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Advances of Molecular Breeding for the Vegetable Crops in the...
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Advances of Molecular Breeding for the Vegetable Crops in the Genomic Era

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 (31 July 2022) | Viewed by 13167

Special Issue Editors

Dr. Honghao Lv

E-Mail Website
Guest Editor
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: vegetable crops; germplasm innovation; genetic breeding; molecular biology; genome editing; plant resistance; haploid induction; male sterility
Special Issues, Collections and Topics in MDPI journals
Dr. Ryo Fujimoto

E-Mail Website
Guest Editor
Graduate School of Agricultural Science, Kobe University, Kobe 6578501, Japan
Interests: epigenetics; hybrid vigor; heterosis; vernalization; Brassica
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Vegetable crops provide humans with abundant and indispensable nutrients, such as vitamins, minerals, fibers and many health-promoting substances. Vegetable crops are also an important source of income for over 1.4 billion farmers around the world, and the harvesting area in 2019 has reached 596.9 million ha according to FAO statistics. However, the production of vegetable crops faces new challenges, such as population explosion and extreme weather conditions, and newly spreading diseases brought by global climate change. In addition, new requirements related to the yield, quality and resistance of the vegetable crops from the producer, consumer and market are put forward. How to meet the new challenges and requirements is a rising question. Fortunately, the genomic era now presents us with a new treasure chest with novel molecular genetics and genomics tools that enable us to solve the problem accurately and efficiently.

This Special Issue will focus on studies and advances concerning the molecular breeding of vegetable crops in the genomic era, including: (i) high-efficiency breeding technologies, such as high-throughput molecular-assisted selection and new generation of male sterility breeding systems; (ii) germplasm innovation technologies, such as molecular assisted distant hybridization and cross-species gene transformation; (iii) mining of important trait genes and their molecular mechanism related to yield, abiotic and biotic resistance, quality and nutrients, using multi-omics and molecular biological methods; (iv) genome design breeding, such as genome sequencing, foreground and background selection, gene editing, etc. We invite researchers to submit papers that highlight the above fields, and reviews summarizing past works and bringing new insights and opinions will also be welcome.

Dr. Honghao Lv
Dr. Ryo Fujimoto
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

  • vegetable
  • molecular genetic breeding
  • gene editing
  • genome design
  • multi-omics techniques
  • germplasm innovation

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Published Papers (4 papers)

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Research

11 pages, 2066 KiB  
Article
Identification and Fine-Mapping of Clubroot (Plasmodiophora brassicae) Resistant QTL in Brassica rapa
by Hui Zhang, Xiaochao Ma, Xitong Liu, Shifan Zhang, Fei Li, Guoliang Li, Rifei Sun and Shujiang Zhang
Horticulturae 2022, 8(1), 66; https://doi.org/10.3390/horticulturae8010066 - 11 Jan 2022
Cited by 2 | Viewed by 2359
Abstract
European fodder turnips (Brassica rapa ssp. rapifera) were identified as sources of clubroot resistance (CR) and have been widely used in Brassica resistance breeding. An F2 population derived from a cross between a resistant turnip and a susceptible Chinese cabbage [...] Read more.
European fodder turnips (Brassica rapa ssp. rapifera) were identified as sources of clubroot resistance (CR) and have been widely used in Brassica resistance breeding. An F2 population derived from a cross between a resistant turnip and a susceptible Chinese cabbage was used to determine the inheritance and locating the resistance Quantitative Trait Loci (QTLs). The parents showed to be very resistant/susceptible to the field isolates (pathotype 4) of clubroot from Henan in China. After inoculation, 27 very resistant or susceptible individuals were selected to construct bulks, respectively. Next-generation-sequencing-based Bulk Segregant Analysis Sequencing (BSA-Seq) was used and located resistance QTL on chromosome A03 (3.3–7.5 Mb) and A08 (0.01–6.5 Mb), named Bcr1 and Bcr2, respectively. Furthermore, an F3 population including 180 families derived from F2 individuals was phenotyped and used to verify and narrow candidate regions. Ten and seven Kompetitive Allele-Specific PCR (KASP) markers narrowed the target regions to 4.3–4.78 Mb (A03) and 0.02–0.79 Mb (A08), respectively. The phenotypic variation explained (PVE) of the two QTLs were 33.3% and 13.3% respectively. The two candidate regions contained 99 and 109 genes. In the A03 candidate region, there were three candidate R genes, namely Bra006630, Bra006631 and Bra006632. In the A08 candidate region, there were two candidate R genes, namely Bra030815 and Bra030846. Full article
(This article belongs to the Special Issue Advances of Molecular Breeding for the Vegetable Crops in the Genomic Era)
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15 pages, 9039 KiB  
Article
Transcriptional Association between mRNAs and Their Paired Natural Antisense Transcripts Following Fusarium oxysporum Inoculation in Brassica rapa L.
by Mst. Arjina Akter, Hasan Mehraj, Naomi Miyaji, Satoshi Takahashi, Takeshi Takasaki-Yasuda, Motoaki Seki, Elizabeth S. Dennis, Ryo Fujimoto and Kenji Osabe
Horticulturae 2022, 8(1), 17; https://doi.org/10.3390/horticulturae8010017 - 23 Dec 2021
Cited by 5 | Viewed by 3653
Abstract
Long noncoding RNAs (lncRNAs) play important roles in abiotic and biotic stress responses; however, studies on the mechanism of regulation of lncRNA expression are limited in plants. The present study examined the relationship between lncRNA expression level and two active histone modifications (H3K4me3 [...] Read more.
Long noncoding RNAs (lncRNAs) play important roles in abiotic and biotic stress responses; however, studies on the mechanism of regulation of lncRNA expression are limited in plants. The present study examined the relationship between lncRNA expression level and two active histone modifications (H3K4me3 and H3K36me3) in Brassica rapa. Both histone marks were enriched in the chromatin regions encoding lncRNAs, especially around the transcription start site. The transcription level of long intergenic noncoding RNAs was positively associated with the level of H3K4me3 and H3K36me3, while this association was not observed in natural antisense RNAs (NATs) and intronic noncoding RNAs. As coordinate expression of mRNAs and paired NATs under biotic stress treatment has been identified, the transcriptional relationship between mRNAs and their paired NATs following Fusarium oxysporum f. sp. conglutinans (Foc) inoculation was examined. A positive association of expression levels between mRNAs and their paired NATs following Foc inoculation was observed. This association held for several defense-response-related genes and their NAT pairs. These results suggest that coordinate expression of mRNAs and paired NATs plays a role in the defense response against Foc. Full article
(This article belongs to the Special Issue Advances of Molecular Breeding for the Vegetable Crops in the Genomic Era)
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15 pages, 1710 KiB  
Article
Analysis of Glucosinolate Content, Composition and Expression Level of Biosynthesis Pathway Genes in Different Chinese Kale Varieties
by Lu Tong, Shanhan Cheng, Honghao Lv, Chengzhi Zhao, Jie Zhu, Pingwu Liu, Zhiwei Wang, Limei Yang and Yangyong Zhang
Horticulturae 2021, 7(10), 398; https://doi.org/10.3390/horticulturae7100398 - 14 Oct 2021
Cited by 1 | Viewed by 2485
Abstract
The content and component of glucosinolates in edible stems and leaves of eight Chinese kale varieties from Japan and eight varieties from China were determined by HPLC-MS. Simultaneously, the expression levels of glucosinolate biosynthesis pathway genes from four varieties with high and low [...] Read more.
The content and component of glucosinolates in edible stems and leaves of eight Chinese kale varieties from Japan and eight varieties from China were determined by HPLC-MS. Simultaneously, the expression levels of glucosinolate biosynthesis pathway genes from four varieties with high and low total glucosinolate contents were analyzed by the qRT-PCR method. Four types of aliphatic glucosinolates (A-GLSs: GRA, SIN, GNA and GER) and indole glucosinolates (I-GLSs: 4-HGBS, GBS, 4-MGBS and NGBS) were detected in the stems and leaves of 16 varieties, and no aromatic glucosinolates (R-GLSs) were detected. A-GLSs account for more than 80.69% of the total content of total glucosinolates (T-GLSs), in which GNA and GRA are the main components of stems and leaves. Among Japanese varieties, QB1 has higher content of A- and T-GLSs, while that of XLB was lower; however, the corresponding varieties were ZH and DSHH in Chinese varieties. Among the above four varieties, the expression levels of SOT16, CYP83B1, SOT17, CYP83A1 and MAM1 genes were significantly higher in the varieties with higher GLSs; the expression levels of SOT16 and CYP83B1 were consistent with the content of I-GLSs; and SOT17, CYP83A1 and MAM1 expression levels were consistent with A-GLSs content. At the same time, the expression levels of SOT16 and CYP83B1 in the leaves were higher than those in the stems. CYP83A1 and MAM1 genes were less expressed in the leaves than in the stems of lower content varieties. It is speculated that these genes may be the key genes regulating GLS biosynthesis in Chinese kale. Full article
(This article belongs to the Special Issue Advances of Molecular Breeding for the Vegetable Crops in the Genomic Era)
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14 pages, 1218 KiB  
Article
Genetic Architecture of Chile Pepper (Capsicum spp.) QTLome Revealed Using Meta-QTL Analysis
by Dennis N. Lozada, Madelin Whelpley and Andrea Acuña-Galindo
Horticulturae 2021, 7(8), 227; https://doi.org/10.3390/horticulturae7080227 - 5 Aug 2021
Cited by 8 | Viewed by 3701
Abstract
In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS). Meta-QTL analysis for different traits in chile peppers (Capsicum spp.) remains lacking, and therefore it would [...] Read more.
In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS). Meta-QTL analysis for different traits in chile peppers (Capsicum spp.) remains lacking, and therefore it would be necessary to re-evaluate identified QTL for a more precise MAS for genetic improvement. We report the first known meta-QTL analysis for diverse traits in the chile pepper QTLome. A literature survey using 29 published linkage mapping studies identified 766 individual QTL from five different trait classes. A total of 311 QTL were projected into a consensus map. Meta-analysis identified 30 meta-QTL regions distributed across the 12 chromosomes of Capsicum. MQTL5.1 and MQTL5.2 related to Phytophthora capsici fruit and root rot resistance were delimited to < 1.0 cM confidence intervals in chromosome P5. Candidate gene analysis for the P5 meta-QTL revealed functions related to histone methylation and demethylation, indicating the potential role of epigenetics for P. capsici resistance. Allele-specific markers for the meta-QTL will be developed and validated for MAS of P. capsici resistant lines. Altogether, results from meta-QTL analysis for chile pepper QTLome rendered further insights into the genetic architecture of different traits for this valuable horticultural crop. Full article
(This article belongs to the Special Issue Advances of Molecular Breeding for the Vegetable Crops in the Genomic Era)
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