Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Horticultural Plants

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: 30 June 2024 | Viewed by 8442

Special Issue Editors


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Guest Editor
College of Horticulture, Qingdao Agriculture University, Qingdao 266109, China
Interests: molecular biology of vegetables; vegetable growth and development; ideotype; sex differentiation; plant biotic and abiotic stresses; mineral element absorption
Special Issues, Collections and Topics in MDPI journals
School of Life Sciences, Liaocheng University, Liaocheng 252000, China
Interests: temperature stress; drought stress; hormone metabolism and signaling; molecular breeding; vegetable crop

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Guest Editor
College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
Interests: grafting; vegetables
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticutural plants including fruit, vegetable and ornamental crops contain many health-promoting substances and play a vital role in sustaining human life. Among them, fruit and vegetable crops are main sources of nutrition, and some of them also are staple foods for human health. With the worsening global environment, the fast growth of the global population and the improvement in people's living standards, the market demand for high-quantity and high-quality fruit is expanding dramatically. The conventional breeding practices for horticutural plant improvement are far from meeting the demands of the times, especially with the declining genetic base and the crossing of barriers in wild and cultivated species. Therefore, transgenic research and genome engineering approaches are hot areas in modern agriculture due to their precise and rapid characteristics. In order to develop new crops by a genetic approach, it is necessary to carry out genome-wide identification and expression analysis of target genes, which control important traits, quality characters and stress tolerances and provide new insights into the crucial genes underlying these traits and their molecular regulation mechanisms.

Over the past decade, people ha e not been satisfied with the conventional breeding approaches for germplasm innovation to cope with harsh environments, and instead have preferred modern technology like transgenic technology, genomics-assisted breeding, genome editing, etc. Therefore, analyses of target genes accurately and systematically lay the foundation to research their functions. This Special Issue on “Genome-Wide Identification and Expression Analysis for the Genetic Improvement of Horticultural Plants”welcomes the submission of review and research papers or short communications on the following topics: crop traits, metabolism, biotic stress and abiotic stress. Bioinformation on both genes or transcript factors and their function verification in horticultural crops are needed. The aim of this Special Issue is to provide new key genes and and valuable reference genes for revealng their molecular regulation mechanisms of important traits, metabolic pathways and resistant tolerance through the advanced technologies of molecular genetics.

Prof. Dr. Huasen Wang
Dr. Fei Ding
Dr. Li Miao
Guest Editors

Manuscript Submission Information

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Keywords

  • horticutural plants
  • genome-wide identification
  • expression analysis
  • genetic improvement

Published Papers (8 papers)

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Research

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15 pages, 9374 KiB  
Article
Genome-Wide Identification and Expression Analysis of Beta-Galactosidase Family Members in Chinese Bayberry (Myrica rubra)
by Li Sun, Qinpei Yu, Shuwen Zhang, Zheping Yu, Senmiao Liang, Xiliang Zheng, Haiying Ren and Xingjiang Qi
Horticulturae 2024, 10(3), 225; https://doi.org/10.3390/horticulturae10030225 - 26 Feb 2024
Viewed by 642
Abstract
Fruit development and softening play pivotal roles in determining fruit quality and post-harvest shelf life in Chinese bayberry (Myrica rubra). However, the specific role of beta (β)-galactosidase, particularly β-galactosidase of M. rubra (MrBGAL), in facilitating fruit softening remains unclear. [...] Read more.
Fruit development and softening play pivotal roles in determining fruit quality and post-harvest shelf life in Chinese bayberry (Myrica rubra). However, the specific role of beta (β)-galactosidase, particularly β-galactosidase of M. rubra (MrBGAL), in facilitating fruit softening remains unclear. In this study, we aimed to address this gap by investigating the involvement of MrBGALs genes in fruit softening. We identified all 15 MrBGALs and conducted a comprehensive analysis, including phylogenetic relationships, gene structure, protein motifs, co-linearity, and expression patterns. Using phylogenetic analysis, we classified all MrBGALs into five distinct groups. Additionally, cis-element prediction and comparative genome analysis provided insightful clues about the functionality of MrBGALs. Transcriptome data revealed unique expression patterns of MrBGALs throughout various fruit development stages. These findings introduce valuable candidate genes that can contribute to unraveling the functions and molecular mechanisms governing fruit development and softening in Chinese bayberry. Full article
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19 pages, 31769 KiB  
Article
Genome-Wide Identification of MYB Transcription Factors and Their Function on Floral Volatile Compounds Biosynthesis in Antirrhinum majus L.
by Xiaohui Song, Senbao Shi, Yulai Kong, Fengyi Wang, Shaorong Dong, Chong Ma, Longqing Chen and Zhenglin Qiao
Horticulturae 2024, 10(2), 136; https://doi.org/10.3390/horticulturae10020136 - 30 Jan 2024
Viewed by 885
Abstract
The v-MYB avivan myoblastsis virus oncogene homolog (MYB) family is the largest gene family of the transcription factor in plants, involved in plant growth and development, secondary metabolism and resistance to biotic/abiotic stress. Antirrhinum majus (snapdragon) is an ideal material for studying ornamental [...] Read more.
The v-MYB avivan myoblastsis virus oncogene homolog (MYB) family is the largest gene family of the transcription factor in plants, involved in plant growth and development, secondary metabolism and resistance to biotic/abiotic stress. Antirrhinum majus (snapdragon) is an ideal material for studying ornamental traits. Nevertheless, there has been no systematic investigation into the AmMYB family of snapdragons. In this study, we identified a total of 162 members of the AmMYB gene family in snapdragons. Gene structure analysis showed that the AmMYB family within the same subgroup had a similar structure and motifs. Analysis of gene duplication events revealed that the amplification of the AmMYB family was driven by whole-genome duplication (WGD) and dispersed duplication. The analysis of cis-acting elements in the promoter region of AmMYB genes reveals a collaborative involvement of light-responsive growth and development elements, stress resistance elements, and hormone-responsive elements jointly participating in the regulation of the AmMYB gene. Collinearity analysis demonstrates significant functional distinctions between AmMYB and monocotyledonous plants. The classification of AmMYB members results in 3 main subgroups with 36 smaller subgroups. All AmMYB genes are distributed across all eight chromosomes, with no apparent correlation between subfamily distribution and chromosome length. Through phylogenetic analysis and RNA-seq analysis, we have identified 9 R2R3-MYB genes that potentially play a role in the regulation of floral volatile organic compounds (FVOCs) biosynthesis. Their expression patterns were verified by qRT-PCR experiments. This study establishes a robust foundation for further investigations into the functionality of AmMYB genes and their molecular mechanisms underlying FVOC biosynthesis in snapdragons. Full article
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16 pages, 3733 KiB  
Article
Comparative Analysis of TPR Gene Family in Cucurbitaceae and Expression Profiling under Abiotic Stress in Cucumis melo L.
by Shuoshuo Wang, Yuchen Meng, Fei Ding, Kuo Yang, Chuang Wang, Hengjia Zhang and Han Jin
Horticulturae 2024, 10(1), 83; https://doi.org/10.3390/horticulturae10010083 - 15 Jan 2024
Viewed by 823
Abstract
Tetratricopeptide repeat (TPR) proteins play numerous roles in plant growth and development by mediating protein–protein interactions in biological systems by binding to peptide ligands. Although genome-wide analyses of the TPR gene family in other species have been performed, its evolution and function in [...] Read more.
Tetratricopeptide repeat (TPR) proteins play numerous roles in plant growth and development by mediating protein–protein interactions in biological systems by binding to peptide ligands. Although genome-wide analyses of the TPR gene family in other species have been performed, its evolution and function in Cucurbitaceae remain unclear. In this study, 144 TPR genes from 11 genomes of eight Cucurbitaceae species with a heterogeneous distribution on the chromosomes were characterized. Based on the homology between Cucurbitaceae and Arabidopsis, the TPR genes were divided into four groups, and the evolutionary relationships of the Benincaceae and Cucurbitaceae tribes were also represented in a phylogenetic tree. Using the ‘DHL92′ genome as a reference, an integrated chromosome map was obtained containing 34 loci, 4 of which were common to the Cucurbitaceae. Cis-regulatory element analysis showed that these elements are essential for melon development and responses to light, phytohormones, and various stresses. CmTPR tissue- and development-specific expression analysis revealed differential expression patterns under normal growth conditions. Furthermore, the CmTPR genes responded to various abiotic stressors. Overall, this study offers insights into the evolutionary history of the TPR gene family in Cucurbitaceae and provides valuable information for elucidating the potential role of CmTPR genes during development and under different stresses in melon. Full article
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17 pages, 26161 KiB  
Article
Genome-Wide Identification, Evolution, and Expression Analysis of the MAPK Gene Family in Rosaceae Plants
by Yongjuan Yang, Hao Tang, Yuchen Huang, Yanyi Zheng, Yuanyuan Sun and Qi Wang
Horticulturae 2023, 9(12), 1328; https://doi.org/10.3390/horticulturae9121328 - 11 Dec 2023
Viewed by 926
Abstract
Mitogen-activated protein kinases (MAPKs) are crucial regulators in coping with abiotic and biotic stresses, including drought, salinity, fungi, and pathogens. However, little is known about the characteristics, evolution process, and functional divergence of the MAPK gene family in Rosaceae plants. A total of [...] Read more.
Mitogen-activated protein kinases (MAPKs) are crucial regulators in coping with abiotic and biotic stresses, including drought, salinity, fungi, and pathogens. However, little is known about the characteristics, evolution process, and functional divergence of the MAPK gene family in Rosaceae plants. A total of 97 MAPK members were identified in six Rosaceae species, including 12 genes in Fragaria vesca, 22 genes in Malus domestica, 23 genes in Pyrus bretschneideri, 12 genes in Prunus mume, 14 genes in Prunus persica, and 14 genes in Rosa chinensis. All MAPK members of six Rosaceae plants were categorized into four clusters by the phylogenetic relationship analysis. Collinearity analysis discovered that both segmental duplication and tandem duplication contributed to the expansion of MAPK family genes in Rosaceae plants. And the analysis of motifs and gene structures indicated that the evolution of the MAPK gene family was highly conserved among phylogenetic clusters in Rosaceae species. In addition, the dN/dS rates of MAPK paralogous gene pairs were below one, suggesting the MAPK gene family in Rosaceae was driven by purifying selective pressure. Furthermore, functional divergence analysis discovered that 14 amino acid residues were detected as potentially key sites for functional divergence of MAPK family genes between different cluster pairs, specifically Type I functional divergence. The analysis of functional distance indicated that cluster C retained more of the original functional features, while cluster B exhibited functional specialization. Moreover, the expression profiles revealed that PmMAPK8, PmMAPK9, and PmMAPK10 were both highly expressed under drought stress and low temperature conditions. This study aims to comprehensively analyze the evolutionary process and functional analyses of the MAPK gene family in Rosaceae plants, which will lay the foundation for future studies into MAPK genes of Rosaceae in response to drought and cold stress. Full article
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19 pages, 12002 KiB  
Article
Genome-Wide Identification of Mango (Mangifera indica L.) MADS-Box Genes Related to Fruit Ripening
by Bin Zheng, Songbiao Wang, Hongxia Wu, Xiaowei Ma, Wentian Xu, Kunliang Xie, Lingfei Shangguan and Jinggui Fang
Horticulturae 2023, 9(12), 1289; https://doi.org/10.3390/horticulturae9121289 - 30 Nov 2023
Viewed by 937
Abstract
MADS-box genes play a crucial role in fruit ripening, yet limited research has been conducted on mango. Based on the conserved domains of this gene family, 84 MADS-box genes were identified in the mango genome, including 22 type I and 62 type II [...] Read more.
MADS-box genes play a crucial role in fruit ripening, yet limited research has been conducted on mango. Based on the conserved domains of this gene family, 84 MADS-box genes were identified in the mango genome, including 22 type I and 62 type II MADS-box genes. Gene duplication analysis revealed that both tandem duplication and segmental replication significantly contributed to the expansion of MADS-box genes in the mango genome, with purifying selection playing a vital role in the segmental duplication events within the MiMADS gene family. Cis-acting element analysis demonstrated that most MiMADS genes were hormonally regulated and participated in the growth, development, and stress resistance of mango fruit. Moreover, through expression pattern analysis and phylogenetic tree construction, we identified six MiMADS genes belonging to the SEP1 subfamily and two belonging to the AG subfamily as potential candidates involved in mango ripening regulation. Notably, Mi08g17750 and Mi04g18430 from the SEP1 subfamily were identified as key regulators inhibiting mango fruit maturation; their interaction network was also analyzed. These findings provide a foundation for further investigation into the regulatory mechanisms underlying mango ripening. Full article
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19 pages, 5934 KiB  
Article
Transcriptome Analyses Reveal Distinct Defense Strategies in Chili Plants under Soilborne Disease Intervention
by Yuyu Zhang, Zhixiong Chen, Fang Chen, Jinqiang Yan, Junyu Wu, Jie Wang and Shumei Ge
Horticulturae 2023, 9(12), 1267; https://doi.org/10.3390/horticulturae9121267 - 25 Nov 2023
Viewed by 789
Abstract
Chili (Capsicum annuum L.) is highly susceptible to soilborne diseases, thereby presenting a significant threat that results in considerable yield losses in chili production. The exploration of genes conferring resistance and the underlying defense mechanisms presents a promising strategy for bolstering plant [...] Read more.
Chili (Capsicum annuum L.) is highly susceptible to soilborne diseases, thereby presenting a significant threat that results in considerable yield losses in chili production. The exploration of genes conferring resistance and the underlying defense mechanisms presents a promising strategy for bolstering plant disease control. In this study, we selected two distinct cultivars, the disease-sensitive ‘Hailan 99’ and the disease-tolerant ‘Sanxiaqing’, to elucidate the molecular basis of their responses to soilborne disease intervention. We conducted a comprehensive analysis of root morphological characteristics and transcriptome profiles under stress conditions. Our findings revealed that, when subjected to soilborne disease intervention, these two cultivars exhibited contrasting root system characteristics and responses, reflecting diverse defense strategies. The disease-resistant cultivar demonstrated superior adaptability, possibly owing to its capacity for swift recognition of pathogen effectors, activation of defense responses, and effective containment of infection at localized sites, thus impeding disease progression. Noteworthy genes such as T459_04053, implicated in effector recognition; MSTRG.26158, MSTRG.30886, and T459_22510, associated with secondary metabolite biosynthesis; and T459_05615, partaking in the autophagy pathway, along with other differentially expressed genes linked to effector recognition, immune activation, and modulation of cell death processes, offer valuable insights into enhancing soilborne disease resistance in chili. Furthermore, these findings contribute to an enhanced understanding of the molecular mechanisms underlying soilborne disease resistance in diverse plant crops. Full article
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16 pages, 7258 KiB  
Article
Genome-Wide Identification and Expression Analysis of the CmHAK Gene Family in Melon (Cucumis melo L.)
by Lina Fu, Huizhi Wang, Xifang Leng, Xinsheng Zhang, Baoying Xiao, Hui Liu, Dongxu Xue, Yangyang Wang, Chunyan Wu and Wei Wang
Horticulturae 2023, 9(10), 1138; https://doi.org/10.3390/horticulturae9101138 - 16 Oct 2023
Viewed by 1236
Abstract
(1) Background: As the largest family of potassium transporters in plants, KT/HAK/KUP plays an important function in plant growth, development, and stress, especially for potassium-loving plants such as melon. (2) Methods: The members of the KT/HAK/KUP gene family in the melon genome were [...] Read more.
(1) Background: As the largest family of potassium transporters in plants, KT/HAK/KUP plays an important function in plant growth, development, and stress, especially for potassium-loving plants such as melon. (2) Methods: The members of the KT/HAK/KUP gene family in the melon genome were identified by bioinformatics technology. The gene structure, chromosome location, phylogeny, and expression analysis were comprehensively and systematically analyzed. (3) Results: The results showed that there are 14 members of the KT/HAK/KUP gene family in melon, which are distributed on seven chromosomes. Each member contains 3–11 introns and 4–12 exons, and could be divided into three distinct branches in phylogeny. The number of amino acid residues encoded by each member varies between 610 and 878. In terms of expression, after 12 h of chilling stress, most of the CmHAK genes were expressed in two melon varieties with different chilling resistances. The expression levels of CmHAK6 and CmHAK8 were downregulated in chilling-resistant varieties, but there was no significant change in chilling-sensitive varieties, indicating that CmHAK6 and CmHAK8 genes may play a negative regulatory role in chilling-resistant varieties. (4) Conclusions: The study provides a theoretical basis for in-depth analysis of the functions of KT/HAK/KUP gene family and cultivation of high-potassium stress-resistant melon varieties. Full article
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Review

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16 pages, 1385 KiB  
Review
Application and Expansion of Virus-Induced Gene Silencing for Functional Studies in Vegetables
by Zheng Wang, Shoujun Cao, Xinyang Xu, Yanjun He, Weisong Shou, Eduardo D. Munaiz, Chao Yu and Jia Shen
Horticulturae 2023, 9(8), 934; https://doi.org/10.3390/horticulturae9080934 - 17 Aug 2023
Cited by 1 | Viewed by 1416
Abstract
Increased consumption of vegetables has been recommended worldwide as a part of a healthy diet; therefore, determining gene function among breeding materials is crucial for vegetable improvement to meet the sustainable development of new vegetable varieties. However, genetic transformation is time-consuming and laborious, [...] Read more.
Increased consumption of vegetables has been recommended worldwide as a part of a healthy diet; therefore, determining gene function among breeding materials is crucial for vegetable improvement to meet the sustainable development of new vegetable varieties. However, genetic transformation is time-consuming and laborious, which limits the exploration of gene function for various vegetable crops. Virus-Induced Gene Silencing (VIGS) can perform large-scale and rapid gene silencing in plants due to a reduction in the experimental period and its independence from the stable genetic transformation, providing an excellent opportunity for functional research. VIGS can accelerate model plant research and make it easier to analyze gene function and validation in vegetable crops. Moreover, with the advent of technologies such as virus-mediated heterologous protein expression and the development of CRISPR/Cas9 technology, virus-mediated genetic tools have ushered in a new era in genetics and crop improvement. This study summarizes recent achievements in VIGS and Virus-Induced Gene Editing (VIGE) in vegetables. We also identify several challenges in the current state of VIGS technology in vegetables, serving as a guide for future research. Full article
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