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A Decade of Research towards to Horticultural Crop from Omics...
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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: closed (20 April 2024) | Viewed by 12535

Special Issue Editor

Dr. Silvia Farinati

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Guest Editor
Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020 Legnaro, PD, Italy
Interests: plant breeding; plant biotechnology; gene expression
Special Issues, Collections and Topics in MDPI journals

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

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. Horticulturae is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant breeding
  • plant stress response
  • assisted evolution techniques

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Published Papers (6 papers)

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Research

18 pages, 3702 KiB  
Article
The Complete Chloroplast Genome of an Epiphytic Leafless Orchid, Taeniophyllum complanatum: Comparative Analysis and Phylogenetic Relationships
by Zhuang Zhou, Jinliao Chen, Fei Wang, Xiaopei Wu, Zhongjian Liu, Donghui Peng and Siren Lan
Horticulturae 2024, 10(6), 660; https://doi.org/10.3390/horticulturae10060660 - 20 Jun 2024
Viewed by 1341
Abstract
Taeniophyllum is a distinct taxon of epiphytic leafless plants in the subtribe Aeridinae of Orchidaceae. The differences in chloroplast genomes between extremely degraded epiphytic leafless orchids and other leafy orchids, as well as their origins and evolution, raise intriguing questions. Therefore, we report [...] Read more.
Taeniophyllum is a distinct taxon of epiphytic leafless plants in the subtribe Aeridinae of Orchidaceae. The differences in chloroplast genomes between extremely degraded epiphytic leafless orchids and other leafy orchids, as well as their origins and evolution, raise intriguing questions. Therefore, we report the chloroplast genome sequence of Taeniophyllum complanatum, including an extensive comparative analysis with other types of leafless orchids. The chloroplast genome of T. complanatum exhibited a typical quadripartite structure, and its overall structure and gene content were relatively conserved. The entire chloroplast genome was 141,174 bp in length, making it the smallest known chloroplast genome of leafless epiphytic orchids. It encoded a total of 120 genes, including repetitive genes, comprising 74 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted on the chloroplast genomes of 43 species belonging to five subfamilies of Orchidaceae. The results showed that the five subfamilies were monophyly, with nearly all segments having a 100% bootstrap value. T. complanatum and Chiloschista were clustered together as a sister group to Phalaenopsis and occupied the highest position in the Epidendroideae. Phylogenetic analysis suggested that T. complanatum and other leafless orchids within the Orchidaceae evolved independently. This study may provide the foundation for research on phylogenetic and structural diversity in leafless epiphytic orchids, thereby enhancing the resources available for chloroplast genome studies in Orchidaceae. Full article
(This article belongs to the Special Issue A Decade of Research towards to Horticultural Crop from Omics to Biotechnology)
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19 pages, 4815 KiB  
Article
Combined Metabolomic and Transcriptomic Analysis Reveals Candidate Genes for Anthocyanin Accumulation in Ginkgo biloba Seed Exocarp
by Jianlu Tang, Zhi Feng, Xiangyue Xiang, Yiqiang Wang and Meng Li
Horticulturae 2024, 10(6), 540; https://doi.org/10.3390/horticulturae10060540 - 22 May 2024
Viewed by 1154
Abstract
Anthocyanin is an important pigment that affects plant color change. In this study, the color parameters and anthocyanin content of Ginkgo biloba seed exocarp at different periods were measured, and it was determined that the a* value (redness value) of the seed exocarp [...] Read more.
Anthocyanin is an important pigment that affects plant color change. In this study, the color parameters and anthocyanin content of Ginkgo biloba seed exocarp at different periods were measured, and it was determined that the a* value (redness value) of the seed exocarp was closely related to the color change occurring during the development of the seed exocarp, and the anthocyanin content in the seed exocarp showed an increasing trend. The molecular mechanism of anthocyanin biosynthesis in Ginkgo biloba seed exocarp is still unclear. In order to further understand the molecular mechanism of color change in Ginkgo biloba seed exocarp, the regulation mechanism and accumulation mode of anthocyanin in the seed exocarp at three different periods were analyzed using transcriptomic and metabolomic. A total of four key anthocyanins were screened from the metabolome, including three kinds of Cyanidin 3-arabinoside, Malvidin 3-glucoside and Cyanidin 3-sambubioside 5-glucoside with increased content. Among them, Cyanidin 3-arabinosidehad a strong correlation with the a* value (PCC = 0.914), which have a great influence on the color change of the seed exocarp, and Delphinidin 3-O-3″,6″-O-dimalonylglucoside with decreased content might jointly affect the formation of exocarp color. The transcriptome data show that among the structural genes, ANS (Gb_33402) had the highest correlation with Cyanidin 3-arabinoside (PCC = 0.9217) and in GbANS, only Gb_33402 showed an upregulated expression trend in the three stages of seed exocarp development, which suggesting that it plays an important role in anthocyanin accumulation in the seed exocarp and it may be the key structural gene affecting the formation of seed exocarp color. Among the transcription factors, the differential expression of most transcription factors (MYB, bHLH, b-ZIP, NAC, WDR and AP2/ERF) may jointly affect the formation of seed exocarp color by promoting anthocyanin accumulation. This study elucidates the main anthocyanins that cause the color change of the seed exocarp of Ginkgo biloba and reveals the molecular regulation mechanism of anthocyanins at different developmental stages of the seed exocarp. It provides a theoretical basis and insights for understanding the color change of Ginkgo biloba seed exocarp. Full article
(This article belongs to the Special Issue A Decade of Research towards to Horticultural Crop from Omics to Biotechnology)
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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
Cited by 1 | Viewed by 2771
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
(This article belongs to the Special Issue A Decade of Research towards to Horticultural Crop from Omics to Biotechnology)
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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
Cited by 2 | Viewed by 2059
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
(This article belongs to the Special Issue A Decade of Research towards to Horticultural Crop from Omics to Biotechnology)
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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 2 | Viewed by 2102
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
(This article belongs to the Special Issue A Decade of Research towards to Horticultural Crop from Omics to Biotechnology)
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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 7 | Viewed by 1831
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
(This article belongs to the Special Issue A Decade of Research towards to Horticultural Crop from Omics to Biotechnology)
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