, pepper, broccoli, eggplant, celery, watermelon, pumpkin, cucumber, etc., are indispensable to human health, as they provide a large amount of nutritional value. Given the increasing world population, climate changes, and changes in consumer behavior, high-quality vegetable cultivars urgently need to be cultivated. Specifically, these vegetables should carry high yield potential, high resistance to abiotic (such as drought, salinity, temperatures, etc.) and biotic stress (fungi, bacteria, insects, etc.), high resistance to bolting, and other important agronomic traits (plant height, leaf shape, color, fruit size, etc.). Advanced next-generation DNA sequencing technologies allow us to rapidly discover candidate regions that control traits of interest based on pooled sequencing (such as QTL-seq, BSA-seq, MutMap, etc.) or genome-wide association studies, and provide a number of variants (SNPs and Indels) for gene/QTL fine mapping. Together, the sequencing technologies or new breeding techniques (e.g., gene editing) provide exciting opportunities for efficient breeding programs of vegetable crops.

Therefore, this Special Issue on “Vegetable Genetic Breeding” welcomes original research articles and reviews highlighting all aspects of vegetable genetic breeding, such as gene/QTL mapping, Mendelian inheritance, transcriptomics, genetic variation, genetic diversity, functional genomics, genomic selection, gene editing, new breeding techniques, and plant genetic resources.

Dr. Wei Qian
Dr. Jian Wu
Dr. Hongbing She
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. Genes 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 2600 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
  • molecular breeding
  • plant genetic resources
  • marker-assisted selection
  • plant genetic resources
  • agronomic trait

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Published Papers (6 papers)

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Research

19 pages, 16645 KiB  
Article
Genome-Wide Identification and Expression Profiling Analysis of the CCT Gene Family in Solanum lycopersicum and Solanum melongena
by Liangyu Cai, Rui Xiang, Yaqin Jiang, Weiliu Li, Qihong Yang, Guiyun Gan, Wenjia Li, Chuying Yu and Yikui Wang
Genes 2024, 15(11), 1385; https://doi.org/10.3390/genes15111385 - 28 Oct 2024
Viewed by 801
Abstract
CCT family genes play crucial roles in photoperiodic flowering and environmental stress response; however, there are limited reports in Solanum species with considerable edible and medicinal value. In this study, we conducted genome-wide characterization and expression profiling analysis of the CCT gene family [...] Read more.
CCT family genes play crucial roles in photoperiodic flowering and environmental stress response; however, there are limited reports in Solanum species with considerable edible and medicinal value. In this study, we conducted genome-wide characterization and expression profiling analysis of the CCT gene family in two Solanum species: tomato (Solanum lycopersicum L.) and eggplant (Solanum melongena L.). A total of 27 SlCCT and 29 SmCCT genes were identified in the tomato and eggplant genomes, respectively. Phylogenetic analysis showed that the CCT gene family could be divided into six subgroups (COL I, COL II, COL III, PRR, CMF I, and CMF II) in Oryza sativa and Arabidopsis thaliana. The similarity in the distribution of exon–intron structures and conserved motifs within the same subgroup indicated the conservation of SlCCT and SmCCT genes during evolution. Intraspecies collinearity analysis revealed that six pairs of SlCCT genes and seven pairs of SmCCT genes showed collinear relationships, suggesting that segmental duplication played a vital role in the expansion of the SlCCT and SmCCT family genes. Cis-acting element prediction indicated that SlCCT and SmCCT were likely to be involved in multiple responses stimulated by light, phytohormones, and abiotic stress. RT-qPCR analysis revealed that SmCCT15, SlCCT6/SlCCT14, and SlCCT23/SmCCT9 responded significantly to salt, drought, and cold stress, respectively. Our comprehensive analysis of the CCT gene family in tomato and eggplant provides a basis for further studies on its molecular role in regulating flowering and resistance to abiotic stress, and provides valuable candidate gene resources for tomato and eggplant molecular breeding. Full article
(This article belongs to the Special Issue Vegetable Genetic Breeding)
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21 pages, 4499 KiB  
Article
Transcriptional Comparison Reveals Differential Resistance Mechanisms between CMV-Resistant PBC688 and CMV-Susceptible G29
by Guangjun Guo, Baogui Pan, Chengsheng Gong, Shubin Wang, Jinbing Liu, Changzhou Gao and Weiping Diao
Genes 2024, 15(6), 731; https://doi.org/10.3390/genes15060731 - 2 Jun 2024
Viewed by 949
Abstract
The Cucumber mosaic virus (CMV) presents a significant threat to pepper cultivation worldwide, leading to substantial yield losses. We conducted a transcriptional comparative study between CMV-resistant (PBC688) and -susceptible (G29) pepper accessions to understand the mechanisms of CMV resistance. PBC688 effectively suppressed CMV [...] Read more.
The Cucumber mosaic virus (CMV) presents a significant threat to pepper cultivation worldwide, leading to substantial yield losses. We conducted a transcriptional comparative study between CMV-resistant (PBC688) and -susceptible (G29) pepper accessions to understand the mechanisms of CMV resistance. PBC688 effectively suppressed CMV proliferation and spread, while G29 exhibited higher viral accumulation. A transcriptome analysis revealed substantial differences in gene expressions between the two genotypes, particularly in pathways related to plant–pathogen interactions, MAP kinase, ribosomes, and photosynthesis. In G29, the resistance to CMV involved key genes associated with calcium-binding proteins, pathogenesis-related proteins, and disease resistance. However, in PBC688, the crucial genes contributing to CMV resistance were ribosomal and chlorophyll a–b binding proteins. Hormone signal transduction pathways, such as ethylene (ET) and abscisic acid (ABA), displayed distinct expression patterns, suggesting that CMV resistance in peppers is associated with ET and ABA. These findings deepen our understanding of CMV resistance in peppers, facilitating future research and variety improvement. Full article
(This article belongs to the Special Issue Vegetable Genetic Breeding)
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14 pages, 3682 KiB  
Article
Integrated Analysis of Transcriptome and Metabolome Reveals Differential Responses to Alternaria brassicicola Infection in Cabbage (Brassica oleracea var. capitata)
by Jinzhou Lei, Wei Zhang, Fangwei Yu, Meng Ni, Zhigang Liu, Cheng Wang, Jianbin Li, Jianghua Song and Shenyun Wang
Genes 2024, 15(5), 545; https://doi.org/10.3390/genes15050545 - 25 Apr 2024
Viewed by 1228
Abstract
Black spot, caused by Alternaria brassicicola (Ab), poses a serious threat to crucifer production, and knowledge of how plants respond to Ab infection is essential for black spot management. In the current study, combined transcriptomic and metabolic analysis was employed to [...] Read more.
Black spot, caused by Alternaria brassicicola (Ab), poses a serious threat to crucifer production, and knowledge of how plants respond to Ab infection is essential for black spot management. In the current study, combined transcriptomic and metabolic analysis was employed to investigate the response to Ab infection in two cabbage (Brassica oleracea var. capitata) genotypes, Bo257 (resistant to Ab) and Bo190 (susceptible to Ab). A total of 1100 and 7490 differentially expressed genes were identified in Bo257 (R_mock vs. R_Ab) and Bo190 (S_mock vs. S_Ab), respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that “metabolic pathways”, “biosynthesis of secondary metabolites”, and “glucosinolate biosynthesis” were the top three enriched KEGG pathways in Bo257, while “metabolic pathways”, “biosynthesis of secondary metabolites”, and “carbon metabolism” were the top three enriched KEGG pathways in Bo190. Further analysis showed that genes involved in extracellular reactive oxygen species (ROS) production, jasmonic acid signaling pathway, and indolic glucosinolate biosynthesis pathway were differentially expressed in response to Ab infection. Notably, when infected with Ab, genes involved in extracellular ROS production were largely unchanged in Bo257, whereas most of these genes were upregulated in Bo190. Metabolic profiling revealed 24 and 56 differentially accumulated metabolites in Bo257 and Bo190, respectively, with the majority being primary metabolites. Further analysis revealed that dramatic accumulation of succinate was observed in Bo257 and Bo190, which may provide energy for resistance responses against Ab infection via the tricarboxylic acid cycle pathway. Collectively, this study provides comprehensive insights into the Ab–cabbage interactions and helps uncover targets for breeding Ab-resistant varieties in cabbage. Full article
(This article belongs to the Special Issue Vegetable Genetic Breeding)
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18 pages, 14236 KiB  
Article
Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Bolting Periods in Spinacia oleracea
by Hao Wu, Zhilong Zhang, Zhiyuan Liu, Qing Meng, Zhaosheng Xu, Helong Zhang, Wei Qian and Hongbing She
Genes 2024, 15(1), 36; https://doi.org/10.3390/genes15010036 - 26 Dec 2023
Cited by 1 | Viewed by 1496
Abstract
Bolting is a symbol of the transition from vegetative to reproductive growth in plants. Late bolting can effectively prolong the commercial value of spinach and is of great importance for spinach breeding. Bolting has complex regulatory networks, and current research on spinach bolting [...] Read more.
Bolting is a symbol of the transition from vegetative to reproductive growth in plants. Late bolting can effectively prolong the commercial value of spinach and is of great importance for spinach breeding. Bolting has complex regulatory networks, and current research on spinach bolting is relatively weak, with specific regulatory pathways and genes unclear. To clarify the regulatory characteristics and key genes related to bolting in spinach, we conducted a comparative transcriptome analysis. In this study, 18 samples from three periods of bolting-tolerant spinach material 12S3 and bolting-susceptible material 12S4 were analyzed using RNA-seq on, resulting in 10,693 differentially expressed genes (DEGs). Functional enrichment and co-expression trend analysis indicated that most DEGs were enriched in the photoperiod pathway, the hormone signaling pathway, and the cutin, suberin, and wax biosynthetic pathways. According to the weighted gene co-expression network analysis (WGCNA), SpFT (SOV4g003400), SOV4g040250, and SpGASA1 (SOV6g017600) were likely to regulate bolting through the gibberellin and photoperiod pathways, and SpELF4 (SOV1g028600) and SpPAT1 (SOV4g058860) caused differences in early and late bolting among different cultivars. These results provide important insights into the genetic control of bolting in spinach and will help elucidate the molecular mechanisms of bolting in leafy vegetables. Full article
(This article belongs to the Special Issue Vegetable Genetic Breeding)
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16 pages, 2551 KiB  
Article
Construction and Application of an F1-Derived Doubled-Haploid Population and High-Density Genetic Map for Ornamental Kale Breeding
by Ning Guo, Shuo Han, Mei Zong, Guixiang Wang, Mengmeng Duan and Fan Liu
Genes 2023, 14(11), 2104; https://doi.org/10.3390/genes14112104 - 20 Nov 2023
Viewed by 1356
Abstract
Ornamental kale (Brassica oleracea var. acephala) is an attractive ornamental plant with a range of leaf colors and shapes. Breeding new varieties of ornamental kale has proven challenging due to its lengthy breeding cycle and the limited availability of genetic markers. [...] Read more.
Ornamental kale (Brassica oleracea var. acephala) is an attractive ornamental plant with a range of leaf colors and shapes. Breeding new varieties of ornamental kale has proven challenging due to its lengthy breeding cycle and the limited availability of genetic markers. In this study, a F1DH ornamental kale population comprising 300 DH lines was constructed using microspore culture. A high-density genetic map was developed by conducting whole-genome sequencing on 150 individuals from the F1DH population. The genetic map contained 1696 bin markers with 982,642 single-nucleotide polymorphisms (SNPs) spanning a total distance of 775.81 cM on all nine chromosomes with an average distance between markers of 0.46 cM. The ornamental kale genetic map contained substantially more SNP markers compared with published genetic maps for other B. oleracea crops. Furthermore, utilizing this high-density genetic map, we identified seven quantitative trait loci (QTLs) that significantly influence the leaf shape of ornamental kale. These findings are valuable for understanding the genetic basis of key agronomic traits in ornamental kale. The F1DH progenies provide an excellent resource for germplasm innovation and breeding new varieties of ornamental kale. Additionally, the high-density genetic map provides crucial insights for gene mapping and unraveling the molecular mechanisms behind important agronomic traits in ornamental kale. Full article
(This article belongs to the Special Issue Vegetable Genetic Breeding)
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16 pages, 2974 KiB  
Article
Genome-Wide Identification and Expression Analysis of Respiratory Burst Oxidase Homolog (RBOH) Gene Family in Eggplant (Solanum melongena L.) under Abiotic and Biotic Stress
by Lihui Du, Zheng Jiang, Yadong Zhou, Lei Shen, Jie He, Xin Xia, Longhao Zhang and Xu Yang
Genes 2023, 14(9), 1665; https://doi.org/10.3390/genes14091665 - 23 Aug 2023
Cited by 5 | Viewed by 1701
Abstract
Respiratory burst oxidase homologs (RBOHs) are important proteins that catalyze the production of reactive oxygen species (ROS), which play important roles in growth and stress response. For a comprehensive analysis of SmRBOH genes, we conducted genome-wide identification of the SmRBOH gene [...] Read more.
Respiratory burst oxidase homologs (RBOHs) are important proteins that catalyze the production of reactive oxygen species (ROS), which play important roles in growth and stress response. For a comprehensive analysis of SmRBOH genes, we conducted genome-wide identification of the SmRBOH gene family in eggplant (Solanum melongena L.) and analyzed the expression of SmRBOHs under abiotic (salt, high-temperature, and low-temperature) and biotic stress (Verticillium dahliae inoculation) by quantitative real-time PCR (qRT-PCR). The result showed that a total of eight SmRBOH members were identified from the genome database of eggplant, and they were relatively evenly distributed across seven chromosomes. The analysis of Motif and the conserved domain showed that SmRBOHs have high similarity in protein sequences and functions. Based on phylogenetics, SmRBOHs were classified into three distinct clades. Furthermore, the promoter regions of SmRBOHs were found to contain different cis-elements. Additionally, the results of the qRT-PCR demonstrated differential expression patterns of SmRBOHs in different tissues (the roots, stems, and leaves) and stress conditions. SmRBOHB, SmRBOHD, SmRBOHH1, and SmRBOHH2 showed significant upregulation (>20-fold) under at least one stress condition. Subcellular localization analysis of the above four members further confirmed that they localized on the plasma membrane. This study provides a theoretical foundation for understanding the functions of SmRBOHs in eggplant. Full article
(This article belongs to the Special Issue Vegetable Genetic Breeding)
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