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Omics Technologies and Their Applications in Vegetable Plant Research

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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: closed (5 March 2023) | Viewed by 33527

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Prof. Dr. Ai-Sheng Xiong

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State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
Interests: plant growth regulators; circadian clock; plant biotechnology; plant genetics and breeding
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Dr. Mengyao Li

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College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
Interests: vegetable genetics and functional genomics; bioinformatics; abiotic stress response; biotechnology
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Dr. Guanglong Wang

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School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
Interests: vegetable biotechnology; abiotic stress response; vegetable quality regulation; hormones in horticultural plants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Vegetable crops contain a large number of species based on plant classification. Multi-omics studies into vegetable plants are of important theoretical value and economic significance. The development of sequencing technology and related bioinformatics tools greatly facilitate molecular biology studies of vegetable plants. Based on the large amount of sequence data produced by omics technologies, researchers in vegetable plant science are expected to carry out in-depth molecular genetics research and identify functional genes, which is expected to promote basic research and accelerate the creation of new varieties.

The development of omics technologies drives new progress in vegetable plant research. Hence, this Special Issue aims to integrate omics technologies and their applications, such as genomics, proteinomics, metabolomics, transcriptomics, and other related topics which can help to unearth the underlying biological mechanism in vegetable plants.

We invite researchers to contribute both original research articles and reviews to this Special Issue.

Prof. Dr. Aisheng Xiong
Dr. Mengyao Li
Dr. Guanglong Wang
Guest Editors

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Keywords

Multi-omics technologies (genomics, proteinomics, metabolomics, transcriptomics, etc.)
comparative genomics
bioinformatics
QTL mapping and GWAS
Breeding
genetic diversity
functional genes

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Published Papers (10 papers)

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Research

12 pages, 2546 KiB

Open AccessArticle

Identification of Genes of Molecular Marker TGS0892 on Chromosome 6 and Its Mechanism of Soluble Solids Metabolism in Tomato

by Rong-Rong Zhang, Jian-Ping Tao, Liu-Xia Song, Jia-Qi Zhang, Hui Liu, Wei-Min Zhu, Tong-Min Zhao and Ai-Sheng Xiong

Horticulturae 2023, 9(1), 52; https://doi.org/10.3390/horticulturae9010052 - 3 Jan 2023

Cited by 3 | Viewed by 2963

Abstract

Tomato (Solanum lycopersicum L.) is one of the vegetables widely cultivated in the world, whose fruits are rich in nutrients. Soluble solids content (SSC) is one of the important factors affecting tomato fruit flavor and plays a decisive role in improving tomato quality. Molecular markers are genetic markers that reveal plant genetic polymorphism at the DNA level, which have the advantages of improving breeding purposes, increasing selection efficiency, and shortening breeding years. The molecular marker TGS0892 is located on chromosome 6 of the tomato genome and is closely related to soluble solids. In the present work, five different tomato cultivars were used as experimental materials. The results showed that ‘TD-10’ had the lightest single fruit weight and the highest soluble solids content, while ‘TD-8’ and ‘TD-9’ had heavier single fruit weight and lowered soluble solids content. Seventeen genes within 50 kb upstream and downstream of the molecular marker TGS0892 were identified using bioinformatics methods, and their structural analysis and functional annotation were performed. Quantitative reverse transcription PCR (RT-qPCR) showed that the expression levels of the 17 genes in different tomato cultivars were classified into two major categories, with the highest expression in ‘TD-7’ and other cultivars, respectively. Soly065970 and Soly066010 were significantly more expressed in high soluble solids tomato cultivars (‘TD-7’ and ‘TD-10’) and less expressed in the low soluble solids tomato cultivar (‘TD-9’). The results suggested that Soly065970 and Soly066010 may be involved in regulating the soluble solids metabolic process, which provides a reference for studying the formation mechanism of highly soluble solids in tomatoes. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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12 pages, 1850 KiB

Open AccessArticle

Identification of QTLs Controlling Radish Root Shape Using Multiple Populations

by Qingzhen Wei, Jinglei Wang, Wuhong Wang, Haijiao Hu, Yaqin Yan, Chonglai Bao and Tianhua Hu

Horticulturae 2022, 8(10), 931; https://doi.org/10.3390/horticulturae8100931 - 10 Oct 2022

Cited by 4 | Viewed by 3904

Abstract

Root shape is an important characteristic that affects the commodity of radish (Raphanus sativus L.), which can be measured using the ratio of root length (RL) to root diameter (RD). Although it is known that root shape is controlled by quantitative trait loci (QTLs), reliable QTLs for radish root shape are still lacking. In the present study, we used three F₂ populations (1902, 1908 and 1909) derived from the crossing of five radish cultivars with highly divergent root shapes to perform QTL-seq. A total of 1282 individuals of the three F₂ populations were measured to determine the root length and maximum diameter. High-depth resequencing of six extreme pools and five parents was performed, and QTL-seq was used to detect the QTLs controlling the radish root shape. We identified seven QTLs for root shape distributing on five radish chromosomes (R1, R2, R4, R5 and R7), among which rs7.1 and rs7.2 had an overlap of 1.02 Mb (13.79–14.81 Mb). In addition, two QTLs, rs4.1 and rs4.2, were adjacent to each other on chromosome R4. In conclusion, this study provides an important foundation for the fine mapping and functional analysis of the QTLs controlling the root shape and breeding for root shape in radish. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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16 pages, 3116 KiB

Open AccessArticle

Transcriptome Analysis of the Development of Pedicel Abscission Zone in Tomato

by Xiufen Dong, Yue Wang, Yanyan Yan and Huasen Wang

Horticulturae 2022, 8(10), 865; https://doi.org/10.3390/horticulturae8100865 - 22 Sep 2022

Cited by 3 | Viewed by 2412

Abstract

Plant organ abscission is a common phenomenon that occurs at a specific position called the abscission zone (AZ). The differentiation and development of the pedicel AZ play important roles in flower and fruit abscission, which are of great significance for abscission in tomatoes before harvest. Previous studies have reported some genes involved in AZ differentiation; however, the genes regulating pedicel AZ cell development in tomatoes after AZ differentiation remain poorly understood. In this study, transcriptome analyses of tomato pedicel AZ samples were performed at 0, 5, 15, and 30 days post-anthesis (DPA). Pedicel AZ growth was mainly observed before 15 DPA. A principal component analysis and a correlation analysis were carried out in order to compare the repeatability and reliability for different samples. We observed 38 up-regulated and 31 down-regulated genes that were significantly altered during 0 to 5 DPA, 5 to 15 DPA, and 0 to 15 DPA, which may play key roles in AZ cell enlargement. GO and KEGG enrichment analyses of the selected DEGs under all three different comparisons were conducted. Auxin-signaling-related genes were analyzed, as well as AUX/IAA, GH3, and small auxin up-regulated RNA (SAUR) gene expression patterns. The presented results provide information on pedicel AZ development, which might help in regulating flower or fruit pedicel abscission in tomato production facilities. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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15 pages, 4628 KiB

Open AccessArticle

Identification and Expression Analysis of CKX Gene Family in Brassica juncea var. tumida and Their Functional Analysis in Stem Development

by Mengyao Li, Jin Zhou, Li Gong, Ran Zhang, Yan Wang, Chao Wang, Xiaoming Du, Ya Luo, Yong Zhang, Xiaorong Wang and Haoru Tang

Horticulturae 2022, 8(8), 705; https://doi.org/10.3390/horticulturae8080705 - 3 Aug 2022

Cited by 6 | Viewed by 2837

Abstract

Cytokinin oxidase/dehydrogenase (CKX) is a specific enzyme affecting plant growth, development, and yield by mediating the metabolism of endogenous cytokinins in a dual catalytic mode. This study aims to reveal the distribution and associated properties of CKX gene family members in the whole genome of Brassica juncea, lay a theoretical basis for further exploration of the biological function of BjuCKX genes, and provide genetic resources to improve the breeding quality of B. juncea. We screened BjuCKX genes with typical FAD-binding and CK binding domains and identified them using bioinformatics methods. In addition, we analyzed physicochemical properties, phylogenetic relationship, gene structure, conservative motif, cis-acting element of promoter, and expression pattern of BjuCKX gene family members. Endogenous hormone levels (GA3, ZR, IAA, ABA, BR and MeJA) were also determined in different developmental periods using an indirect enzyme-linked immunosorbent assay (ELISA). A total of 23 BjuCKX genes were identified, and they were renamed BjuCKX01~BjuCKX23. Further analysis revealed that the amino acid number of 23 BjuCKX proteins ranged from 333 to 1337 aa, the molecular weight ranged 36.58 to 148.49 kDa, whereas the theoretical isoelectric point ranged from 4.94 to 9.10. The phylogenetic tree clustering analysis can group family members into four subgroups. Collinearity analysis revealed that genes were not evenly distributed on the chromosome, with a pair of tandem repeats. Meanwhile, BjuCKX genes located on each chromosome revealed cross collinearity caused by fragment replication. The genes were more conserved in structure. In the upstream region of promoter, there were several cis-acting elements, including plant growth and development, hormone response, and biological and abiotic stress. Combined with transcriptome data, BjuCKX gene expression has been demonstrated to be different at varying developmental stages of the stem. RT-qPCR further confirmed that BjuCKX genes were involved in stem development and affects growth by regulating endogenous hormone levels. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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16 pages, 2531 KiB

Open AccessEditor’s ChoiceArticle

Integrated Metabolomic and Transcriptomic Analysis Reveals the Effect of Artificial Shading on Reducing the Bitter Taste of Bamboo Shoots

by Yongjian Huang, Hang Xun, Guilin Yi, Ti Li, Xi Yao and Feng Tang

Horticulturae 2022, 8(7), 594; https://doi.org/10.3390/horticulturae8070594 - 1 Jul 2022

Cited by 11 | Viewed by 3198

Abstract

Bamboo shoot is a delicious and nutritious forest vegetable. It has been found that bamboo shoots collected from low-light environments have a less bitter taste. The molecular mechanism of light in the regulation of bitter substance accumulation in bamboo shoots is still unclear. In this study, we applied a shading treatment to Pleioblastus amarus bamboo shoots in the preharvesting period. The reduction in the bitterness intensity was confirmed by a sensory test. An integrated metabolomic and transcriptomic analysis was performed on P. amarus bamboo shoots grown under shading treatment and normal growing conditions, and 56 differentially accumulated metabolites and 178 differentially expressed genes were identified. The results showed that the contents of a series of phenolic acids related to the tyrosine metabolism pathway were downregulated under shading treatment, revealing that shading decreased the accumulation of phenolic acids and further mediated the resulting bitter taste of the bamboo shoots. This work will be helpful for understanding the regulatory mechanisms governing the bitter tasting substances in bamboo shoots grown under a shading treatment and provides a reference for the use of shading treatment in cultivation practices to improve the taste of bamboo shoots. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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16 pages, 2483 KiB

Open AccessArticle

Effect of CaCl₂ Treatment on Enzymatic Browning of Fresh-Cut Luffa (Luffa cylindrica)

by Yingna Feng, Cui Feng, Yuanhua Wang, Shuai Gao, Pengpeng Sun, Zhiming Yan, Xiaojun Su, Ying Sun and Qianqian Zhu

Horticulturae 2022, 8(6), 473; https://doi.org/10.3390/horticulturae8060473 - 26 May 2022

Cited by 10 | Viewed by 3033

Abstract

Enzymatic browning is a major issue that reduces the commercial value of Luffa cylindrica during storage, processing, and transportation. Our results showed that 1% CaCl₂ treatment was optimal for reducing the surface browning of fresh-cut luffa. After storage at 25 °C for four days, the treated luffa had a significantly higher total phenolic (TP) content than the untreated luffa. At the end of the storage period, the calcium treatment showed low malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) accumulation in the luffa. The treated luffa maintained higher superoxide dismutase (SOD), catalase (CAT), and phenylalanine ammonia lyase (PAL) activities and lower polyphenol oxidase (PPO) activity as compared to the untreated luffa. Furthermore, the genes regulating SOD (e.g., SOD1, SOD2, and SOD3), CAT (e.g., LcCAT1 and CAT2), and PAL (e.g., PAL1 and PAL2) in calcium-treated luffa were upregulated to varying degrees, suggesting that Ca²⁺ inhibited the browning of fresh-cut tissue by regulating the activities of those enzymes. Ultrastructure images showed that the treated luffa could maintain the relative integrity of the cell membrane and organelles. Therefore, Ca²⁺ might act as a second messenger to reduce ROS oxidative damage and maintain the cell membrane integrity. This study provides new insights into the breeding of new luffa varieties that are resistant to browning and post-harvest treatments to reduce the browning of luffa tissue. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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16 pages, 3151 KiB

Open AccessArticle

Expression Analysis and Interaction Protein Screening of CRY1 in Strawberry

by Yuyun Ye, Ruiling Li, Wenchao Pu, Yunting Zhang, Leiyu Jiang, Hao Li, Yongqiang Liu, Yuntian Ye, Maolan Yue, Yuanxiu Lin, Qing Chen, Yong Zhang, Ya Luo, Mengyao Li, Xiaorong Wang and Haoru Tang

Horticulturae 2022, 8(5), 460; https://doi.org/10.3390/horticulturae8050460 - 20 May 2022

Cited by 2 | Viewed by 3167

Abstract

Cryptochrome 1 (CRY1), a main blue light receptor protein, plays a significant role in several biological processes. However, the expression patterns and function of CRY1 in strawberry have not been identified. Here, the expression profile of CRY1 in different tissues and developmental stages of strawberry fruit, and expression patterns response to abiotic stresses (low temperature, salt and drought) were analyzed. Its subcellular localization, interaction proteins and heterologous overexpression in tobacco were also investigated. The results showed that CRY1 was mainly expressed in leaves and fruits with an expression peak at the initial red stage in strawberry fruit. Abiotic stresses could significantly induce the expression of CRY1. The CRY1 protein was located in both nucleus and cytoplasm. Five proteins (CSN5a-like, JAZ5, eIF3G. NF-YC9, and NDUFB9) interacting with CRY1 were discovered. Genes related flowering times, such as HY5 and CO, in three overexpressed FaCRY1 tobacco lines, were significantly upregulated. Taken together, our results suggested CRY1 have a broad role in biological processes in strawberry. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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10 pages, 1861 KiB

Open AccessArticle

Callogenesis and Plant Regeneration in Peony (Paeonia × suffruticosa) Using Flower Petal Explants

by Xia Chen, Chengyang Ye, Hongmin Yang, Wen Ji, Zhen Xu, Sanchun Ye, Huasen Wang, Songheng Jin, Chao Yu and Xiangtao Zhu

Horticulturae 2022, 8(5), 357; https://doi.org/10.3390/horticulturae8050357 - 20 Apr 2022

Cited by 10 | Viewed by 3818

Abstract

Peony is a traditional Chinese flower with significant ornamental and medicinal value. However, there are still problems, such as serious browning, difficulties in differentiation, and rooting and low regeneration efficiency in the process of the regeneration system established, which have hindered the development of transgenic peony technology. Establishing an efficient regeneration system is considered to be an important goal among peony researchers. Here, we describe a protocol for high-frequency callus induction and establishment of peony plants using flower petals as explants. Murashige and Skoog (MS) medium supplemented with 2.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D), 1.5 mg/L N-(phenylmethyl)-9H-purin-6-amine (6-BA), and 0.3 mg/L 1-naphthylacetic acid (NAA) was identified as the best medium for callus induction, achieving an induction rate of up to 98.52%. The highest peony proliferation rate (234%) was achieved on MS supplemented with 0.2 mg/L NAA and 3.0 mg/L 6-BA. The highest callus differentiation rate (34.81%) was achieved on MS supplemented with 2.0 mg/L 6-BA and 0.5 mg/L zeatin (ZT). The highest rooting rate was 23.33% when using 1/2 MS supplemented with 0.1 mg/L NAA and 0.05 mg/L 3-indolebutyric acid (IBA). After acclimation, the plants were transferred to pots, where they showed robust growth. We also observed the surface structures of the calluses using scanning electron microscopy and found that the differentiation characteristics of the calluses were hugely variable and that different surface structures appeared to affect bud differentiation efficiency. The efficient and rapid system for regenerating peonies using petal cultures established here will create new opportunities for the mass reproduction and genetic engineering of peony plants. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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14 pages, 3187 KiB

Open AccessArticle

Transcriptome Profiling Unravels the Involvement of Phytohormones in Tomato Resistance to the Tomato Yellow Leaf Curl Virus (TYLCV)

by Liuxia Song, Yinlei Wang, Liping Zhao and Tongmin Zhao

Horticulturae 2022, 8(2), 143; https://doi.org/10.3390/horticulturae8020143 - 8 Feb 2022

Cited by 8 | Viewed by 3152

Abstract

Tomato yellow leaf curl virus (TYLCV) is a serious pathogen transmitted by the whitefly (Bemisia tabaci). Due to the quick spread of the virus, which is assisted by its vector, tomato yield and quality have suffered a crushing blow. Resistance to TYLCV has been intensively investigated in transmission, yet the mechanism of anti-TYLCV remains elusive. Herein, we conducted transcriptome profiling with a TYLCV-resistant cultivar (CLN2777A) and a susceptible line (Moneymaker) to identify the potential mechanism of resistance to TYLCV. Compared to the susceptible line, CLN2777A maintained a lower level of lipid peroxidation (LPO) after TYLCV infection. Through RNA-seq, over 1000 differentially expressed genes related to the metabolic process, cellular process, response to stimulus, biological regulation, and signaling were identified, indicating that the defense response was activated after the virus attack. Further analysis showed that TYLCV infection could induce the expression of the genes involved in salicylic and jasmonic acid biosynthesis and the signal transduction of phytohormones, which illustrated that phytohormones were essential for tomatoes to defend against TYLCV. These findings provide greater insight into the effective source of resistance for TYLCV control, indicating a potential molecular tool for the design of TYLCV-resistant tomatoes. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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13 pages, 1472 KiB

Open AccessArticle

Identification and Expression Analysis of Zinc Finger A20/AN1 Stress-Associated Genes SmSAP Responding to Abiotic Stress in Eggplant

by Faxiang Wan, Yuhu Xu, Sulong Wang, Jun Gao, Dan Lu, Chenghong Zhou, Yanqing Liao, Yanyan Ma and Yu Zheng

Horticulturae 2022, 8(2), 108; https://doi.org/10.3390/horticulturae8020108 - 25 Jan 2022

Cited by 7 | Viewed by 3141

Abstract

Stress-associated proteins (SAP), a class of zinc-finger proteins, have been identified as novel stress regulatory proteins in stress responses. However, SAP genes in eggplant (SmSAP) have been little reported. It has important significance in identifying SAP members, understanding the molecular mechanisms underlying stress responses, and tolerance. We performed a comprehensive study of the A20/AN1 domains, motifs, gene structures, phylogenetic relationships, chromosomal locations, gene replications, collinearity, cis-acting elements, and expression pattern responses to various abiotic stresses. Twenty-one SAP genes were identified in eggplant (SmSAP) and were localized on 10 chromosomes. A phylogenetic analysis revealed that most of the SmSAP proteins showed a high homology with the tomato SAP members, and 21 members were divided into four groups based on the homology of the SAP members in eggplant, tomato, rice, and Arabidopsis. Further analysis revealed that SmSAP proteins contain the characteristic A20/AN1 domains, the A20 domain composed of motif 2 (ILCINNCGFFGSPATMNLCSKCYKDMJLK). Four pairs of tandem duplications were found in eggplant, and 10 SmSAP genes had collinearity with SAP genes from Arabidopsis, potato, or tomato, but only four SmSAP genes were collinear with SAP genes in the three species mentioned above. Moreover, the promoters of SmSAP genes were predicted to contain many cis-acting elements that respond to abiotic stress and hormones. A qRT-PCR analysis of the four selected SmSAP genes exhibited diverse expression levels in response to various environmental stresses. These results provided a comprehensive analysis of the SmSAP genes and lay a solid foundation for improving the understanding of the functional diversification of SAP genes under various environmental stresses in eggplant. Full article

(This article belongs to the Special Issue Omics Technologies and Their Applications in Vegetable Plant Research)

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