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New Horizons in Vegetable Genetics and Genetic Breeding 2.0
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New Horizons in Vegetable Genetics and Genetic Breeding 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 August 2024 | Viewed by 4776

Special Issue Editor

Prof. Dr. Yangyong Zhang

E-Mail Website
Guest Editor
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing 100081, China
Interests: vegetable breeding; genetics and genomics; marker‑assisted selection; gene/QTL mapping; distant hybridization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Traditional breeding has contributed to the improvement of vegetable varieties; however, traditional breeding faces challenges regarding precise selection from large populations, rapid production and the specific improvement of elite parental lines. Current advances in sequencing technologies and bio-informatics have facilitated genetic and genomic studies, including genome assembly, omics studies (transcriptomic, proteomic and epigenetic sequencing), gene/QTL mapping, genome-wide association studies, (high-throughput) marker-assisted selection, and genomic selection. These advances have contributed to prediction and selection in plant breeding populations, thus accelerating the breeding of new vegetables. In addition, genome-editing tools, such as CRISPR/Cas tools targeting nuclear genomes and TALEN-based tools targeting cytoplasmic genomes, are particularly useful in the oriented modification of desirable breeding lines. Additionally, the utilization of in vivo haploid/diploid production tools via the manipulation of certain genetic factors has become a promising strategy for accelerating the production of homozygous lines.

This Special Issue, entitled "New Horizons in Vegetable Genetics and Genetic Breeding", invites reviews, research and opinion articles on the advanced tools, approaches and models of genetics and genomics employed to improve the quality of vegetables. This Special Issue will also accept submissions that focus on the high-throughput genotyping and phenotyping of important traits, applications of genome editing tools, and the generation and application of haploid/diploid inducer systems.

Prof. Dr. Yangyong Zhang
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • vegetable breeding
  • marker-assisted selection
  • genomic selection
  • QTL/gene mapping
  • ge-nome-wide association studies
  • omics studies
  • bio-informatics tools
  • genome editing
  • in vivo haploid/diploid induction

Published Papers (4 papers)

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Research

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16 pages, 4490 KiB  
Article
A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (Phaseolus vulgaris L.)
by Osvin Arriagada, Bárbara Arévalo, Igor Pacheco, Andrés R. Schwember, Lee A. Meisel, Herman Silva, Katherine Márquez, Andrea Plaza, Ricardo Pérez-Diáz, José Pico-Mendoza, Ricardo A. Cabeza, Gerardo Tapia, Camila Fuentes, Yohaily Rodríguez-Alvarez and Basilio Carrasco
Int. J. Mol. Sci. 2024, 25(7), 4081; https://doi.org/10.3390/ijms25074081 - 06 Apr 2024
Viewed by 530
Abstract
The domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of [...] Read more.
The domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of 281 common bean landraces from Chile was analyzed using a 12K-SNP microarray. Additionally, 401 accessions representing the rest of the five common bean races were analyzed. A total of 2543 SNPs allowed us to differentiate a genetic group of 165 accessions that corresponds to the race Chile, 90 of which were classified as pure accessions, such as the bean types ‘Tórtola’, ‘Sapito’, ‘Coscorrón’, and ‘Frutilla’. Our genetic analysis indicates that the race Chile has a close relationship with accessions from Argentina, suggesting that nomadic ancestral peoples introduced the bean seed to Chile. Previous archaeological and genetic studies support this hypothesis. Additionally, the low genetic diversity (π = 0.053; uHe = 0.53) and the negative value of Tajima’ D (D = −1.371) indicate that the race Chile suffered a bottleneck and a selective sweep after its introduction, supporting the hypothesis that a small group of Argentine bean genotypes led to the race Chile. A total of 235 genes were identified within haplotype blocks detected exclusively in the race Chile, most of them involved in signal transduction, supporting the hypothesis that intracellular signaling pathways play a fundamental role in the adaptation of organisms to changes in the environment. To date, our findings are the most complete investigation associated with the origin of the race Chile of common bean. Full article
(This article belongs to the Special Issue New Horizons in Vegetable Genetics and Genetic Breeding 2.0)
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22 pages, 11158 KiB  
Article
Transcriptome Analysis Reveals the Mechanism of Exogenous Selenium in Alleviating Cadmium Stress in Purple Flowering Stalks (Brassica campestris var. purpuraria)
by Zhi Huang, Shiling Meng, Juan Huang, Wende Zhou, Xiaoli Song, Peiyao Hao, Peigen Tang, Yihan Cao, Fen Zhang, Huanxiu Li, Yi Tang and Bo Sun
Int. J. Mol. Sci. 2024, 25(3), 1800; https://doi.org/10.3390/ijms25031800 - 01 Feb 2024
Cited by 1 | Viewed by 827
Abstract
In China, cadmium (Cd) stress has a significant role in limiting the development and productivity of purple flowering stalks (Brassica campestris var. purpuraria). Exogenous selenium supplementation has been demonstrated in earlier research to mitigate the effects of Cd stress in a [...] Read more.
In China, cadmium (Cd) stress has a significant role in limiting the development and productivity of purple flowering stalks (Brassica campestris var. purpuraria). Exogenous selenium supplementation has been demonstrated in earlier research to mitigate the effects of Cd stress in a range of plant species; nevertheless, the physiological and molecular processes by which exogenous selenium increases vegetable shoots’ resistance to Cd stress remain unclear. Purple flowering stalks (Brassica campestris var. purpuraria) were chosen as the study subject to examine the effects of treatment with sodium selenite (Na2SeO3) on the physiology and transcriptome alterations of cadmium stress. Purple flowering stalk leaves treated with exogenous selenium had higher glutathione content, photosynthetic capacity, and antioxidant enzyme activities compared to the leaves treated with Cd stress alone. Conversely, the contents of proline, soluble proteins, soluble sugars, malondialdehyde, and intercellular CO2 concentration tended to decrease. Transcriptome analysis revealed that 2643 differentially expressed genes (DEGs) were implicated in the response of exogenous selenium treatment to Cd stress. The metabolic pathways associated with flavonoid production, carotenoid synthesis, glutathione metabolism, and glucosinolate biosynthesis were among those enriched in these differentially expressed genes. Furthermore, we discovered DEGs connected to the production route of glucosinolates. This work sheds fresh light on how purple flowering stalks’ tolerance to cadmium stress is improved by exogenous selenium. Full article
(This article belongs to the Special Issue New Horizons in Vegetable Genetics and Genetic Breeding 2.0)
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20 pages, 5164 KiB  
Article
Evolution and Dynamic Transcriptome of Key Genes of Photoperiodic Flowering Pathway in Water Spinach (Ipomoea aquatica)
by Xin Wang, Yuanyuan Hao, Muhammad Ahsan Altaf, Huangying Shu, Shanhan Cheng, Zhiwei Wang and Guopeng Zhu
Int. J. Mol. Sci. 2024, 25(3), 1420; https://doi.org/10.3390/ijms25031420 - 24 Jan 2024
Viewed by 704
Abstract
The photoperiod is a major environmental factor in flowering control. Water spinach flowering under the inductive short-day condition decreases the yield of vegetative tissues and the eating quality. To obtain an insight into the molecular mechanism of the photoperiod-dependent regulation of the flowering [...] Read more.
The photoperiod is a major environmental factor in flowering control. Water spinach flowering under the inductive short-day condition decreases the yield of vegetative tissues and the eating quality. To obtain an insight into the molecular mechanism of the photoperiod-dependent regulation of the flowering time in water spinach, we performed transcriptome sequencing on water spinach under long- and short-day conditions with eight time points. Our results indicated that there were 6615 circadian-rhythm-related genes under the long-day condition and 8691 under the short-day condition. The three key circadian-rhythm genes, IaCCA1, IaLHY, and IaTOC1, still maintained single copies and similar IaCCA1, IaLHY, and IaTOC1 feedback expression patterns, indicating the conservation of reverse feedback. In the photoperiod pathway, highly conserved GI genes were amplified into two copies (IaGI1 and IaGI2) in water spinach. The significant difference in the expression of the two genes indicates functional diversity. Although the photoperiod core gene FT was duplicated to three copies in water spinach, only IaFT1 was highly expressed and strongly responsive to the photoperiod and circadian rhythms, and the almost complete inhibition of IaFT1 in water spinach may be the reason why water spinach does not bloom, no matter how long it lasts under the long-day condition. Differing from other species (I. nil, I. triloba, I. trifida) of the Ipomoea genus that have three CO members, water spinach lacks one of them, and the other two CO genes (IaCO1 and IaCO2) encode only one CCT domain. In addition, through weighted correlation network analysis (WGCNA), some transcription factors closely related to the photoperiod pathway were obtained. This work provides valuable data for further in-depth analyses of the molecular regulation of the flowering time in water spinach and the Ipomoea genus. Full article
(This article belongs to the Special Issue New Horizons in Vegetable Genetics and Genetic Breeding 2.0)
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Review

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22 pages, 2336 KiB  
Review
Advances and Prospects of Virus-Resistant Breeding in Tomatoes
by Zolfaghar Shahriari, Xiaoxia Su, Kuanyu Zheng and Zhongkai Zhang
Int. J. Mol. Sci. 2023, 24(20), 15448; https://doi.org/10.3390/ijms242015448 - 22 Oct 2023
Cited by 2 | Viewed by 2387
Abstract
Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, [...] Read more.
Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies. Full article
(This article belongs to the Special Issue New Horizons in Vegetable Genetics and Genetic Breeding 2.0)
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