A Decade of Research towards to Horticultural Crop from Omics to Biotechnology

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: 20 April 2024 | Viewed by 5598

Special Issue Editor

Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Campus of Agripolis, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD, Italy
Interests: plant breeding; plant biotechnology; gene expression

Special Issue Information

Dear Colleagues,

Climate change and the associated economic crisis have highlighted the need for a resistant horticulture sector, which is one of the most intensive agricultural systems, guarenteeing access to an adequate supply of food. The development of new solutions to improve the agricultural system for horticultural crops cannot be separated from the genetic improvement of crops.

At the "state of the art" level, much remains to be discovered about the mechanisms underlying the gene expression of plant species, and how this knowledge can be applied to varietal selection plans.

The purpose of this Special Issue “A Decade of Research Towards to Horticultural Crop from Omics to Biotechnology” is to present innovative studies, tools, approaches, and techniques that have been successful in addressing some of these topics, and any other innovation that has improved the efficiency and sustainability of horticultural crops. These scientific contributions can help to improve understanding around molecular mechanisms that govern the physiological processes of the crops under examination, often not yet thoroughly studied at the genomic level, providing knowledge that is potentially extendable to other plant species.

Moreover, evaluating the integration of conventional methods with Biotech analyses across a variety selection protocols can provide useful information on genetic improvement plans.

Dr. Silvia Farinati
Guest Editor

Manuscript Submission Information

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Keywords

  • plant breeding
  • plant stress response
  • assisted evolution techniques

Published Papers (4 papers)

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Research

19 pages, 4159 KiB  
Article
Genome-Wide Classification and Evolutionary Analysis of the KNOX Gene Family in Plants
by Zhi-Meng Gan, Xiao-Yan Ai, Chun-Gen Hu and Jin-Zhi Zhang
Horticulturae 2023, 9(11), 1174; https://doi.org/10.3390/horticulturae9111174 - 27 Oct 2023
Viewed by 1246
Abstract
The Knotted1-like homeobox (KNOX) gene family plays a pivotal role in regulating meristem activity, organ differentiation, and cell meristematic identity. However, there has been a lack of large-scale, systematic, and comprehensive comparative analyses to explore their expression patterns and evolutionary mechanisms. [...] Read more.
The Knotted1-like homeobox (KNOX) gene family plays a pivotal role in regulating meristem activity, organ differentiation, and cell meristematic identity. However, there has been a lack of large-scale, systematic, and comprehensive comparative analyses to explore their expression patterns and evolutionary mechanisms. In this study, a total of 1425 KNOX genes were identified across 118 plant species. The result showed that higher plants exhibited a significantly higher abundance of KNOX genes compared to lower plants. Phylogenetic analysis revealed that all KNOX genes can be divided into two classes (class I and II) and evolved independently after species differentiation. An analysis of gene duplication or loss showed that gene loss was more common than gene duplication in lower plants within the KNOX gene family. These findings suggest that gene loss in the KNOX gene family occurs after events such as whole-genome duplication (WGD) or whole-genome triplication (WGT). In addition, conserved motif analysis was also conducted to uncover the evolutionary trajectories of KNOX genes. We found that three motifs (M1, M2, and M4) were present in nearly all KNOX genes, while four novel motifs (M7–M10) were lost in lower plants but present in higher plants. Moreover, the loss of certain motifs in the KNOX genes was also observed in higher plants, indicating sequence divergence in KNOX genes throughout evolution. To understand the expression patterns of KNOX genes, a gene expression pattern analysis was performed in A. thaliana and O. sativa. The results showed that class I KNOX genes exhibit conserved high expression in stems, suggesting their potential similar biological roles across different plant species and the conservation of their functions during evolution. Additionally, we analyzed the KNOX genes in the Citrus genus and closely related species, and we found that the number of KNOX genes evolved at a slower rate in these species, indicating a relatively conservative nature. In conclusion, this study provides valuable resources for the investigation of KNOX gene family evolution and function in plants. Full article
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17 pages, 6066 KiB  
Article
RVE1, DBB1b, and COL2 Transcription Factors Are Responsive to Combined Stress by UV-B Radiation and Cold in Bell Pepper (Capsicum annuum)
by Brandon Estefano Morales-Merida, Jesús Christian Grimaldi-Olivas, Abraham Cruz-Mendívil, Claudia Villicaña, José Benigno Valdez-Torres, José Basilio Heredia, Rubén León-Chan, Luis Alberto Lightbourn-Rojas and Josefina León-Félix
Horticulturae 2023, 9(6), 699; https://doi.org/10.3390/horticulturae9060699 - 14 Jun 2023
Viewed by 1146
Abstract
Ultraviolet-B radiation (UV-B) and cold limit the growth and development of plants, which generates changes in gene expression. This allows plants to respond to stress through regulatory proteins, such as transcription factors, that activate or repress the expression of stress-response genes. RNA-Seq data [...] Read more.
Ultraviolet-B radiation (UV-B) and cold limit the growth and development of plants, which generates changes in gene expression. This allows plants to respond to stress through regulatory proteins, such as transcription factors, that activate or repress the expression of stress-response genes. RNA-Seq data and WGCNA analyses were utilized to identify the hub genes. Our study found a total of 25, 24, and 29 transcription factors at different time points T1, T2, and T3, respectively, under combined stress (ultraviolet-B radiation and cold). RVE1 (MYB-related), COL2 (CO-like), and DBB1b (DBB) were identified as candidate hub genes. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed that RVE1, DBB1b, and COL2 were mostly involved in energy production, the antioxidant system (enzymatic and non-enzymatic), signaling through abscisic acid and CA2+, response to light stimulus, and cellular homeostasis. These findings provide the basis for further investigation related to UV-B radiation and cold stress response mechanisms in plants. Full article
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16 pages, 3111 KiB  
Article
Metabolomic and Transcriptomic Analysis Reveals the Mechanisms Underlying the Difference in Anthocyanin Accumulation in Apple Fruits at Different Altitudes
by Caiyun Shi, Zhifeng Wei, Li Liu, Ming Li, Junwei Liu and Dengtao Gao
Horticulturae 2023, 9(4), 475; https://doi.org/10.3390/horticulturae9040475 - 11 Apr 2023
Cited by 1 | Viewed by 1298
Abstract
The red color of apple peel is an important phenotypic and economic trait mainly attributed to anthocyanin accumulation. Apples show a deeper red color at higher altitudes than at lower ones; however, the molecular regulatory network underlying color variation along altitudinal gradients has [...] Read more.
The red color of apple peel is an important phenotypic and economic trait mainly attributed to anthocyanin accumulation. Apples show a deeper red color at higher altitudes than at lower ones; however, the molecular regulatory network underlying color variation along altitudinal gradients has not been investigated. In this study, the effects of environmental conditions associated with low (124 m) and high (1901 m) altitudes on peel color were assessed through physiological, metabolomic, transcriptomic, and qRT-PCR analyses in Huashuo apple and its sister line, Huarui apple. The content of cyanidin-3-O-galactoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-xyloside was abundant in the high-altitude environment and may contribute to the deeper red color. Transcript levels of structural genes in the anthocyanin synthesis pathway, especially MdCHI, MdCHS, MdANS, and MdDFR, in apple peel were significantly higher at high altitude than at low altitude. Based on the protein interaction prediction and correlation analyses, four transcription factors (MDP0000127691, MDP0000284922, MDP0000758053, and MDP0000074681) could interact with anthocyanin synthesis-related proteins, showing high correlation with anthocyanin accumulation. Therefore, the abovementioned four genes and four transcription factors were predicted to account for the color differences between high and low altitudes. These results provide genetic resources and a theoretical basis for color-oriented fruit improvement. Full article
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6 pages, 732 KiB  
Communication
Rapid Genetic Assessment of Carrot Varieties Based on AFLP Analysis
by Arthur Domblides and Elena Domblides
Horticulturae 2023, 9(3), 298; https://doi.org/10.3390/horticulturae9030298 - 22 Feb 2023
Cited by 1 | Viewed by 1068
Abstract
It is necessary to regard the biodiversity of carrot as a genetic source of useful and indispensable components for the human diet. Amplified fragment length polymorphism (AFLP) markers were used to discriminate eight carrot genotypes with different root colors. With the combination of [...] Read more.
It is necessary to regard the biodiversity of carrot as a genetic source of useful and indispensable components for the human diet. Amplified fragment length polymorphism (AFLP) markers were used to discriminate eight carrot genotypes with different root colors. With the combination of enzymes Tru9I, PstI, and three sets of primer pairs corresponding to adapters joint to the restricted sites, 92 loci were produced, including 60 polymorphic ones. Each of the three primer sets showed high efficiency, according to estimations of PIC (0.34, 0.34, and 0.41), D (0.36, 0.67, and 0.67), Rp (5.5, 11.3, and 15), and HE (0.32, 0.49, and 0.49). The genetic distances were calculated using values of Nei’s coefficient. The most genetically similar were Chantenay Coeur Rouge and Colmar a Coeur Rouge at a distance of 0.12, whereas the most distant were Saint Valery and Purple Dragon at the highest distance of 0.34. Confirming its genetic identity, Purple Dragon and Gelber Goliath with purple and yellow roots were the most detached varieties from others at distances of 0.23–0.34 and 0.23–0.28, respectively. Male sterile Berlicum breeding accessions were well distinct from other orange-colored varieties at the highest distance of 0.30 from Deep Purple F1. Slight modifications including the facilitation of gel staining enables the wide use of the AFLP method for genetic diversity assessment in carrot breeding accessions. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: A RAPID GENETIC ASSESSMENT OF CARROT VARIETIES BASED ON AFLP-ANALYSIS
Author: Domblides
Highlights: A rapid protocol of AFLP-analysis has been offered to estimate the genetic variation among carrot varieties. AFLPs showed the high productivity in generation of 92 countable fragments with three pair pairs and corresponded enzymes. Eight carrot breeding accessions were well distinguished and genetic distances were established between genotype with different root color.

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