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Horticultural Crop Improvement: A New Era for Plant Molecular Research

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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 (30 April 2023) | Viewed by 13877

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Prof. Dr. Bo Sun

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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

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Guest Editor

College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
Interests: evolution of plant metabolic network; 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 a type of 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 the highly diverse and complex genome, which brought challenges to systematic studies around 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 of 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 applications of molecular biology, such as whole-genome resequencing, transcriptomics, proteomics, metabolomics, and genome editing, towards horticultural crop improvement. The topics include but are not limited to the 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

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Keywords

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

Published Papers (8 papers)

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Research

14 pages, 4268 KiB

Open AccessArticle

Genome-Wide Identification and Functional Analysis of the AP2/ERF Transcription Factor Family in Citrus Rootstock under Waterlogging Stress

by Wen He, Liang Luo, Rui Xie, Jiufeng Chai, Hao Wang, Yan Wang, Qing Chen, Zhiwei Wu, Shaofeng Yang, Mengyao Li, Yuanxiu Lin, Yunting Zhang, Ya Luo, Yong Zhang, Haoru Tang and Xiaorong Wang

Int. J. Mol. Sci. 2023, 24(10), 8989; https://doi.org/10.3390/ijms24108989 - 19 May 2023

Cited by 1 | Viewed by 1521

Abstract

Citrus plants are sensitive to waterlogging, and the roots are the first plant organ affected by hypoxic stress. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) can modulate plant growth and development. However, the information on AP2/ERF genes in citrus rootstock and their involvement in waterlogging conditions is limited. Previously, a rootstock cultivar, Citrus junos cv. Pujiang Xiangcheng was found to be highly tolerant to waterlogging stress. In this study, a total of 119 AP2/ERF members were identified in the C. junos genome. Conserved motif and gene structure analyses indicated the evolutionary conservation of PjAP2/ERFs. Syntenic gene analysis revealed 22 collinearity pairs among the 119 PjAP2/ERFs. The expression profiles under waterlogging stress showed differential expression of PjAP2/ERFs, of which, PjERF13 was highly expressed in both root and leaf. Furthermore, the heterologous expression of PjERF13 significantly enhanced the tolerance of transgenic tobacco to waterlogging stress. The overexpression of PjERF13 decreased the oxidative damage in the transgenic plants by reducing the H₂O₂ and MDA contents and increasing the antioxidant enzyme activities in the root and leaf. Overall, the current study provided basic information on the AP2/ERF family in the citrus rootstock and uncovered their potential function in positively regulating the waterlogging stress response. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research)

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13 pages, 6487 KiB

Open AccessArticle

TcbHLH14 a Jasmonate Associated MYC2-like Transcription Factor Positively Regulates Pyrethrin Biosynthesis in Tanacetum cinerariifolium

by Tuo Zeng, Qin Yu, Junzhong Shang, Zhizhuo Xu, Li Zhou, Wei Li, Jinjin Li, Hao Hu, Liyong Zhu, Jiawen Li and Caiyun Wang

Int. J. Mol. Sci. 2023, 24(8), 7379; https://doi.org/10.3390/ijms24087379 - 17 Apr 2023

Viewed by 1208

Abstract

Natural pyrethrins have high application value, and are widely used as a green pesticide in crop pest prevention and control. Pyrethrins are mainly extracted from the flower heads of Tanacetum cinerariifolium; however, the natural content is low. Therefore, it is essential to understand the regulatory mechanisms underlying the synthesis of pyrethrins through identification of key transcription factors. We identified a gene encoding a MYC2-like transcription factor named TcbHLH14 from T. cinerariifolium transcriptome, which is induced by methyl jasmonate. In the present study, we evaluated the regulatory effects and mechanisms of TcbHLH14 using expression analysis, a yeast one-hybrid assay, electrophoretic mobility shift assay, and overexpression/virus-induced gene silencing experiments. We found that TcbHLH14 can directly bind to the cis-elements of the pyrethrins synthesis genes TcAOC and TcGLIP to activate their expression. The transient overexpression of TcbHLH14 enhanced expression of the TcAOC and TcGLIP genes. Conversely, transient silencing of TcbHLH14 downregulated the expression of TcAOC and TcGLIP and reduced the content of pyrethrins. In summary, these results indicate that the potential application of TcbHLH14 in improving the germplasm resources and provide a new insight into the regulatory network of pyrethrins biosynthesis of T. cinerariifolium to further inform the development of engineering strategies for increasing pyrethrins contents. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research)

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18 pages, 96649 KiB

Open AccessArticle

KNOX Genes Were Involved in Regulating Axillary Bud Formation of Chrysanthemum × morifolium

by Qingqing Yang, Tianci Cong, Yicen Yao, Tangren Cheng, Cunquan Yuan and Qixiang Zhang

Int. J. Mol. Sci. 2023, 24(8), 7081; https://doi.org/10.3390/ijms24087081 - 11 Apr 2023

Cited by 4 | Viewed by 1448

Abstract

Branching is an important agronomic and economic trait in cut chrysanthemums. The axillary meristem (AM) formation of the axillary buds of cut chrysanthemums has a decisive role in its branching characteristics. However, little is known about the regulation mechanism of axillary meristem formation in chrysanthemums at the molecular level. Members of the Homeobox gene family especially genes belonging to the class I KNOX branch play a key role in regulating the axillary bud growth and development processes of plants. In this study, three genes belonging to the class I KNOX branch, CmKNAT1, CmKNAT6, and CmSTM were cloned from chrysanthemums, and their functions in regulating axillary bud formation were examined. The subcellular localization test showed that these three KNOX genes were expressed in the nucleus, so all of them might function as transcription factors. The results of the expression profile analysis showed that these three KNOX genes were highly expressed in the AM formation stage of axillary buds. Overexpression of KNOX genes result in a wrinkled leaf phenotype in tobacco and Arabidopsis, which may be related to the excessive division of leaf cells, resulting in the proliferation of leaf tissue. Furthermore, overexpression of these three KNOX genes enhances the regeneration ability of tobacco leaves, indicating that these three KNOX genes may participate in the regulation of cell meristematic ability, thus promoting the formation of buds. In addition, the results of fluorescence quantitative testing showed that these three KNOX genes may promote the formation of chrysanthemum axillary buds by promoting the cytokinin pathway while inhibiting the auxin and gibberellin pathways. In conclusion, this study demonstrated that CmKNAT1, CmKNAT6, and CmSTM genes were involved in regulating axillary bud formation of Chrysanthemum × morifolium and preliminarily revealed the molecular mechanism of their regulation of AM formation. These findings may provide a theoretical basis and candidate gene resources for genetic engineering breeding of new varieties of cut chrysanthemums without lateral branches. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research)

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19 pages, 3809 KiB

Open AccessArticle

Characterization of the Difference between Day and Night Temperatures on the Growth, Photosynthesis, and Metabolite Accumulation of Tea Seedlings

by Xiaoqin Tan, Huili Li, Zhongyue Zhang, Yanjuan Yang, Zhen Jin, Wei Chen, Dandan Tang, Chaoling Wei and Qian Tang

Int. J. Mol. Sci. 2023, 24(7), 6718; https://doi.org/10.3390/ijms24076718 - 04 Apr 2023

Cited by 3 | Viewed by 2127

Abstract

Currently, the effects of the differences between day and night temperatures (DIFs) on tea plant are poorly understood. In order to investigate the influence of DIFs on the growth, photosynthesis, and metabolite accumulation of tea plants, the plants were cultivated under 5 °C (25/20 °C, light/dark), 10 °C (25/15 °C, light/dark), and 15 °C (25/10 °C, light/dark). The results showed that the growth rate of the new shoots decreased with an increase in the DIFs. There was a downward trend in the photosynthesis among the treatments, as evidenced by the lowest net photosynthetic rate and total chlorophyll at a DIF of 15 °C. In addition, the DIFs significantly affected the primary and secondary metabolites. In particular, the 10 °C DIF treatment contained the lowest levels of soluble sugars, tea polyphenols, and catechins but was abundant in caffeine and amino acids, along with high expression levels of theanine synthetase (TS3) and glutamate synthase (GOGAT). Furthermore, the transcriptome data revealed that the differentially expressed genes were enriched in valine, leucine, and isoleucine degradation, flavone/flavonol biosyntheses, flavonoid biosynthesis, etc. Therefore, we concluded that a DIF of 10 °C was suitable for the protected cultivation of tea plants in terms of the growth and the quality of a favorable flavor of tea, which provided a scientific basis for the protected cultivation of tea seedlings. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research)

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14 pages, 6920 KiB

Open AccessArticle

A Joint Transcriptomic and Metabolomic Analysis Reveals the Regulation of Shading on Lignin Biosynthesis in Asparagus

by Junying Ma, Xiaoyan Li, Maolin He, Yanwen Li, Wei Lu, Mengyao Li, Bo Sun and Yangxia Zheng

Int. J. Mol. Sci. 2023, 24(2), 1539; https://doi.org/10.3390/ijms24021539 - 12 Jan 2023

Cited by 6 | Viewed by 1722

Abstract

Asparagus belongs to the Liliaceae family and has important economic and pharmacological value. Lignin plays a crucial role in cell wall structural integrity, stem strength, water transport, mechanical support and plant resistance to pathogens. In this study, various biological methods were used to study the mechanism of shading on the asparagus lignin accumulation pathway. The physiological results showed that shading significantly reduced stem diameter and cell wall lignin content. Microstructure observation showed that shading reduced the number of vascular bundles and xylem area, resulting in decreased lignin content, and thus reducing the lignification of asparagus. Cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol are crucial intermediate metabolites in the process of lignin synthesis. Metabolomic profiling showed that shading significantly reduced the contents of cinnamic acid, caffeic acid, ferulic acid and sinapyl alcohol. Transcriptome profiling identified 37 differentially expressed genes related to lignin, including PAL, C4H, 4CL, CAD, CCR, POD, CCoAOMT, and F5H related enzyme activity regulation genes. The expression levels of POD, CCoAOMT, and CCR genes were significantly decreased under shading treatment, while the expression levels of CAD and F5H genes exhibited no significant difference with increased shading. The downregulation of POD, CCoAOMT genes and the decrease in CCR gene expression levels inhibited the activities of the corresponding enzymes under shading treatment, resulting in decreased downstream content of caffeic acid, ferulic acid, sinaperol, chlorogenic acid and coniferin. A significant decrease in upstream cinnamic acid content was observed with shading, which also led to decreased downstream metabolites and reduced asparagus lignin content. In this study, transcriptomic and metabolomic analysis revealed the key regulatory genes and metabolites of asparagus lignin under shading treatment. This study provides a reference for further understanding the mechanism of lignin biosynthesis and the interaction of related genes. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research)

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16 pages, 3647 KiB

Open AccessArticle

The Functional Characterization of Carboxylesterases Involved in the Degradation of Volatile Esters Produced in Strawberry Fruits

by Lingjie Zhang, Kang Zhou, Maohao Wang, Rui Li, Xinlong Dai, Yajun Liu, Xiaolan Jiang, Tao Xia and Liping Gao

Int. J. Mol. Sci. 2023, 24(1), 383; https://doi.org/10.3390/ijms24010383 - 26 Dec 2022

Cited by 2 | Viewed by 1771

Abstract

Volatile ester compounds are important contributors to the flavor of strawberry, which affect consumer preference. Here, the GC-MS results showed that volatile esters are the basic aroma components of strawberry, banana, apple, pear, and peach, and the volatile esters were significantly accumulated with the maturation of strawberry fruits. The main purpose of this study is to discuss the relationship between carboxylesterases (CXEs) and the accumulation of volatile ester components in strawberries. FaCXE2 and FaCXE3 were found to have the activity of hydrolyzing hexyl acetate, Z-3-hexenyl acetate, and E-2-hexenyl acetate to the corresponding alcohols. The enzyme kinetics results showed that FaCXE3 had the higher affinity for hexyl acetate, E-2-hexenyl acetate, and Z-3-hexenyl acetate compared with FaCXE2. The volatile esters were mainly accumulated at the maturity stages in strawberry fruits, less at the early stages, and the least during the following maturation stages. The expression of FaCXE2 gradually increased with fruit ripening and the expression level of FaCXE3 showed a decreasing trend, which suggested the complexity of the true function of CXEs. The transient expression of FaCXE2 and FaCXE3 genes in strawberry fruits resulted in a significantly decreased content of volatile esters, such as Z-3-hexenyl acetate, methyl hexanoate, methyl butyrate, and other volatile esters. Taken together, FaCXE2 and FaCXE3 are indeed involved in the regulation of the synthesis and degradation of strawberry volatile esters. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research)

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16 pages, 6170 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Molecular Regularity Mechanism Underlying Stem Bulblet Formation in Oriental Lily ‘Siberia’; Functional Characterization of the LoLOB18 Gene

by Shaozhong Fang, Chenglong Yang, Muhammad Moaaz Ali, Mi Lin, Shengnan Tian, Lijuan Zhang, Faxing Chen and Zhimin Lin

Int. J. Mol. Sci. 2022, 23(23), 15246; https://doi.org/10.3390/ijms232315246 - 03 Dec 2022

Cited by 3 | Viewed by 1488

Abstract

The formation of underground stem bulblets in lilies is a complex biological process which is key in their micropropagation. Generally, it involves a stem-to-bulblet transition; however, the underlying mechanism remains elusive. It is important to understand the regulatory mechanism of bulblet formation for the reproductive efficiency of Lilium. In this study, we investigated the regulatory mechanism of underground stem bulblet formation under different conditions regarding the gravity point angle of the stem, i.e., vertical (control), horizontal, and slanting. The horizontal and slanting group displayed better formation of bulblets in terms of quality and quantity compared with the control group. A transcriptome analysis revealed that sucrose and starch were key energy sources for bulblet formation, auxin and cytokinin likely promoted bulblet formation, and gibberellin inhibited bulblet formation. Based on transcriptome analysis, we identified the LoLOB18 gene, a homolog to AtLOB18, which has been proven to be related to embryogenic development. We established the stem bud growth tissue culture system of Lilium and silenced the LoLOb18 gene using the VIGS system. The results showed that the bulblet induction was reduced with down-regulation of LoLOb18, indicating the involvement of LoLOb18 in stem bulblet formation in lilies. Our research lays a solid foundation for further molecular studies on stem bulblet formation of lilies. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research)

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21 pages, 2659 KiB

Open AccessArticle

Metabolic and Transcriptomic Profiling Reveals Etiolated Mechanism in Huangyu Tea (Camellia sinensis) Leaves

by Xin Mei, Kaikai Zhang, Yongen Lin, Hongfeng Su, Chuyuan Lin, Baoyi Chen, Haijun Yang and Lingyun Zhang

Int. J. Mol. Sci. 2022, 23(23), 15044; https://doi.org/10.3390/ijms232315044 - 30 Nov 2022

Cited by 8 | Viewed by 1687

Abstract

Leaf color is one of the key factors involved in determining the processing suitability of tea. It relates to differential accumulation of flavor compounds due to the different metabolic mechanisms. In recent years, photosensitive etiolation or albefaction is an interesting direction in tea research field. However, the molecular mechanism of color formation remains unclear since albino or etiolated mutants have different genetic backgrounds. In this study, wide-target metabolomic and transcriptomic analyses were used to reveal the biological mechanism of leaf etiolation for ‘Huangyu’, a bud mutant of ‘Yinghong 9’. The results indicated that the reduction in the content of chlorophyll and the ratio of chlorophyll to carotenoids might be the biochemical reasons for the etiolation of ‘Huangyu’ tea leaves, while the content of zeaxanthin was significantly higher. The differentially expressed genes (DEGs) involved in chlorophyll and chloroplast biogenesis were the biomolecular reasons for the formation of green or yellow color in tea leaves. In addition, our results also revealed that the changes of DEGs involved in light-induced proteins and circadian rhythm promoted the adaptation of etiolated tea leaves to light stress. Variant colors of tea leaves indicated different directions in metabolic flux and accumulation of flavor compounds. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research)

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