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Horticulturae
Special Issues
Genomics and Bioinformatics Applications in Horticulture
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Genomics and Bioinformatics Applications in Horticulture

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 March 2022) | Viewed by 18700

Special Issue Editors

Dr. Renesh Bedre

E-Mail Website
Guest Editor
Texas A&M AgriLife Research & Extension Center, Texas A&M University, 2415 E. Hwy. 83, Weslaco, TX 78596, USA
Interests: bioinformatics; computational biology; genomics; transcriptomics; quantitative genetics; biostatistics; machine learning
Dr. Devi R. Kandel

E-Mail Website
Guest Editor
Texas A&M AgriLife Research & Extension Center, Texas A&M University, 2415 E. Hwy. 83, Weslaco, TX 78596, USA
Interests: high-throughput sequencing; horticulture; plant breeding; quantitative genetics

Special Issue Information

Dear Researchers,

Horticulture plays a vital role in human lives by providing fruits, vegetables, medicines, spices, ornamentals, and beverages. Horticultural plants are getting increasing attention for balanced nutrition for better human health and a clean environment. Research into horticultural plants has emphasized improving quality and health-promoting beneficial compounds, shelf-life extension, increasing yield, and development of varieties resistant to biotic and abiotic stresses.

Continuous development in low-cost and high-throughput sequencing technologies provides a wealth of genetic information to study the complex gene regulatory mechanisms and defense systems in the plants. Modern genomics and bioinformatics have surged the genome sequencing and molecular research of horticultural plants. This Special Issue focuses on genomics and bioinformatics analysis of horticultural plants, which can add value to the improvement of horticultural plants.

This Special Issue covers broad topics on horticultural plants genomics, including but not limited to the following:

  1. Transcriptomics and genomics analysis in response to biotic and abiotic stresses
  2. Comparative genomics analysis
  3. Population genomics
  4. Genome- and transcriptome-wide association analysis
  5. Molecular marker discovery
  6. Plant–pathogen interactions
  7. Development of new computational tools, functional databases, and genetic information resources
  8. Machine learning in genomics analysis

Dr. Renesh Bedre
Dr. Devi R. Kandel
Guest Editors

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

  • horticultural plants
  • genomics
  • transcriptomics
  • proteomics
  • bioinformatics
  • computational biology
  • RNA-seq
  • high-throughput sequencing
  • plant–pathogen interactions
  • computational tools and databases
  • machine learning

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

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Research

18 pages, 5650 KiB  
Article
Metabolome and Transcriptome Analyses Unravels Molecular Mechanisms of Leaf Color Variation by Anthocyanidin Biosynthesis in Acer triflorum
by Anran Sun, Xiaona Pei, Shikai Zhang, Zhiming Han, Ying Xie, Guanzheng Qu, Xiaoqing Hu, Mulualem Tigabu and Xiyang Zhao
Horticulturae 2022, 8(7), 635; https://doi.org/10.3390/horticulturae8070635 - 14 Jul 2022
Cited by 4 | Viewed by 2348
Abstract
Acer triflorum Komarov is an important ornamental tree, and its seasonal change in leaf color is the most striking feature. However, the quantifications of anthocyanin and the mechanisms of leaf color change in this species remain unknown. Here, the combined analysis of metabolome [...] Read more.
Acer triflorum Komarov is an important ornamental tree, and its seasonal change in leaf color is the most striking feature. However, the quantifications of anthocyanin and the mechanisms of leaf color change in this species remain unknown. Here, the combined analysis of metabolome and transcriptome was performed on green, orange, and red leaves. In total, 27 anthocyanin metabolites were detected and cyanidin 3-O-arabinoside, pelargonidin 3-O-glucoside, and peonidin 3-O-gluside were significantly correlated with the color development. Several structural genes in the anthocyanin biosynthesis process, such as chalcone synthase (CHS), flavanone 3-hydroxylase (F3H), and dihydroflavonol 4-reductase (DFR), were highly expressed in red leaves compared to green leaves. Most regulators (MYB, bHLH, and other classes of transcription factors) were also upregulated in red and orange leaves. In addition, 14 AtrMYBs including AtrMYB68, AtrMYB74, and AtrMYB35 showed strong interactions with the genes involved in anthocyanin biosynthesis, and, thus, could be further considered the hub regulators. The findings will facilitate genetic modification or selection for further improvement in ornamental qualities of A. triflorum. Full article
(This article belongs to the Special Issue Genomics and Bioinformatics Applications in Horticulture)
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15 pages, 4454 KiB  
Article
Genome-Wide Identification and Expression Analysis of RR-Type MYB-Related Transcription Factors in Tomato (Solanum lycopersicum L.)
by Jiaying Sun and Changkui Guo
Horticulturae 2022, 8(5), 399; https://doi.org/10.3390/horticulturae8050399 - 2 May 2022
Cited by 5 | Viewed by 3071
Abstract
Evidence have indicated that RR-type MYB-related transcription factors (TFs) are functionally diverse in regulating floral development, fruit development, leaf senescence, ABA response, and drought and salt responses. Several RR-type MYB-related TFs in Arabidopsis, Antirrhinum and rice are identified and characterized. However, the [...] Read more.
Evidence have indicated that RR-type MYB-related transcription factors (TFs) are functionally diverse in regulating floral development, fruit development, leaf senescence, ABA response, and drought and salt responses. Several RR-type MYB-related TFs in Arabidopsis, Antirrhinum and rice are identified and characterized. However, the complete RR-type MYB-related family in tomato has not been studied to date. Here, a genome-wide identification of tomato RR-type MYB-related TFs (SlMYBR) was performed by bioinformatics analysis, and their expression patterns were analyzed. A total of thirteen SlMYBR genes, which were mainly distributed in the head or tail of the chromosome, were identified from tomato and were divided into three groups. Group II was all MYBR genes from eudicots without genes from monocots. For Group I and Group III, the phylogenetic tree was in accord with the evolutionary relationship of these species. SlMYBR proteins were unstable proteins and located in the nucleus. The promoters of SlMYBR contained multiple important cis-acting elements related to abiotic stress or hormone responses. SlMYBR genes had various temporal and spatial expression patterns. Experiments of spraying exogenous hormone demonstrated that the expression of most genes containing hormone response elements was changed, indicating that the expression patterns were associated with the amount of cis-acting elements. The comprehensive investigation of tomato SlMYBR genes in the present study helps to clearly understand the evolution of RR-type MYB-related TFs and provides a useful reference for the further functional study of SlMYBR genes in tomato. Full article
(This article belongs to the Special Issue Genomics and Bioinformatics Applications in Horticulture)
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21 pages, 4107 KiB  
Article
An Integrative Volatile Terpenoid Profiling and Transcriptomics Analysis in Hoya cagayanensis, Hoya lacunosa and Hoya coriacea (Apocynaceae, Marsdenieae)
by Syazwani Basir, Muhamad Afiq Akbar, Noraini Talip, Syarul Nataqain Baharum and Hamidun Bunawan
Horticulturae 2022, 8(3), 224; https://doi.org/10.3390/horticulturae8030224 - 4 Mar 2022
Cited by 4 | Viewed by 3573
Abstract
Hoya’s R.Br. attractive flower shapes and unique scents make it suitable to be exploited as a new source of tropical fragrance. Therefore, this study aims to elucidate the biosynthesis of secondary metabolites using phytochemical and transcriptomic approaches to understand the mechanisms of scents [...] Read more.
Hoya’s R.Br. attractive flower shapes and unique scents make it suitable to be exploited as a new source of tropical fragrance. Therefore, this study aims to elucidate the biosynthesis of secondary metabolites using phytochemical and transcriptomic approaches to understand the mechanisms of scents biosynthesis, especially terpenoid in Hoya. Three Hoya flower species were selected in this study: Hoya cagayanensis, Hoya lacunosa, and Hoya coriacea. The secondary metabolite profiles characterizing scents on flowers were performed using head space solid phase microextraction (HS-SPME). Gas chromatography-mass spectrometry (GC-MS) revealed 23 compounds from H. cagayanensis, 14 from H. lacunose, and 36 from H. coriacea. Volatiles from the three species had different fragrance profiles, with β-ocimene and methyl salicylate compounds dominating the odor in H. cagayanensis. The 1-octane-3-ol was found highest in H. lacunosa, and (Z)-acid butyric, 3-hexenyl ester was found highest in H. coriacea. Subsequent studies were conducted to identify the biosynthesis pathway of secondary metabolites responsible for the aroma profile released by Hoya flowers through transcriptome sequencing using the Illumina Hiseq 4000 platform. A total of 109,240 (75.84%) unigenes in H. cagayanensis, 42,479 (69.00%) in H. lacunosa and 72,610 (70.55%) in H. coriacea of the total unigenes were successfully annotated using public databases such as NCBI-Nr, KEGG, InterPro, and Gene Ontology (GO). In conclusion, this study successfully identified the complete outline of terpenoid biosynthesis pathways for the first time in Hoya. This discovery could lead to the exploitation of new knowledge in producing high-value compounds using the synthetic biology approach. Full article
(This article belongs to the Special Issue Genomics and Bioinformatics Applications in Horticulture)
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10 pages, 1770 KiB  
Communication
Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach
by Zhijiang Wu, Haiyan Deng, Guidong Liang, Xiaoying Ye, Yonghua Qin and Lifang Huang
Horticulturae 2021, 7(12), 534; https://doi.org/10.3390/horticulturae7120534 - 2 Dec 2021
Cited by 3 | Viewed by 4095
Abstract
Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of [...] Read more.
Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species. Full article
(This article belongs to the Special Issue Genomics and Bioinformatics Applications in Horticulture)
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22 pages, 10684 KiB  
Article
Genome-Wide Analysis and Functional Characterization of the UDP-Glycosyltransferase Family in Grapes
by Yongzan Wei, Huayuan Mu, Guangzhao Xu, Yi Wang, Yang Li, Shaohua Li and Lijun Wang
Horticulturae 2021, 7(8), 204; https://doi.org/10.3390/horticulturae7080204 - 21 Jul 2021
Cited by 14 | Viewed by 3788
Abstract
Grape (Vitis vinifera) produces a variety of secondary metabolites, which can enhance nutrients and flavor in fruit and wine. Uridine diphosphate-glycosyltransferases (UGTs) are primarily responsible for the availability of secondary metabolites by glycosylation modification. Here, a total of 228 putative UGTs [...] Read more.
Grape (Vitis vinifera) produces a variety of secondary metabolites, which can enhance nutrients and flavor in fruit and wine. Uridine diphosphate-glycosyltransferases (UGTs) are primarily responsible for the availability of secondary metabolites by glycosylation modification. Here, a total of 228 putative UGTs were identified in V. vinifera, and VvUGTs were clustered into 15 groups (A to O) and unevenly distributed on 18 chromosomes. Diverse VvUGT members from 12 groups were transcribed, and they responded to different external stresses. More than 72% of VvUGT members were expressed at one or more stages of grape fruit development, and the expression levels of 34 VvUGT members increased gradually with fruit ripening. The VvUGT members of different groups may be involved in the synthesis and accumulation of flavonoid glycosides, glycosidically bound volatiles, and stilbenes. These results will provide guidance for further research on the functions and regulating mechanisms of UGT genes. Full article
(This article belongs to the Special Issue Genomics and Bioinformatics Applications in Horticulture)
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