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Vegetable Genetics and Genomics 2.0

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: closed (25 August 2024) | Viewed by 12107

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”.

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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Related Special Issues

Published Papers (8 papers)

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Research

25 pages, 17436 KiB  
Article
Genome-Wide Identification, Expression, and Protein Analysis of CKX and IPT Gene Families in Radish (Raphanus sativus L.) Reveal Their Involvement in Clubroot Resistance
by Haohui Yang, Xiaochun Wei, Weiwei Lei, Henan Su, Yanyan Zhao, Yuxiang Yuan, Xiaowei Zhang and Xixiang Li
Int. J. Mol. Sci. 2024, 25(16), 8974; https://doi.org/10.3390/ijms25168974 - 17 Aug 2024
Viewed by 1185
Abstract
Cytokinins (CKs) are a group of phytohormones that are involved in plant growth, development, and disease resistance. The isopentenyl transferase (IPT) and cytokinin oxidase/dehydrogenase (CKX) families comprise key enzymes controlling CK biosynthesis and degradation. However, an integrated analysis of these two gene families [...] Read more.
Cytokinins (CKs) are a group of phytohormones that are involved in plant growth, development, and disease resistance. The isopentenyl transferase (IPT) and cytokinin oxidase/dehydrogenase (CKX) families comprise key enzymes controlling CK biosynthesis and degradation. However, an integrated analysis of these two gene families in radish has not yet been explored. In this study, 13 RsIPT and 12 RsCKX genes were identified and characterized, most of which had four copies in Brassica napus and two copies in radish and other diploid Brassica species. Promoter analysis indicated that the genes contained at least one phytohormone or defense and stress responsiveness cis-acting element. RsIPTs and RsCKXs were expanded through segmental duplication. Moreover, strong purifying selection drove the evolution of the two gene families. The expression of the RsIPT and RsCKX genes distinctly showed diversity in different tissues and developmental stages of the root. Expression profiling showed that RsCKX1-1/1-2/1-3 was significantly upregulated in club-resistant materials during primary infection, suggesting their vital function in clubroot resistance. The interaction network of CKX proteins with similar 3D structures also reflected the important role of RsCKX genes in disease resistance. This study provides a foundation for further functional study on the IPT and CKX genes for clubroot resistance improvement in Raphanus. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics 2.0)
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13 pages, 2996 KiB  
Article
Novel Allelic Gene Variations in CmCLAVATA3 (CmCLV3) Were Identified in a Genetic Population of Melon (Cucumis melo L.)
by Hangyu Wu, Yue Jia, Xinxiu Chen, Naiyu Jiang, Zhonghua Zhang and Sen Chai
Int. J. Mol. Sci. 2024, 25(11), 6011; https://doi.org/10.3390/ijms25116011 - 30 May 2024
Viewed by 612
Abstract
Carpel number (CN) is an important trait affecting the fruit size and shape of melon, which plays a crucial role in determining the overall appearance and market value. A unique non-synonymous single nucleotide polymorphism (SNP) in CmCLAVATA3 (CmCLV3) is responsible for [...] Read more.
Carpel number (CN) is an important trait affecting the fruit size and shape of melon, which plays a crucial role in determining the overall appearance and market value. A unique non-synonymous single nucleotide polymorphism (SNP) in CmCLAVATA3 (CmCLV3) is responsible for the variation of CN in C. melo ssp. agrestis (hereafter agrestis), but it has been unclear in C. melo ssp. melo (hereafter melo). In this study, one major locus controlling the polymorphism of 5-CN (multi-CN) and 3-CN (normal-CN) in melo was identified using bulked segregant analysis (BSA-seq). This locus was then fine-mapped to an interval of 1.8 Mb on chromosome 12 using a segregating population containing 1451 progeny. CmCLV3 is still present in the candidate region. A new allele of CmCLV3, which contains five other nucleotide polymorphisms, including a non-synonymous SNP in coding sequence (CDS), except the SNP reported in agrestis, was identified in melo. A cis-trans test confirmed that the candidate gene, CmCLV3, contributes to the variation of CNs in melo. The qRT-PCR results indicate that there is no significant difference in the expression level of CmCLV3 in the apical stem between the multi-CN plants and the normal-CN plants. Overall, this study provides a genetic resource for melon fruit development research and molecular breeding. Additionally, it suggests that melo has undergone similar genetic selection but evolved into an independent allele. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics 2.0)
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20 pages, 10550 KiB  
Article
Genome-Wide Identification of Glutathione S-Transferase Genes in Eggplant (Solanum melongena L.) Reveals Their Potential Role in Anthocyanin Accumulation on the Fruit Peel
by Hesbon Ochieng Obel, Xiaohui Zhou, Songyu Liu, Yan Yang, Jun Liu and Yong Zhuang
Int. J. Mol. Sci. 2024, 25(8), 4260; https://doi.org/10.3390/ijms25084260 - 11 Apr 2024
Viewed by 1660
Abstract
Anthocyanins are ubiquitous pigments derived from the phenylpropanoid compound conferring red, purple and blue pigmentations to various organs of horticultural crops. The metabolism of flavonoids in the cytoplasm leads to the biosynthesis of anthocyanin, which is then conveyed to the vacuoles for storage [...] Read more.
Anthocyanins are ubiquitous pigments derived from the phenylpropanoid compound conferring red, purple and blue pigmentations to various organs of horticultural crops. The metabolism of flavonoids in the cytoplasm leads to the biosynthesis of anthocyanin, which is then conveyed to the vacuoles for storage by plant glutathione S-transferases (GST). Although GST is important for transporting anthocyanin in plants, its identification and characterization in eggplant (Solanum melongena L.) remains obscure. In this study, a total of 40 GST genes were obtained in the eggplant genome and classified into seven distinct chief groups based on the evolutionary relationship with Arabidopsis thaliana GST genes. The seven subgroups of eggplant GST genes (SmGST) comprise: dehydroascorbate reductase (DHAR), elongation factor 1Bγ (EF1Bγ), Zeta (Z), Theta(T), Phi(F), Tau(U) and tetra-chlorohydroquinone dehalogenase TCHQD. The 40 GST genes were unevenly distributed throughout the 10 eggplant chromosomes and were predominantly located in the cytoplasm. Structural gene analysis showed similarity in exons and introns within a GST subgroup. Six pairs of both tandem and segmental duplications have been identified, making them the primary factors contributing to the evolution of the SmGST. Light-related cis-regulatory elements were dominant, followed by stress-related and hormone-responsive elements. The syntenic analysis of orthologous genes indicated that eggplant, Arabidopsis and tomato (Solanum lycopersicum L.) counterpart genes seemed to be derived from a common ancestry. RNA-seq data analyses showed high expression of 13 SmGST genes with SmGSTF1 being glaringly upregulated on the peel of purple eggplant but showed no or low expression on eggplant varieties with green or white peel. Subsequently, SmGSTF1 had a strong positive correlation with anthocyanin content and with anthocyanin structural genes like SmUFGT (r = 0.9), SmANS (r = 0.85), SmF3H (r = 0.82) and SmCHI2 (r = 0.7). The suppression of SmGSTF1 through virus-induced gene silencing (VIGs) resulted in a decrease in anthocyanin on the infiltrated fruit surface. In a nutshell, results from this study established that SmGSTF1 has the potential of anthocyanin accumulation in eggplant peel and offers viable candidate genes for the improvement of purple eggplant. The comprehensive studies of the SmGST family genes provide the foundation for deciphering molecular investigations into the functional analysis of SmGST genes in eggplant. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics 2.0)
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17 pages, 4068 KiB  
Article
Exploring the Regulatory Dynamics of BrFLC-Associated lncRNA in Modulating the Flowering Response of Chinese Cabbage
by Yun Dai, Xinyu Gao, Shifan Zhang, Fei Li, Hui Zhang, Guoliang Li, Rifei Sun, Shujiang Zhang and Xilin Hou
Int. J. Mol. Sci. 2024, 25(3), 1924; https://doi.org/10.3390/ijms25031924 - 5 Feb 2024
Cited by 1 | Viewed by 1265
Abstract
Vernalization plays a crucial role in the flowering and yield of Chinese cabbage, a process intricately influenced by long non-coding RNAs (lncRNAs). Our research focused on lncFLC1, lncFLC2a, and lncFLC2b, which emerged as key players in this process. These lncRNAs [...] Read more.
Vernalization plays a crucial role in the flowering and yield of Chinese cabbage, a process intricately influenced by long non-coding RNAs (lncRNAs). Our research focused on lncFLC1, lncFLC2a, and lncFLC2b, which emerged as key players in this process. These lncRNAs exhibited an inverse expression pattern to the flowering repressor genes FLOWERING LOCUS C 1 (BrFLC1) and FLOWERING LOCUS C 2 (BrFLC2) during vernalization, suggesting a complex regulatory mechanism. Notably, their expression in the shoot apex and leaves was confirmed through in fluorescent in situ hybridization (FISH). Furthermore, when these lncRNAs were overexpressed in Arabidopsis, a noticeable acceleration in flowering was observed, unveiling functional similarities to Arabidopsis’s COLD ASSISTED INTRONIC NONCODING RNA (COOLAIR). This resemblance suggests a potentially conserved regulatory mechanism across species. This study not only enhances our understanding of lncRNAs in flowering regulation, but also opens up new possibilities for their application in agricultural practices. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics 2.0)
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15 pages, 7655 KiB  
Article
Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale
by Shuo Han, Xiaowen Han, Chuandong Qi, Fengling Guo, Junliang Yin, Yiqing Liu and Yongxing Zhu
Int. J. Mol. Sci. 2024, 25(2), 929; https://doi.org/10.3390/ijms25020929 - 11 Jan 2024
Cited by 3 | Viewed by 1514
Abstract
The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger [...] Read more.
The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics 2.0)
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15 pages, 3568 KiB  
Article
Lipid-Related Domestication Accounts for the Extreme Cold Sensitivity of Semiwild and Tropic Xishuangbanna Cucumber (Cucumis sativus L. var. xishuangbannanesis)
by Rui-Jing Zhang, Bin Liu, Shan-Shan Song, Radwa Salah, Chang-Jiang Song, Shi-Wei Xia, Qian Hao, Yan-Jun Liu, Yu Li and Yun-Song Lai
Int. J. Mol. Sci. 2024, 25(1), 79; https://doi.org/10.3390/ijms25010079 - 20 Dec 2023
Cited by 2 | Viewed by 1085
Abstract
Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannanesis) is a semiwild variety originating from low latitude tropic areas, and therefore shows extreme cold sensitivity and heat tolerance. Here, we mapped the quantitative trait loci (QTLs) that control the cold sensitivity and [...] Read more.
Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannanesis) is a semiwild variety originating from low latitude tropic areas, and therefore shows extreme cold sensitivity and heat tolerance. Here, we mapped the quantitative trait loci (QTLs) that control the cold sensitivity and heat tolerance of XIS cucumber seedlings. Using bulked segregant analysis (BSA), we identified three QTLs (HTT1.1, HTT3.1, and HTT3.2, with a total length of 11.98 Mb) for heat tolerance and two QTLs (LTT6.1 and LTT6.2, with a total length of 8.74 Mb) for cold sensitivity. The QTL LTT6.1 was then narrowed down to a length of 641 kb by using kompetitive allele-specific PCR (KASP) markers. Based on structural variants (SVs) and single-nucleotide polymorphisms (SNPs), we found the LTT6.1 is covered by a high divergent region including a 50 kb deletion in the XIS49 genome, which affects the gene structure of lipase abhydrolase domain containing 6 (ABHD6, Csa_6G032560). Accordingly, there is a very big difference in lipid composition, but not in other osmoprotectants like free amino acids and fatty acids, between XIS49 and cultivated cucumber CL. Moreover, we calculated the composite likelihood ratio (CLR) and identified selective sweeps from 115 resequencing data, and found that lipid- and fatty-acid-related processes are major aspects in the domestication of the XIS group cucumber. LTT6.1 is a particularly special region positioned nearby lipid-related selective sweeps. These studies above suggested that the lipid-related domestication of XIS cucumbers should account for their extreme cold sensitivity. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics 2.0)
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17 pages, 8820 KiB  
Article
Genome-Wide Identification and Expression Analysis of the SWEET Gene Family in Capsicum annuum L.
by Xiaowen Han, Shuo Han, Yongxing Zhu, Yiqing Liu, Shenghua Gao, Junliang Yin, Fei Wang and Minghua Yao
Int. J. Mol. Sci. 2023, 24(24), 17408; https://doi.org/10.3390/ijms242417408 - 12 Dec 2023
Cited by 4 | Viewed by 2153
Abstract
Sugars will eventually be exported transporters (SWEETs) are a novel class of sugar transport proteins that play a crucial role in plant growth, development, and response to stress. However, there is a lack of systematic research on SWEETs in Capsicum annuum L. In this [...] Read more.
Sugars will eventually be exported transporters (SWEETs) are a novel class of sugar transport proteins that play a crucial role in plant growth, development, and response to stress. However, there is a lack of systematic research on SWEETs in Capsicum annuum L. In this study, 33 CaSWEET genes were identified through bioinformatics analysis. The Ka/Ks analysis indicated that SWEET genes are highly conserved not only among peppers but also among Solanaceae species and have experienced strong purifying selection during evolution. The Cis-elements analysis showed that the light-responsive element, abscisic-acid-responsive element, jasmonic-acid-responsive element, and anaerobic-induction-responsive element are widely distributed in the promoter regions of CaSWEETs. The expression pattern analysis revealed that CaSWEETs exhibit tissue specificity and are widely involved in pepper growth, development, and stress responses. The post-transcription regulation analysis revealed that 20 pepper miRNAs target and regulate 16 CaSWEETs through cleavage and translation inhibition mechanisms. The pathogen inoculation assay showed that CaSWEET16 and CaSWEET22 function as susceptibility genes, as the overexpression of these genes promotes the colonization of pathogens, whereas CaSWEET31 functions as a resistance gene. In conclusion, through systematic identification and characteristic analysis, a comprehensive understanding of CaSWEET was obtained, which lays the foundation for further studies on the biological functions of SWEET genes. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics 2.0)
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18 pages, 2486 KiB  
Article
A Comprehensive Genome-Wide Association Study of Carotenoid and Capsaicinoid Contents in Capsicum chinense Germplasm
by Mesfin Haile, Nayoung Ro, Ho-Cheol Ko, Hyeonseok Oh and Gi-An Lee
Int. J. Mol. Sci. 2023, 24(18), 13885; https://doi.org/10.3390/ijms241813885 - 9 Sep 2023
Cited by 5 | Viewed by 1720
Abstract
Pepper is a highly important vegetable globally, both economically and nutritionally. However, to efficiently select and identify genetic resources for pepper breeding programs, it is crucial to understand the association between important traits and genetic factors. In this study, we investigated the genetic [...] Read more.
Pepper is a highly important vegetable globally, both economically and nutritionally. However, to efficiently select and identify genetic resources for pepper breeding programs, it is crucial to understand the association between important traits and genetic factors. In this study, we investigated the genetic basis of carotenoid and capsaicinoid content in 160 Capsicum chinense germplasms. The study observed significant variability in carotenoid and capsaicinoid content among the germplasms. Correlation analysis revealed a strong positive correlation between violaxanthin and antheraxanthin. In contrast, capsaicin and dihydrocapsaicin displayed negative correlations with individual carotenoids but exhibited a strong positive correlation between the two compounds (r = 0.90 ***). Genotyping-by-sequencing (GBS) was performed on 160 genotypes of pepper germplasm, which identified 47,810 high-quality SNPs. A comprehensive genome-wide association analysis was performed using these SNPs to identify SNPs associated with carotenoids and capsaicinoids, revealing 193 SNPs that exhibited significant associations. Specifically, 4 SNPs were associated with violaxanthin, 2 with antheraxanthin, 86 with capsorubin, 5 with capsanthin, 63 with zeaxanthin, 3 with β-cryptoxanthin, and 2 with α-carotene. With further studies, the significantly associated SNPs identified in this study have the potential to be utilized for selecting pepper accessions with high carotenoid and capsaicinoid contents. Additionally, the genes associated with these significant SNPs will be used to understand their roles and involvement in the biosynthesis pathway of carotenoids and capsaicinoids. Understanding the function of these genes can provide insights into the molecular mechanisms underlying the production of these bioactive compounds in pepper. The findings of this study hold valuable implications for selecting pepper varieties with desirable traits and developing breeding programs aimed at enhancing the nutritional and medicinal properties of pepper. Full article
(This article belongs to the Special Issue Vegetable Genetics and Genomics 2.0)
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