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New Trends in Genomics and Metabolomics of Horticultural Plants at Fujian Agriculture and Forestry University 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 October 2024) | Viewed by 4593

Special Issue Editor

Prof. Dr. Yuling Lin

E-Mail Website
Guest Editor
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: genomics and biotechnology; plant tissue culture; non-coding RNA; molecular biology; somatic embryogenesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Throughout the life of a plant, temperature, water and salt stresses may recur over time and gradually affect its normal physiological activities. Due to abiotic and biotic stresses, the growth and development of horticultural plants such as fruit trees, vegetables, flowers, tea plants, become constrained. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance. With advances in high-throughput sequencing technology, multiomics such as pan-genomics, transcriptomics and genome-wide non-coding RNAs have rapidly developed. Plant metabolomics is a set of nimble, analytical and chemometric tools and methods for plant functional genomics, phenotyping and systems biology. Genomics and metabolomics of horticultural plants are paving the way for a comprehensive and holistic understanding the growth, development, defense and productivity of horticultural plants.

This Special Issue aims to provide a platform for molecular mechanistic research on horticultural plants, with a special focus on genomics and metabolomes. We warmly welcome your submissions of original papers and reviews based on results from molecular viewpoints.

This Special Issue is supervised by Dr. Yuling Lin and assisted by our Topical Advisory Panel Member Dr. Shijiang Cao (College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China).

Prof. Dr. Yuling Lin
Guest Editor

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.

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Keywords

  • genomics
  • metabolomics
  • non-coding RNA
  • transcriptomics
  • horticultural plants

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Related Special Issue

Published Papers (4 papers)

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20 pages, 12433 KiB  
Article
Genome-Wide Identification and Expression Analysis Unveil the Involvement of the Succinic Semialdehyde Dehydrogenase (SSADH) Gene Family in Banana Low Temperature Stress
by Xiong Guo, Fengjie Yang, Xueying Zhang, Mengjie Tang, Kui Wan, Chunwang Lai, Zhongxiong Lai and Yuling Lin
Int. J. Mol. Sci. 2025, 26(7), 3006; https://doi.org/10.3390/ijms26073006 - 26 Mar 2025
Viewed by 265
Abstract
Banana (Musa spp.) is susceptible to low-temperature stress and other environmental stresses, which can hinder the growth and development. Succinic semialdehyde dehydrogenase (SSADH) is critical for GABA biosynthesis and plays a crucial role in plants. However, the SSADH genes of [...] Read more.
Banana (Musa spp.) is susceptible to low-temperature stress and other environmental stresses, which can hinder the growth and development. Succinic semialdehyde dehydrogenase (SSADH) is critical for GABA biosynthesis and plays a crucial role in plants. However, the SSADH genes of bananas have not been studied. This study found 19 MaSSADHs, 18 MbSSADHs, and 18 MiSSADHs from the banana genome. According to the phylogenetic tree, these genes can be categorized into five branches. This study cloned the MaSSADH1-14 from banana. The subcellular localization assays of MaSSADH1-14 in tobacco leaves confirmed that the presence of SSADH was not only localized mitochondrion but also localized chloroplast. The cis-elements of the SSADH gene family are related to the potential regulation of the banana SSADH gene family; their involvement in diverse stress responses. Transcriptomic data was utilized to examine the effect of MaSSADH genes under cold stress in bananas. The results of RT-qPCR were consistent with transcriptome data. These results showed that most MaSSADHs are passively responsive to low-temperature treatment. In addition, transient overexpression of MaSSADH1-14 in Nicotiana benthamiana leaves resulted in the content of GABA increasing, indicating that MaSSADH1-14 may be involved in the accumulation of GABA of banana. Collectively, these results improve knowledge of the SSADH gene family in banana and establish a basis for comprehending its biological roles in response to low temperatures. Full article
(This article belongs to the Special Issue New Trends in Genomics and Metabolomics of Horticultural Plants at Fujian Agriculture and Forestry University 2.0)
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18 pages, 6321 KiB  
Article
Mining of Candidate Genes Associated with Leaf Shape Traits in Grapes
by Chuan Zhang, Vivek Yadav and Liwen Cui
Int. J. Mol. Sci. 2024, 25(22), 12101; https://doi.org/10.3390/ijms252212101 - 11 Nov 2024
Viewed by 951
Abstract
As the most important organ for photosynthesis, leaves provide the main energy source for plant growth. Leaf traits affect light energy utilization and, thus, plant development and biomass. Given the high morphological variability of leaves between and within grape genotypes, phenotypic analysis is [...] Read more.
As the most important organ for photosynthesis, leaves provide the main energy source for plant growth. Leaf traits affect light energy utilization and, thus, plant development and biomass. Given the high morphological variability of leaves between and within grape genotypes, phenotypic analysis is challenging. This study first evaluated leaf shape trait parameters using a specific leaf profile and area analyzer, along with genome-wide association study (GWAS) analyses, to identify additional candidate genes related to grape leaf shape traits. In the two-year analysis, 89 single-nucleotide polymorphisms (SNPs) were found to be significantly associated with leaf shape traits. These SNP loci were distributed on 18 chromosomes, of which chromosome 15 had the most relevant SNPs. We found that leaf shape-associated genes included mainly plant hormone-, ubiquitin ligase-, serine/threonine protein kinase-, transcription factor-, and cell wall metabolism-related genes. By analyzing the expression of these candidate genes on the chip, we found that they exhibited diverse expression levels in leaves at different developmental stages (young, mature, and senescent). This suggests that these genes could be considered candidates for grape leaf improvement. Full article
(This article belongs to the Special Issue New Trends in Genomics and Metabolomics of Horticultural Plants at Fujian Agriculture and Forestry University 2.0)
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20 pages, 8124 KiB  
Article
Identification and Characterization of the DOF Gene Family in Phoebe bournei and Its Role in Abiotic Stress—Drought, Heat and Light Stress
by Kehui Zheng, Mengmeng Lv, Jiaying Qian, Yiran Lian, Ronglin Liu, Shuhao Huo, Obaid Ur Rehman, Qinmin Lin, Zhongyang Zhou, Xiaomin Liu and Shijiang Cao
Int. J. Mol. Sci. 2024, 25(20), 11147; https://doi.org/10.3390/ijms252011147 - 17 Oct 2024
Cited by 1 | Viewed by 1146
Abstract
Phoebe bournei is a second-class endangered and protected species unique to China, and it holds significant ecological and economic value. DNA binding one zinc finger (Dof) transcription factors are plant-specific regulators. Numerous studies have demonstrated that Dof genes are involved in plant growth, [...] Read more.
Phoebe bournei is a second-class endangered and protected species unique to China, and it holds significant ecological and economic value. DNA binding one zinc finger (Dof) transcription factors are plant-specific regulators. Numerous studies have demonstrated that Dof genes are involved in plant growth, development and responses to abiotic stress. In this study, we identified and analyzed 34 PbDof gene members at the whole-genome level. The results indicated that the 34 PbDof genes were unevenly distributed across 12 chromosomes. We utilized the Dof genes from Arabidopsis thaliana and P. bournei to construct a phylogenetic tree and categorized these genes into eight subgroups. In the collinearity analysis, there were 16 homologous gene pairs between AtDof and PbDof and nine homologous gene pairs between ZmDof and PbDof. We conducted a cis-acting element analysis and found that cis-acting elements involved in light response were the most abundant in PbDof genes. Through SSR site prediction, we analyzed that the evolution level of Dof genes is low. Additionally, we assessed the expression profiles of eight PbDof genes under high temperature, drought, and light stress using qRT-PCR. In particular, PbDof08 and PbDof16 are significantly upregulated under the three stresses. This study provides foundational information for PbDof genes and offers new insights for further research on the mechanism of Dof transcription factors responding to stress, as well as the adaptation of P. bournei to environmental changes. Full article
(This article belongs to the Special Issue New Trends in Genomics and Metabolomics of Horticultural Plants at Fujian Agriculture and Forestry University 2.0)
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24 pages, 5440 KiB  
Article
Comprehensive Expression Analysis of the WRKY Gene Family in Phoebe bournei under Drought and Waterlogging Stresses
by Zhongxuan Wang, Limei You, Na Gong, Can Li, Zhuoqun Li, Jun Shen, Lulu Wan, Kaijin Luo, Xiaoqing Su, Lizhen Feng, Shipin Chen and Wenjun Lin
Int. J. Mol. Sci. 2024, 25(13), 7280; https://doi.org/10.3390/ijms25137280 - 2 Jul 2024
Cited by 5 | Viewed by 1441
Abstract
In response to biotic and abiotic stresses, the WRKY gene family plays a crucial role in plant growth and development. This study focused on Phoebe bournei and involved genome-wide identification of WRKY gene family members, clarification of their molecular evolutionary characteristics, and comprehensive [...] Read more.
In response to biotic and abiotic stresses, the WRKY gene family plays a crucial role in plant growth and development. This study focused on Phoebe bournei and involved genome-wide identification of WRKY gene family members, clarification of their molecular evolutionary characteristics, and comprehensive mapping of their expression profiles under diverse abiotic stress conditions. A total of 60 WRKY gene family members were identified, and their phylogenetic classification revealed three distinct groups. A conserved motif analysis underscored the significant conservation of motif 1 and motif 2 among the majority of PbWRKY proteins, with proteins within the same class sharing analogous gene structures. Furthermore, an examination of cis-acting elements and protein interaction networks revealed several genes implicated in abiotic stress responses in P. bournei. Transcriptomic data were utilized to analyze the expression patterns of WRKY family members under drought and waterlogged conditions, with subsequent validation by quantitative real-time PCR (RT-qPCR) experiments. Notably, PbWRKY55 exhibited significant expression modulation under drought stress; PbWRKY36 responded prominently to waterlogging stress; and PbWRKY18, PbWRKY38, and PbWRKY57 demonstrated altered expression under both drought and waterlogging stresses. This study revealed the PbWRKY candidate genes that potentially play a pivotal role in enhancing abiotic stress resilience in P. bournei. The findings have provided valuable insights and knowledge that can guide further research aimed at understanding and addressing the impacts of abiotic stress within this species. Full article
(This article belongs to the Special Issue New Trends in Genomics and Metabolomics of Horticultural Plants at Fujian Agriculture and Forestry University 2.0)
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