The Role of Transcription Factors in Horticultural Plants

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Developmental Physiology, Biochemistry, and Molecular Biology".

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 4421

Special Issue Editors

CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy
Interests: transcriptional regulation; plant biotechnologies; food science
Special Issues, Collections and Topics in MDPI journals
Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy
Interests: plant development; plant disease resistance; transcriptional regulation
Research and Development, Sacco SRL, 22071 Cadorago, Italy
Interests: plant growth promoters; plant physiology; crop genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the field of plant sciences, great efforts have been devoted to the identification and functional characterization of transcription factors (TFs), and to the investigation of the complex regulatory networks they are part of. The role of TFs has been extensively explored for many model organisms and crop species, shedding much light on the regulation of all aspects related to plant development, metabolism, and responsive physiology. All studies related to the translation—and expansion—of this body of knowledge, from model organisms to horticultural species, have therefore had enormous impact on the field’s improvement, both in terms of meeting the interests of producers and consumers, and in addressing the challenges represented by climate change and the growing need for agricultural sustainability.

This Special Issue welcomes your contributions to the study of TFs in horticultural species, and aims to explore the subject by means of a multidisciplinary approach related to plant development, basic genetics and breeding, physiology and agronomy.

Best regards

Dr. Dario Paolo
Dr. Chiara Mizzotti
Dr. Francesco Vuolo
Guest Editors

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Keywords

  • horticultural species
  • transcriptional regulation
  • stress resistance
  • food quality

Published Papers (3 papers)

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Research

12 pages, 6460 KiB  
Article
Identification and Expression Analysis of the bHLH Gene Family Members in Diospyros kaki
by Weijuan Han, Qi Zhang, Yujing Suo, Huawei Li, Songfeng Diao, Peng Sun, Lin Huang and Jianmin Fu
Horticulturae 2023, 9(3), 380; https://doi.org/10.3390/horticulturae9030380 - 15 Mar 2023
Cited by 1 | Viewed by 1402
Abstract
Basic helix–loop–helix (bHLH) proteins belong to one of the largest families involved in plant growth, development, signal transduction, and secondary metabolism. Although bHLH genes have been previously identified in persimmon (Diospyros kaki), systematic studies have not been reported. A total of [...] Read more.
Basic helix–loop–helix (bHLH) proteins belong to one of the largest families involved in plant growth, development, signal transduction, and secondary metabolism. Although bHLH genes have been previously identified in persimmon (Diospyros kaki), systematic studies have not been reported. A total of 59 bHLH family members have been identified from the “Xiaoguotianshi” persimmon transcriptome. These proteins were clustered into 12 groups from I to XII based on their phylogenetic relationships with Arabidopsis thaliana. Combined with the phylogenetic analysis, in silico expression patterns of five developmental stages, the protein–protein interaction analysis between DkbHLH and DkMYB proteins showed that the bHLH_Cluster-15548.1 protein sequence was identified to be highly similar to the AtGL3 (AT5G41315.1) protein, which is associated with flavonoid and proanthocyanidin (PA) biosynthesis. This study presents the systematic analysis of bHLH genes from D. kaki and provides valuable information for further research on the involvement of bHLH protein in anthocyanin biosynthesis. Full article
(This article belongs to the Special Issue The Role of Transcription Factors in Horticultural Plants)
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14 pages, 7171 KiB  
Article
Genome-Wide Identification and Expression Analysis of the PME and PMEI Gene Families in Diospyros kaki: A Bioinformatics Study
by Qi Zhang, Tingting Pu, Yiru Wang, Yue Bai, Yujing Suo and Jianmin Fu
Horticulturae 2022, 8(12), 1159; https://doi.org/10.3390/horticulturae8121159 - 07 Dec 2022
Cited by 3 | Viewed by 1280
Abstract
Pectins are major components of cell walls in plants. Pectin methylesterases (PMEs) and pectin methylesterase inhibitors (PMEIs) play crucial roles in pectin synthesis and metabolism. Overall, 28 putative DkPMEs and 29 putative DkPMEIs were identified from the D. kaki genome. According to phylogenetic [...] Read more.
Pectins are major components of cell walls in plants. Pectin methylesterases (PMEs) and pectin methylesterase inhibitors (PMEIs) play crucial roles in pectin synthesis and metabolism. Overall, 28 putative DkPMEs and 29 putative DkPMEIs were identified from the D. kaki genome. According to phylogenetic analysis, DkPME/DkPMEI proteins can be classified into four and five clades, respectively. Motif and gene structure analysis showed that DkPME/DkPMEI are highly conserved in the same clades, which indicates that the function of these DkPME/DkPMEI were similar. Besides, DkPME/DkPMEI genes were distributed unevenly on their corresponding chromosomes. Synteny analysis showed that PME or PMEI gene usually matched with more than one DkPME/DkPMEI in D. oleifera, D. lotus, and A. thaliana, implying that the function of these genes in D. kaki may be diverse. Expression analysis showed that DkPME/DkPMEI from the same clade exhibited diverse expression patterns, indicating that these genes might have diverse functions. Functional protein–protein interaction network analysis showed that DkPMEI21 and DkPMEI15 were core nodes and were, respectively, positive and negative regulators for carbohydrate metabolism, stress responses, and sugar signaling. This study provides a theoretical basis for the functional characteristics, evolutionary relationship, and role of these gene families in developing persimmon fruit. Full article
(This article belongs to the Special Issue The Role of Transcription Factors in Horticultural Plants)
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16 pages, 7411 KiB  
Article
Transcriptome-Based Identification, Characterization, Evolutionary Analysis, and Expression Pattern Analysis of the WRKY Gene Family and Salt Stress Response in Panax ginseng
by Tao Liu, En Yu, Lihe Hou, Panpan Hua, Mingzhu Zhao, Yanfang Wang, Jian Hu, Meiping Zhang, Kangyu Wang and Yi Wang
Horticulturae 2022, 8(9), 756; https://doi.org/10.3390/horticulturae8090756 - 23 Aug 2022
Cited by 4 | Viewed by 1278
Abstract
WRKY transcription factors are some of the most important transcription factors in planta, and they are involved in biological and abiotic stresses, growth and development, and biochemical processes. The WRKY gene family has been found in many higher plants, while little is known [...] Read more.
WRKY transcription factors are some of the most important transcription factors in planta, and they are involved in biological and abiotic stresses, growth and development, and biochemical processes. The WRKY gene family has been found in many higher plants, while little is known about WRKY-encoding genes in ginseng. As a traditional and important economic medicinal herb and health food, ginseng has been a model species for other related medicinal plants. Here, we analyze the WRKY transcript factor gene family in ginseng from a genetics and genomics perspective in the hope that this study can create a new avenue for understanding the role of PgWRKYs. By identifying and analyzing all candidate WRKY transcription factor family members based on the transcriptome of ginseng, a total of 118 PgWRKY genes was obtained following gene classification, the phylogenetic relationship, conserved domain structure, functional differentiation, and an expression activity analysis. A phylogenetic analysis revealed that the PgWRKYs were clustered into three groups: I, II, and III transcription factors. Members in group Ⅱ were further divided into five sub-groups: Ⅱa to Ⅱe. An expression analysis showed a trend of co-expression among most PgWRKY genes, forming an interaction network. The coding sequences were WRKYGQK; only two genes were WRKYGKK, and only one gene was WSKYGQK. Moreover, a salt stress treatment analysis of the response of PgWRKY39-01, PgWRKY062, and PgWRKY064 genes was investigated using RT-qPCR. After salt stress treatment, the expression of three PgWRKY genes was increased, indicating that PgWRKYs can participate in regulating the response to salt stresses in ginseng. These comprehensive data provide a reference for elucidating the functions of this transcription factor family in the growth, development, and salt stress response of ginseng. Full article
(This article belongs to the Special Issue The Role of Transcription Factors in Horticultural Plants)
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