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Horticulturae
Special Issues
Advances in Horticultural Crops Comparative and Functional Genomics
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Advances in Horticultural Crops Comparative and Functional Genomics

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 (30 April 2022) | Viewed by 12297

Special Issue Editors

Dr. Xin Wang

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Guest Editor
Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
Interests: bioinformatics; comparative and functional genomics; population genomics; genome evolution; epigenetics; genomic selection; genetic diversity
Dr. Jiantao Zhao

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Guest Editor
Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
Interests: GWAS; meta-analysis; evolution and domestication; pan-genome; allele specific expression; flavor; metabolites

Special Issue Information

Dear Colleagues,

Horticultural crops contribute a large portion of vitamins, minerals, antioxidants, and fiber to the human diet. With expanding genomics data and genomic tools, comparative and functional genomics is a useful tool for guiding crop improvement and breeding. By implementing genomics data and bioinformatics approaches, researchers can investigate the genes underlying the important agronomic traits, which could be utilized for crop improvement.

The proposed Special Issue on “Advances in Horticultural Crops Comparative and Functional Genomics” will present crucial findings in horticultural crops obtained by bioinformatics and extensive genomic data. Potential topics include, but are not limited to the following: population genomics, genome evolution, crop epigenetic, meta-analysis, 3D genome, genetic diversity, and genomic selection. We look forward to receiving your manuscripts and sharing your results in this Special Issue.

Dr. Xin Wang
Dr. Jiantao Zhao
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

  • population genomics
  • genome evolution
  • crop epigenetic
  • meta-analysis
  • GWAS
  • QTL-seq
  • 3D Genome
  • genetic diversity
  • genomic selection

Published Papers (4 papers)

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Research

12 pages, 1060 KiB  
Article
Characteristics of Interspecific Hybridization and Inbred Progeny of Pumpkin (Cucurbita moschata Duch.) and Winter Squash (Cucurbita maxima Duch.)
by Zefa Liu, Yanfang Jiang, Xipeng Yang, Xin Deng, Jiancheng Dang, Zhijun Wang, Mohd Rafii Yusop and Shamsiah Abdullah
Horticulturae 2022, 8(7), 596; https://doi.org/10.3390/horticulturae8070596 - 01 Jul 2022
Cited by 3 | Viewed by 2646
Abstract
Hybrid incompatibility and F1 hybrid dysgenesis in the interspecific hybridization between pumpkin (Cucurbita moschata Duch.) and winter squash (Cucurbita maxima Duch.) have been previously noted. For this reason, it is difficult to obtain F2 generations due to F1 [...] Read more.
Hybrid incompatibility and F1 hybrid dysgenesis in the interspecific hybridization between pumpkin (Cucurbita moschata Duch.) and winter squash (Cucurbita maxima Duch.) have been previously noted. For this reason, it is difficult to obtain F2 generations due to F1 sterility. However, back-crossing and add-crossing can be utilized to overcome these incompatibility barriers in interspecific hybridization. To date, few studies have focused on parental selection, the back-crossing process, and offspring characteristics related to interspecific hybridization. Hence, we explored the F1 seed acquisition rate, plant characteristics, and F2 generation fertility after interspecific back-crossing and add-crossing hybridization of C. moschata and C. maxima. Moreover, as a female parent, X-1 (C. moschata) yielded F1 seeds when crossed with winter squash (C. maxima) 10-04-3, 10-37, or 10-05-2. BC1F1 seeds and plants could be obtained with winter squash (C. maxima) as the recurrent parent. Some healthy F2 seeds and plants were obtained from the interspecific hybrids, including ZJ-13, ZJ-8, and ZJ-11. Further fruit nutrition quality analysis showed that the starch, polysaccharide, cellulose, and dry material contents of ZJ-7 and ZJ-8 were significantly higher than those of the parent pumpkin and winter squash lines. The bioflavonoid content of ZJ-8 was lower than that of its parents, and its soluble protein was at the median value. Meanwhile, the bioflavonoid content of ZJ-1 was lower than that of its parents, but its soluble protein was significantly higher. These results suggest that back-crossing and multi-crossing can overcome the barriers to interspecific crossing of C. moschata × C. maxima. Some interspecific hybrid fruits had nutritional contents much higher than those of their parent lines. Additionally, X-1 (C. maxima) was found to act as a bridge species in interspecific hybridization. Collectively, in this study, the barriers to interspecific hybridization of C. moschata × C. maxima were addressed through crossing methods and choice of parents, and the obtained results are expected to provide novel support for interspecific hybrid breeding between C. moschata and C. maxima. Full article
(This article belongs to the Special Issue Advances in Horticultural Crops Comparative and Functional Genomics)
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17 pages, 2195 KiB  
Article
Assessment of Genetic Diversity and Relatedness in an Andean Potato Collection from Argentina by High-Density Genotyping
by Sofía Sucar, Martín Federico Carboni, María Florencia Rey Burusco, Martín Alfredo Castellote, Gabriela Alejandra Massa, Marcelo Nicolás Monte and Sergio Enrique Feingold
Horticulturae 2022, 8(1), 54; https://doi.org/10.3390/horticulturae8010054 - 07 Jan 2022
Cited by 3 | Viewed by 2282
Abstract
Native potatoes are the most diverse among cultivated potato species and thus constitute a valuable source for identifying genes for potato improvement. Nevertheless, high-density mapping, needed to reveal allelic diversity, has not been performed for native Argentinian potatoes. We present a study of [...] Read more.
Native potatoes are the most diverse among cultivated potato species and thus constitute a valuable source for identifying genes for potato improvement. Nevertheless, high-density mapping, needed to reveal allelic diversity, has not been performed for native Argentinian potatoes. We present a study of the genetic variability and population structure of 96 Andigena potatoes from Northwestern Argentina performed using a subset of 5035 SNPs with no missing data and full reproducibility. These high-density markers are distributed across the genome and present a good coverage of genomic regions. A Bayesian approach revealed the presence of: (I) a major group comprised of most of the Andean accessions; (II) a smaller group containing the out-group cv. Spunta and the sequenced genotype DM; and (III) a third group containing colored flesh potatoes. This grouping was also consistent when maximum likelihood trees were constructed and further confirmed by a principal coordinate analysis. A group of 19 accessions stored as Andean varieties clustered consistently with group Tuberosum accessions. This was in agreement with previous studies and we hypothesize that they may be reintroductions of European-bred long day-adapted potatoes. The present study constitutes a valuable source for allele mining of genes of interest and thus provides a tool for association mapping studies. Full article
(This article belongs to the Special Issue Advances in Horticultural Crops Comparative and Functional Genomics)
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26 pages, 80363 KiB  
Article
Genome-Wide Identification and Characterization of DnaJ Gene Family in Grape (Vitis vinifera L.)
by Tianchi Chen, Tao Xu, Tianye Zhang, Tingting Liu, Leyi Shen, Zhihui Chen, Yueyan Wu and Jian Yang
Horticulturae 2021, 7(12), 589; https://doi.org/10.3390/horticulturae7120589 - 18 Dec 2021
Cited by 7 | Viewed by 3035
Abstract
Grape production in southern China suffers great loss due to various environmental stresses. To understand the mechanism of how the grape plants respond to these stresses is an active area of research in developing cultivation techniques. Plant stress resistance is known to rely [...] Read more.
Grape production in southern China suffers great loss due to various environmental stresses. To understand the mechanism of how the grape plants respond to these stresses is an active area of research in developing cultivation techniques. Plant stress resistance is known to rely on special proteins. Amongst them, DnaJ protein (HSP40) serves as co-chaperones of HSP70, playing crucial roles in various stress response. However, the DnaJ proteins encoded by the DnaJ gene family in Vitis vinifera L. have not been fully described yet. In this study, we identified 78 VvDnaJs in the grape genome that can be classified into three groups—namely, DJA, DJB, and DJC. To reveal the evolutionary and stress response mechanisms for the VvDnaJ gene family, their evolutionary and expression patterns were analyzed using the bioinformatic approach and qRT-PCR. We found that the members in the same group exhibited a similar gene structure and protein domain organization. Gene duplication analysis demonstrated that segmental and tandem duplication may not be the dominant pathway of gene expansion in the VvDnaJ gene family. Codon usage pattern analysis showed that the codon usage pattern of VvDnaJs differs obviously from the monocotyledon counterparts. Tissue-specific analysis revealed that 12 VvDnaJs present a distinct expression profile, implying their distinct roles in various tissues. Cis-acting element analysis showed that almost all VvDnaJs contained the elements responsive to either hormones or stresses. Therefore, the expression levels of VvDnaJs subjected to exogenous hormone applications and stress treatments were determined, and we found that VvDnaJs were sensitive to hormone treatments and shade, salt, and heat stresses, especially VIT_00s0324g00040. The findings of this study could provide comprehensive information for the further investigation on the genetics and protein functions of the DnaJ gene family in grape. Full article
(This article belongs to the Special Issue Advances in Horticultural Crops Comparative and Functional Genomics)
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12 pages, 12215 KiB  
Article
The Isolation and Identification of Anthocyanin-Related GSTs in Chrysanthemum
by Yajing Li, Xiaofen Liu, Fang Li, Lili Xiang and Kunsong Chen
Horticulturae 2021, 7(8), 231; https://doi.org/10.3390/horticulturae7080231 - 07 Aug 2021
Cited by 8 | Viewed by 3242
Abstract
Anthocyanin is the crucial pigment for the coloration of red chrysanthemum flowers, which synthesizes in the cytosol and is transported to the vacuole for stable storage. In general, glutathione S-transferases (GSTs) play a vital role in this transport. To date, there is no [...] Read more.
Anthocyanin is the crucial pigment for the coloration of red chrysanthemum flowers, which synthesizes in the cytosol and is transported to the vacuole for stable storage. In general, glutathione S-transferases (GSTs) play a vital role in this transport. To date, there is no functional GST reported in chrysanthemums. Here, a total of 94 CmGSTs were isolated from the chrysanthemum genome, with phylogenetic analysis suggesting that 16 members of them were clustered into the Phi subgroup which was related to anthocyanin transport. Among them, the expression of CmGST1 was positively correlated with anthocyanin accumulation. Protein sequence alignment revealed that CmGST1 included anthocyanin-related GST-specific amino acid residues. Further transient overexpression experiments in tobacco leaves showed that CmGST1 could promote anthocyanin accumulation. In addition, a dual-luciferase assay demonstrated that CmGST1 could be regulated by CmMYB6, CmbHLH2 and CmMYB#7, which was reported to be related to anthocyanin biosynthesis. Taken together, we suggested that CmGST1 played a key role in anthocyanin transport and accumulation in chrysanthemums. Full article
(This article belongs to the Special Issue Advances in Horticultural Crops Comparative and Functional Genomics)
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