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Horticultural Crop Improvement: A New Era for Plant Molecular Research: 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 February 2025 | Viewed by 8459

Special Issue Editors

Prof. Dr. Bo Sun

E-Mail Website
Guest Editor
College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
Interests: brassica vegetables; Chinese kale; mustard; carotenoids; glucosinolate; antioxidants; nutritional quality; postharvest
Special Issues, Collections and Topics in MDPI journals
Dr. Pengxiang Fan

E-Mail Website
Guest Editor
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
Interests: evolution of plant metabolic networks; metabolic network reconstruction; biosynthesis of specialized metabolites; regulation of plant metabolism; plant–herbivore interaction; Solanaceae; glandular trichome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural plants are intensively cultivated crops with high economic value, such as tree fruits, vegetables, ornamental plants, and tea crops. The wide taxonomic distribution and sophisticated domestication history of horticultural crops have led to their highly diverse and complex genomes, which has caused challenges regarding the systematic studies of these plants.

Molecular biology reveals the molecular basis of biological processes in cells, and it is essential for understanding the mechanisms of the execution and regulation of biological processes. Molecular biology technologies have been applied to a wide range of living organisms. However, knowledge about horticultural crops is relatively less available than that on model plants. Recent advances in molecular biology—represented by revolutionary biotechnologies such as plant genome editing and next-generation sequencing—provide unprecedented opportunities to gain insight into the less well-studied horticultural crops.

For this Special Issue, we welcome any original research articles, reviews, short notes, or opinion articles that highlight horticultural crop improvement applications in molecular biology, such as whole-genome resequencing, transcriptomics, proteomics, metabolomics, and genome editing. The topics include, but are not limited to, studies of regulatory mechanisms of plant growth and development, as well as efforts to improve crop yield, quality, and resistance to biotic/abiotic stresses.

Prof. Dr. Bo Sun
Dr. Pengxiang Fan
Guest Editors

Manuscript Submission Information

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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.

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Keywords

  • horticultural plants
  • whole-genome resequencing
  • transcriptomics
  • proteomics
  • metabolomics
  • gene editing
  • gene regulation
  • growth and development
  • yield
  • quality
  • resistance

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Published Papers (8 papers)

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Research

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19 pages, 7280 KiB  
Article
The Impact of Nutrient Solution Electrical Conductivity on Leaf Transcriptome Contributing to the Fruit Quality of Cucumber Grown in Coir Cultivation
by Lizhong He, Wentao Xu, Dongke Zhou, Jun Yan, Haijun Jin, Hongmei Zhang, Jiawei Cui, Chen Miao, Yongxue Zhang, Qiang Zhou, Jizhu Yu, Xiang Yu and Xiaotao Ding
Int. J. Mol. Sci. 2024, 25(22), 11864; https://doi.org/10.3390/ijms252211864 - 5 Nov 2024
Viewed by 416
Abstract
Soilless cultivation is increasingly utilized in supplying essential nutrients for greenhouse crops. However, the impact of coir cultivation under varying electrical conductivity (EC) conditions on cucumber growth and fruit quality, particularly through the regulation of gene expression during the vegetative stage, remains uncertain. [...] Read more.
Soilless cultivation is increasingly utilized in supplying essential nutrients for greenhouse crops. However, the impact of coir cultivation under varying electrical conductivity (EC) conditions on cucumber growth and fruit quality, particularly through the regulation of gene expression during the vegetative stage, remains uncertain. In this study, we performed metabolic measurements on cucumber in both vegetative and reproductive stages under three different EC conditions and found metabolic products such as some primary metabolites (cellulose, many uncharged amino acids) and some secondary metabolites (rutin, cucurbitacin B) accumulated the most under EC of 5 dS·m−1. Next, we conducted transcriptome profiling in cucumber leaves, revealing that the function of genes significantly regulated by EC was associated with photosynthesis, many anabolic processes, and membrane transport. Finally, a set of genes contributed to metabolites related to the fruit quality of cucumber were identified by the Orthogonal Partial Least Squares (O2PLS) analysis, including genes involved in the biosynthesis of amino acids, polysaccharides, and many secondary metabolites. Taken together, these findings suggest that coir cultivation in greenhouses with moderate EC can induce a transcriptome-wide change in gene expression, thereby contributing to enhancing the abundance of metabolites associated with cucumber fruit quality. Full article
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research: 3rd Edition)
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17 pages, 14292 KiB  
Article
Integrated Transcriptomic and Proteomic Analysis of Nutritional Quality-Related Molecular Mechanisms in “Longjia”, “Yangpao”, and “Niangqing” Walnuts (Juglans sigillata)
by Hailang Wang, Yue Su, Xiang Hu, Boxiao Wu, Yun Liu, Huan Kan and Changwei Cao
Int. J. Mol. Sci. 2024, 25(21), 11671; https://doi.org/10.3390/ijms252111671 - 30 Oct 2024
Viewed by 450
Abstract
In this study, “Longjia (LJ)” and “Yangpao (YP)”exhibited higher contents of major nutrients compared to “Niangqing (NQ)” walnuts. The combination of transcriptome and proteome by RNA sequencing and isotope labeling for relative and absolute quantification techniques provides new insights into the molecular mechanisms [...] Read more.
In this study, “Longjia (LJ)” and “Yangpao (YP)”exhibited higher contents of major nutrients compared to “Niangqing (NQ)” walnuts. The combination of transcriptome and proteome by RNA sequencing and isotope labeling for relative and absolute quantification techniques provides new insights into the molecular mechanisms underlying the nutritional quality of the three walnut species. A total of 4146 genes and 139 proteins showed differential expression levels in the three comparison groups. Combined transcriptome and proteome analyses revealed that these genes and proteins were mainly enriched in signaling pathways such as fatty acid biosynthesis, protein processing in endoplasmic reticulum, and amino acid metabolism, revealing their relationship with the nutritional quality of walnut kernels. This study identified key genes and proteins associated with nutrient metabolism and accumulation in walnut kernels, provided transcriptomic and proteomic information on the molecular mechanisms of nutrient differences in walnut kernels, and contributed to the elucidation of the mechanisms of nutrient differences and the selection and breeding of high-quality walnut seedlings. Full article
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research: 3rd Edition)
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18 pages, 3308 KiB  
Article
SSA4 Mediates Cd Tolerance via Activation of the Cis Element of VHS1 in Yeast and Enhances Cd Tolerance in Chinese Cabbage
by Han Zheng, Chao Yuan, Tong Bu, Qun Liu, Jingjuan Li, Fengde Wang, Yihui Zhang, Lilong He and Jianwei Gao
Int. J. Mol. Sci. 2024, 25(20), 11026; https://doi.org/10.3390/ijms252011026 - 14 Oct 2024
Viewed by 728
Abstract
Identifying key genes involved in Cadmium (Cd) response pathways in plants and developing low-Cd-accumulating cultivars may be the most effective and eco-friendly strategy to tackle the problem of Cd pollution in crops. In our previous study, Stressseventy subfamily A 4 (SSA4) [...] Read more.
Identifying key genes involved in Cadmium (Cd) response pathways in plants and developing low-Cd-accumulating cultivars may be the most effective and eco-friendly strategy to tackle the problem of Cd pollution in crops. In our previous study, Stressseventy subfamily A 4 (SSA4) was identified to be associated with Cd tolerance in yeast. Here, we investigated the mechanism of SSA4 in regulating Cd tolerance in yeast. ScSSA4 binds to POre Membrane 34 (POM34), a key component of nuclear pore complex (NPC), and translocates from the cytoplasm to the nucleus, where it regulates the expression of its downstream gene, Viable in a Hal3 Sit4 background 1 (VHS1), resulting in reduced Cd accumulation in yeast cells. Additionally, we identified a Chinese cabbage SSA4 gene, BrSSA4c, which could enhance the Cd tolerance in Chinese cabbage. This study offers new insights into the regulatory mechanisms of Cd tolerance in yeast, a model organism, and paves the way for the genetic enhancement of Cd tolerance in Chinese cabbage. Full article
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research: 3rd Edition)
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14 pages, 3436 KiB  
Article
Chlorophyll and Carotenoid Metabolism Varies with Growth Temperatures among Tea Genotypes with Different Leaf Colors in Camellia sinensis
by Pengfei Xu, Jingbo Yu, Ruihong Ma, Yanyan Ji, Qiang Hu, Yihu Mao, Changqing Ding, Zhengzhen Li, Shibei Ge, Wei-Wei Deng and Xin Li
Int. J. Mol. Sci. 2024, 25(19), 10772; https://doi.org/10.3390/ijms251910772 - 7 Oct 2024
Viewed by 994
Abstract
The phenotype of albino tea plants (ATPs) is significantly influenced by temperature regimes and light conditions, which alter certain components of the tea leaves leading to corresponding phenotypic changes. However, the regulatory mechanism of temperature-dependent changes in photosynthetic pigment contents and the resultant [...] Read more.
The phenotype of albino tea plants (ATPs) is significantly influenced by temperature regimes and light conditions, which alter certain components of the tea leaves leading to corresponding phenotypic changes. However, the regulatory mechanism of temperature-dependent changes in photosynthetic pigment contents and the resultant leaf colors remain unclear. Here, we examined the chloroplast microstructure, shoot phenotype, photosynthetic pigment content, and the expression of pigment synthesis-related genes in three tea genotypes with different leaf colors under different temperature conditions. The electron microscopy results revealed that all varieties experienced the most severe chloroplast damage at 15 °C, particularly in albino cultivar Baiye 1 (BY), where chloroplast basal lamellae were loosely arranged, and some chloroplasts were even empty. In contrast, the chloroplast basal lamellae at 35 °C and 25 °C were neatly arranged and well-developed, outperforming those observed at 20 °C and 15 °C. Chlorophyll and carotenoid measurements revealed a significant reduction in chlorophyll content under low temperature treatment, peaking at ambient temperature followed by high temperatures. Interestingly, BY showed remarkable tolerance to high temperatures, maintaining relatively high chlorophyll content, indicating its sensitivity primarily to low temperatures. Furthermore, the trends in gene expression related to chlorophyll and carotenoid metabolism were largely consistent with the pigment content. Correlation analysis identified key genes responsible for temperature-induced changes in these pigments, suggesting that changes in their expression likely contribute to temperature-dependent leaf color variations. Full article
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research: 3rd Edition)
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22 pages, 13380 KiB  
Article
Integrated Metabolomic–Transcriptomic Analyses of Flavonoid Accumulation in Citrus Fruit under Exogenous Melatonin Treatment
by Chenning Zhao, Zhendong Wang, Zhenkun Liao, Xiaojuan Liu, Yujia Li, Chenwen Zhou, Cui Sun, Yue Wang, Jinping Cao and Chongde Sun
Int. J. Mol. Sci. 2024, 25(12), 6632; https://doi.org/10.3390/ijms25126632 - 16 Jun 2024
Cited by 3 | Viewed by 1330
Abstract
The flavonoids in citrus fruits are crucial physiological regulators and natural bioactive products of high pharmaceutical value. Melatonin is a pleiotropic hormone that can regulate plant morphogenesis and stress resistance and alter the accumulation of flavonoids in these processes. However, the direct effect [...] Read more.
The flavonoids in citrus fruits are crucial physiological regulators and natural bioactive products of high pharmaceutical value. Melatonin is a pleiotropic hormone that can regulate plant morphogenesis and stress resistance and alter the accumulation of flavonoids in these processes. However, the direct effect of melatonin on citrus flavonoids remains unclear. In this study, nontargeted metabolomics and transcriptomics were utilized to reveal how exogenous melatonin affects flavonoid biosynthesis in “Bingtangcheng” citrus fruits. The melatonin treatment at 0.1 mmol L−1 significantly increased the contents of seven polymethoxylated flavones (PMFs) and up-regulated a series of flavonoid pathway genes, including 4CL (4-coumaroyl CoA ligase), FNS (flavone synthase), and FHs (flavonoid hydroxylases). Meanwhile, CHS (chalcone synthase) was down-regulated, causing a decrease in the content of most flavonoid glycosides. Pearson correlation analysis obtained 21 transcription factors co-expressed with differentially accumulated flavonoids, among which the AP2/EREBP members were the most numerous. Additionally, circadian rhythm and photosynthesis pathways were enriched in the DEG (differentially expressed gene) analysis, suggesting that melatonin might also mediate changes in the flavonoid biosynthesis pathway by affecting the fruit’s circadian rhythm. These results provide valuable information for further exploration of the molecular mechanisms through which melatonin regulates citrus fruit metabolism. Full article
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research: 3rd Edition)
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17 pages, 3876 KiB  
Article
Evidence Supporting a Role of Alternative Splicing Participates in Melon (Cucumis melo L.) Fruit Ripening
by Wenjiao Wang, Yuping Wei, Zhaoying Xu, Chengcheng Shen, Ang Li, Dailu Guan, Xuejun Zhang and Bin Liu
Int. J. Mol. Sci. 2024, 25(11), 5886; https://doi.org/10.3390/ijms25115886 - 28 May 2024
Viewed by 1054
Abstract
One key post-transcriptional modification mechanism that dynamically controls a number of physiological processes in plants is alternative splicing (AS). However, the functional impacts of AS on fruit ripening remain unclear. In this research, we used RNA-seq data from climacteric (VED, Harukei 3) and [...] Read more.
One key post-transcriptional modification mechanism that dynamically controls a number of physiological processes in plants is alternative splicing (AS). However, the functional impacts of AS on fruit ripening remain unclear. In this research, we used RNA-seq data from climacteric (VED, Harukei 3) and non-climacteric (PI, PS) melon cultivars to explore alternative splicing (AS) in immature and mature fruit. The results revealed dramatic changes in differential AS genes (DAG) between the young and mature fruit stages, particularly in genes involved in fruit development/ripening, carotenoid and capsaicinoid biosynthesis, and starch and sucrose metabolism. Serine/arginine-rich (SR) family proteins are known as important splicing factors in AS events. From the melon genome, a total of 17 SR members were discovered in this study. These genes could be classified into eight distinct subfamilies based on gene structure and conserved motifs. Promoter analysis detected various cis-acting regulatory elements involved in hormone pathways and fruit development. Interestingly, these SR genes exhibited specific expression patterns in reproductive organs such as flowers and ovaries. Additionally, concurrent with the increase in AS levels in ripening fruit, the transcripts of these SR genes were activated during fruit maturation in both climacteric and non-climacteric melon varieties. We also found that most SR genes were under selection during domestication. These results represent a novel finding of increased AS levels and SR gene expression during fruit ripening, indicating that alternative splicing may play a role in fruit maturation. Full article
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research: 3rd Edition)
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15 pages, 6777 KiB  
Article
Transcriptome Analysis Reveals the Mechanism by Which Exogenous Melatonin Treatment Delays Leaf Senescence of Postharvest Chinese Kale (Brassica oleracea var. alboglabra)
by Hongmei Di, Chenlu Zhang, Aolian Zhou, Huanhuan Huang, Yi Tang, Huanxiu Li, Zhi Huang, Fen Zhang and Bo Sun
Int. J. Mol. Sci. 2024, 25(4), 2250; https://doi.org/10.3390/ijms25042250 - 13 Feb 2024
Cited by 3 | Viewed by 1581
Abstract
Melatonin, a pleiotropic small molecule, is employed in horticultural crops to delay senescence and preserve postharvest quality. In this study, 100 µM melatonin treatment delayed a decline in the color difference index h* and a*, maintaining the content of chlorophyll and [...] Read more.
Melatonin, a pleiotropic small molecule, is employed in horticultural crops to delay senescence and preserve postharvest quality. In this study, 100 µM melatonin treatment delayed a decline in the color difference index h* and a*, maintaining the content of chlorophyll and carotenoids, thereby delaying the yellowing and senescence of Chinese kale. Transcriptome analysis unequivocally validates melatonin’s efficacy in delaying leaf senescence in postharvest Chinese kale stored at 20 °C. Following a three-day storage period, the melatonin treatment group exhibited 1637 differentially expressed genes (DEGs) compared to the control group. DEG analysis elucidated that melatonin-induced antisenescence primarily governs phenylpropanoid biosynthesis, lipid metabolism, plant signal transduction, and calcium signal transduction. Melatonin treatment up-regulated core enzyme genes associated with general phenylpropanoid biosynthesis, flavonoid biosynthesis, and the α-linolenic acid biosynthesis pathway. It influenced the redirection of lignin metabolic flux, suppressed jasmonic acid and abscisic acid signal transduction, and concurrently stimulated auxin signal transduction. Additionally, melatonin treatment down-regulated RBOH expression and up-regulated genes encoding CaM, thereby influencing calcium signal transduction. This study underscores melatonin as a promising approach for delaying leaf senescence and provides insights into the mechanism of melatonin-mediated antisenescence in postharvest Chinese kale. Full article
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research: 3rd Edition)
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Review

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13 pages, 774 KiB  
Review
Emerging Roles of Mitogen-Activated Protein Kinase Signaling Pathways in the Regulation of Fruit Ripening and Postharvest Quality
by Juan Jin, Wei Wang, Dingyu Fan, Qing Hao and Wensuo Jia
Int. J. Mol. Sci. 2024, 25(5), 2831; https://doi.org/10.3390/ijms25052831 - 29 Feb 2024
Cited by 1 | Viewed by 1230
Abstract
Fleshy fruit ripening is a unique biological process that involves dramatic changes in a diverse array of cellular metabolisms. The regulation of these metabolisms is essentially mediated by cellular signal transduction of internal (e.g., hormones) and external cues (i.e., environmental stimuli). Mitogen-activated protein [...] Read more.
Fleshy fruit ripening is a unique biological process that involves dramatic changes in a diverse array of cellular metabolisms. The regulation of these metabolisms is essentially mediated by cellular signal transduction of internal (e.g., hormones) and external cues (i.e., environmental stimuli). Mitogen-activated protein kinase (MAPK) signaling pathways play crucial roles in a diverse array of biological processes, such as plant growth, development and biotic/abiotic responses. Accumulating evidence suggests that MAPK signaling pathways are also implicated in fruit ripening and quality formation. However, while MAPK signaling has been extensively reviewed in Arabidopsis and some crop plants, the comprehensive picture of how MAPK signaling regulates fruit ripening and quality formation remains unclear. In this review, we summarize and discuss research in this area. We first summarize recent studies on the expression patterns of related kinase members in relation to fruit development and ripening and then summarize and discuss the crucial evidence of the involvement of MAPK signaling in fruit ripening and quality formation. Finally, we propose several perspectives, highlighting the research matters and questions that should be afforded particular attention in future studies. Full article
(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research: 3rd Edition)
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