Advances in Brassica Crops Genomics and Breeding, 2nd Edition

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: 15 October 2024 | Viewed by 15741

Special Issue Editors


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Guest Editor
Department of Biotechnology, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: Brassica genomics and genetics; molecular breeding
Special Issues, Collections and Topics in MDPI journals
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: vegetable genetic breeding; genomics; genetic resources; molecular breeding
Special Issues, Collections and Topics in MDPI journals
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: pan-genome; genomics; genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the tremendous success of the first edition of the Special Issue “Advances in Brassica Crops Genomics and Breeding” (https://www.mdpi.com/journal/horticulturae/special_issues/Brassica_Genomics), a second edition is being launched.

Brassica crops include vegetable, oil, ornamental and condimental crops. Many of these, such as Chinese cabbage, cabbage and rapeseed, are cultivated worldwide as important crops. Brassica species are unique not only because of their economic importance, but also because of the domestication of extreme morphological types, such as leafy heading, root/stem enlarging and florescence heading in these species. Moreover, Brassica species represent several important polyploidization events, including paleo-, meso- and present polyploidization, which make them ideal as model species for the investigation of polyploidization.

With the fast progress we are making in sequencing technologies, a number of genomes of Brassica crops species have been sequenced and high-quality chromosome scale assemblies were obtained. Moreover, the large-scale resequencing data of germplasm resources have been made available in B. rapa, B. oleracea, and B. napus, which allows GWAS and domestication analysis in these important crops. These breakthroughs accelerated the investigation into the genomics of the complex Brassica genomes, the evolution of different Brassica species, functional revealing of important genes, and the molecular marker-assisted breeding of Brassica crops. The purpose of this Special Issue is to present the recent advances in genomics and breeding in Brassica crops.

Prof. Dr. Xiaowu Wang
Dr. Jian Wu
Dr. Xu Cai
Guest Editors

Manuscript Submission Information

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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

  • brassica
  • marker-assisted breeding
  • gene mapping
  • QTL
  • SNP
  • GWAS
  • genomics
  • genome structure variation
  • transcriptomics
  • metabolomics

Related Special Issue

Published Papers (10 papers)

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Research

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10 pages, 284 KiB  
Communication
Imidazolinone Resistance in Oilseed Rape (Brassica napus L.): Current Status, Breeding, Molecular Markers and Prospects for Application in Hybrid Seed Purity Improvement
by Elena Victorovna Kozar and Elena Alekseevna Domblides
Horticulturae 2024, 10(6), 553; https://doi.org/10.3390/horticulturae10060553 - 24 May 2024
Viewed by 324
Abstract
Resistance of agricultural crops to herbicides is an important topic that concerns many researchers. One of the most popular groups of herbicides is the imidazolinone group. Resistant forms of crops such as wheat (Triticum aestivum L.), sunflower (Helianthus annuus L.), corn [...] Read more.
Resistance of agricultural crops to herbicides is an important topic that concerns many researchers. One of the most popular groups of herbicides is the imidazolinone group. Resistant forms of crops such as wheat (Triticum aestivum L.), sunflower (Helianthus annuus L.), corn (Zea mays L.), rice (Oryza sativa L.) and oilseed rape (Brassica napus L.) have been developed to this group of herbicides. All crops resistant to this group of herbicides have the commercial name Clearfield®. In this review, the information concerning oilseed rape resistance to the imidazolinone group of herbicides is collected and summarized; it will be useful for breeders and researchers engaged in this direction. This review touches upon the topic of mechanisms of oilseed rape resistance to imidazolinones. Mutation variants known to date, which provide resistance to this group of herbicides, are described, and known molecular markers of them are presented. Approaches to the selection of oilseed rape for resistance to the imidazolinone group of herbicides are mentioned. Various methods of utilizing imidazolinone resistance to improve the purity of hybrid seeds are also considered. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
19 pages, 4698 KiB  
Article
Genetic Variation and Association Analysis of Phenolic Compounds in Rapeseed (Brassica napus L.) Mutant Lines Using Genotyping-by-Sequencing (GBS)
by Dong-Gun Kim, Jaihyunk Ryu, Baul Yang, Ye-Jin Lee, Jae Hoon Kim, Juyoung Kim, Woon Ji Kim, Sang Hoon Kim, Soon-Jae Kwon, Jin-Baek Kim, Si-Yong Kang, Jae Il Lyu, Chang-Hyu Bae and Joon-Woo Ahn
Horticulturae 2023, 9(11), 1204; https://doi.org/10.3390/horticulturae9111204 - 6 Nov 2023
Viewed by 1035
Abstract
The concentration of phenolic compounds in rapeseed is important because they are either anti-nutritional compounds or directly related to antioxidant activity. In this study, single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing (GBS), and an association study was conducted to investigate phenolic content [...] Read more.
The concentration of phenolic compounds in rapeseed is important because they are either anti-nutritional compounds or directly related to antioxidant activity. In this study, single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing (GBS), and an association study was conducted to investigate phenolic content in 95 rapeseed mutant lines derived from gamma rays and their original cultivar. A total of 3,196,318 SNPs were detected, resulting in the identification of a set of 70,208 union SNPs used to perform association studies. Seven compounds were identified, sinapine being the major phenolic compound (91.2–99.2%) in all genotypes. An association study was conducted for seven compounds and total phenolic content (TPC). It identified 241 SNPs that were significantly associated with these compounds, total sinapine content (TSC), and TPC. Based on the SNP markers detected, BnaC02g20420D was associated with dihexose, BnaC08g30570D with progoitrin, BnaA01g06890D with methyl sinapate, BnaA09g16810D with sinapine(4-O-8′)guaiacyl, BnaCnng39930D with trans-sinapine 1, BnaA07g31720D with trans-sinapine 2, BnaC03g31950D with sinapoyl malate, and BnaAnng27700D with TPC. These were selected as candidate genes that may play a key role in rapeseed. The SNP markers associated with these key phenolic compounds can be used as targets in breeding programs to reduce anti-nutritional components. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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18 pages, 2468 KiB  
Article
A Cold Case—Glucosinolate Levels in Kale Cultivars Are Differently Influenced by Cold Temperatures
by Christoph Hahn, Anja Müller, Nikolai Kuhnert and Dirk C. Albach
Horticulturae 2023, 9(9), 953; https://doi.org/10.3390/horticulturae9090953 - 22 Aug 2023
Cited by 2 | Viewed by 1998
Abstract
Among the Brassica oleracea L. crops, kale has gained increased global recognition in recent years as a healthy food item due to its high nutritional value and versatility. Additionally, the diversity of different kale varieties has started to be explored across large latitudes [...] Read more.
Among the Brassica oleracea L. crops, kale has gained increased global recognition in recent years as a healthy food item due to its high nutritional value and versatility. Additionally, the diversity of different kale varieties has started to be explored across large latitudes from the Mediterranean to north temperate climates. Specifically, glucosinolates are the predominant phytochemicals found in kale leaves, contributing to the specific taste of this vegetable, and they are affected by environmental factors such as temperature. To date, no study has investigated the effect of chilling on glucosinolate diversity and, thus, the taste in genetically different kale cultivars at the same time. Given the variability of glucosinolates observed among cultivars, we evaluated the impact of acclimation to cold temperatures on glucosinolate levels in curly kale, Lacinato kale, and a feral type using high-performance liquid chromatography coupled with time-of-flight mass spectrometry (HPLC-ESI-qTOF-MS). We targeted the short-term impact (after 12 h) on glucosinolates as well as the longer-term effect (after seven days) of cold acclimation. Our results revealed different molecular patterns regarding the change in glucosinolates in the feral type compared to curly kale and Lacinato-type kale. In the latter ones, primary aliphatic glucosinolates were induced (the glucoraphanin in Lacinato kale increased by more than 200%). The indole glucobrassicin was not significantly affected. Conversely, in the feral type the indole glucobrassicin was reduced by 35% after cold acclimation, whereas aliphatic glucosinolates were hardly affected. The results indicate that both genetic and environmental factors are important for the composition of glucosinolate patterns in kale. In conclusion, to obtain plants with an improved nutritional value, considering both temperature and the choice of cultivar is crucial during kale cultivation. Future breeding attempts of kale should also emphasize the cultivar-dependent cold acclimation patterns reported here. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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16 pages, 5771 KiB  
Article
Elucidating Quadruplication Event of PHO1 Gene: A Key Regulator of Plant Phosphate Translocation in Brassica rapa
by Dahlia Shahbuddin, Rosazlina Rusly, Ahmad Naqib Shuid and Ahmad Bukhary Ahmad Khair
Horticulturae 2023, 9(7), 845; https://doi.org/10.3390/horticulturae9070845 - 24 Jul 2023
Viewed by 898
Abstract
In response to Pi deprivation, phosphate 1 (PHO1) is a significant regulator at trans-eQTL hotspots in Brassica rapa. Brassica rapa short-read sequencing data analysis revealed four PHO1 paralog genes, PHO1_A, PHO1_B, PHO1_C, and PHO1_D, placed in [...] Read more.
In response to Pi deprivation, phosphate 1 (PHO1) is a significant regulator at trans-eQTL hotspots in Brassica rapa. Brassica rapa short-read sequencing data analysis revealed four PHO1 paralog genes, PHO1_A, PHO1_B, PHO1_C, and PHO1_D, placed in tandem with very high sequence similarity. However, based on short-read genomic sequence data, only three transcripts are accessible. Five bacterial artificial chromosomes (BACs) can be sequenced using a long-read sequencer, which improves de novo assembly and identifies structural variants. The PHO1 gene’s quadruplicating tandem positions in the genomic sequence were confirmed by an analysis of long-read data. Transcript analysis identified only three groups of PHO1 paralogs (ortholog AT1G14040 in Arabidopsis), i.e., PHO1_A, PHO1_B, and PHO1_D, expressed in B. rapa leaf tissues under Pi deficiency. PHO1_A, with transcript ID XM_009150437.2, has five different splice variants found. These splice variants’ truncated proteins demonstrated PHO1_A’s function in P control as opposed to protein encoding. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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15 pages, 3871 KiB  
Article
QTL Mapping of Leaf-Related Traits Using a High-Density Bin Map in Brassica rapa
by Fengming Li, Zhiyuan Liu, Haixu Chen, Jian Wu, Xu Cai, Hui Wang, Xiaowu Wang and Jianli Liang
Horticulturae 2023, 9(4), 433; https://doi.org/10.3390/horticulturae9040433 - 27 Mar 2023
Cited by 1 | Viewed by 1411
Abstract
The species Brassica rapa includes enormous leafy vegetables with extreme leaf morphological diversity. Leaf traits such as size, shape, weight, and ratio of the leaf blade to the petiole contribute to yield, appearance, and desirability to consumers. These leaf-related traits are controlled by [...] Read more.
The species Brassica rapa includes enormous leafy vegetables with extreme leaf morphological diversity. Leaf traits such as size, shape, weight, and ratio of the leaf blade to the petiole contribute to yield, appearance, and desirability to consumers. These leaf-related traits are controlled by quantitative trait loci (QTLs). The construction of high-density bin maps using low-coverage sequencing is a powerful method for QTL fine-mapping and gene identification. In this study, we performed whole-genome re-sequencing of Wutacai ‘Zhongbaye’ and Chinese cabbage ‘HN53’ and 150 F2 individuals to construct a high-density bin map for QTL mapping of 11 leaf-related traits. The parental lines and F2 population were re-sequenced at 10x and 1x coverage, respectively. A map containing 565 bin markers was constructed based on parental single-nucleotide polymorphisms and a modified sliding window approach. The total map length was 944.6 cM and the average distance of the bins was 1.65 cM. In total, 60 significant QTLs controlling 11 leaf-related traits were detected. We further identified candidate genes responsible for these complex leaf-related traits. These findings suggest that this cost-effective bin-mapping approach is capable of rapid identification of QTLs and candidate genes, and will thus facilitate the dissection of the underlying molecular basis of leaf morphological variations and accelerate the improvement of B. rapa vegetable breeding. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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15 pages, 2579 KiB  
Article
Identification of a Monosomic Alien Chromosome Addition Line Responsible for the Purple Color Trait in Heading Chinese Cabbage
by Xiaoyun Xin, Deshuang Zhang, Hong Zhao, Tongbing Su, Xiuyun Zhao, Weihong Wang, Peirong Li, Yangjun Yu, Jiao Wang, Shuancang Yu and Fenglan Zhang
Horticulturae 2023, 9(2), 146; https://doi.org/10.3390/horticulturae9020146 - 21 Jan 2023
Cited by 2 | Viewed by 1662
Abstract
Purple heading Chinese cabbage has become popular in recent years due to its attractive color and health benefits. However, purple varieties remain rare, and the regulation mechanism of anthocyanin accumulation in Chinese cabbage is still largely unknown. By introducing the purple color trait [...] Read more.
Purple heading Chinese cabbage has become popular in recent years due to its attractive color and health benefits. However, purple varieties remain rare, and the regulation mechanism of anthocyanin accumulation in Chinese cabbage is still largely unknown. By introducing the purple color trait from Brassica juncea, a new purple heading Chinese cabbage cultivar (18M-245) was generated with deep purple leaves at both the seedling and adult stages. Anthocyanin accumulation in 18M-245 increased when grown at low temperatures. FISH and genotyping results showed that the purple trait was caused by an alien chromosome addition line derived from the Brassica B genome. The LDOX coding gene BjuB014115 from the addition line was highly expressed in 18M-245, consistent with the results of anthocyanin accumulation. Meanwhile, several MYB and bHLH transcriptional factors from the Brassica A genome were found to directly bind to the promoter of BjuB014115, suggesting that interactions between the Brassica A and B genomes are involved in the regulatory network of anthocyanin biosynthesis in Chinese cabbage. Our results provide new insights into the regulation mechanism of anthocyanin biosynthesis in purple heading Chinese cabbage. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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15 pages, 4257 KiB  
Article
Analysis of Structure Variations and Expression Characteristics of DMP8 and DMP9 Genes in Brassicaceae
by Tingting Zhang, Jianli Liang, Xu Cai, Lei Zhang, Jian Wu and Xiaowu Wang
Horticulturae 2022, 8(11), 1095; https://doi.org/10.3390/horticulturae8111095 - 21 Nov 2022
Viewed by 1769
Abstract
Doubled haploid (DH) technology based on in vivo haploid induction (HI), which is used to obtain true-breeding lines within a single generation, is a technique that significantly increases modern crop-breeding efficiency. Recently, dicot Arabidopsis thaliana lines containing mutations in DMP8/9 were used as [...] Read more.
Doubled haploid (DH) technology based on in vivo haploid induction (HI), which is used to obtain true-breeding lines within a single generation, is a technique that significantly increases modern crop-breeding efficiency. Recently, dicot Arabidopsis thaliana lines containing mutations in DMP8/9 were used as haploid inducer lines, but the use of this new HI mechanism is limited in Brassicaceae species, which include many important vegetable, oil, and fodder crops. Here, we investigated the phylogenetic distribution of the DMP8 and DMP9 homologous genes from 26 sequenced Brassicaceae species. We found that DMP8 only exists in the tribe Arabideae, while multiple copies of the DMP9 gene are presenting in all the investigated Brassicaceae species. The syntenic DMP9 genes were divided into two groups derived from the S genomic block and R genomic block, respectively. We further investigated the duplication, structure variations, and expression of the DMP9 genes in Brassica species that had undergone an extra whole-genome triplication. Our results revealed that DMP9 was lost in the most fractionated (MF2) subgenome, and the retained DMP9s in the least fractionated (LF) subgenome and medium fractionated (MF1) subgenome showed diversified expression patterns, indicating their functional diversification. Our results will be useful for obtaining the target DMP genes for the establishing of HI lines in Brassicaceae crops. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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16 pages, 3605 KiB  
Article
Systematic Characterization of Brassica napus HIR Gene Family Reveals a Positive Role of BnHIR2.7 in Sclerotinia sclerotiorum Resistance
by Mengqi Li, Yuqiao Tang, Mengna Yu, Yonghai Fan, Shahid Ullah Khan, Wei Chang, Xiaodong Li, Siyu Wei, Lijuan Wei, Cunmin Qu, Jiana Li and Kun Lu
Horticulturae 2022, 8(10), 874; https://doi.org/10.3390/horticulturae8100874 - 23 Sep 2022
Cited by 2 | Viewed by 1612
Abstract
Hypersensitive-induced response protein (HIR) is a class of plant immune proteins that play pivotal roles in Sclerotinia sclerotiorum (Lib.) de Bary resistance. However, there has been no systematic investigation and identification of HIR genes in rapeseed (Brassica napus L.). Hence, we identified [...] Read more.
Hypersensitive-induced response protein (HIR) is a class of plant immune proteins that play pivotal roles in Sclerotinia sclerotiorum (Lib.) de Bary resistance. However, there has been no systematic investigation and identification of HIR genes in rapeseed (Brassica napus L.). Hence, we identified 50 BnHIR genes and classified them into four groups. Subcellular localization prediction suggested that HIR proteins are mainly localized in the mitochondria. Cis-acting elements involved in light and diverse abiotic stress were found in the promoter regions of BnHIR. The majority of BnHIR genes in Groups 1/3/4 were expressed in most examined tissues, especially in leaves and siliques pericarp, while the BnHIR genes in Group 2 were not or had low expression in all detected tissues. In the case of S. sclerotiorum inoculation, HIR genes in Groups 1/3/4 were strongly induced, especially homologous genes in Group 1, which exhibited different expression patterns. Moreover, overexpression of BnHIR2.7 in Arabidopsis thaliana illustrated its prominent resistance to S. sclerotiorum. Our study provides insight into the evolutionary relationships of the HIR family genes in B. napus and lays the foundation for their resistance to S. sclerotiorum in B. napus. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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Review

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12 pages, 1653 KiB  
Review
Mechanism of Tolerance to Head-Splitting of Cabbage (Brassica oleracea L. var. capitata L.): A Review of Current Knowledge and Future Directions
by Ying Wang, Qiang Li, Guoli Zhang, Liqiang Gu, Yuqian Zhao, Lei Zhou, Yanqiu Dong, Haiquan Dong and Xiaoming Song
Horticulturae 2023, 9(2), 251; https://doi.org/10.3390/horticulturae9020251 - 12 Feb 2023
Cited by 2 | Viewed by 2041
Abstract
Cabbage (Brassica oleracea L. var. capitata L.) is an important cruciferous vegetable, which is rich in dietary fiber, vitamins, beta-carotene and even good for cancer prevention. So, it is widely planted around the world. However, in the production of cabbage, the property [...] Read more.
Cabbage (Brassica oleracea L. var. capitata L.) is an important cruciferous vegetable, which is rich in dietary fiber, vitamins, beta-carotene and even good for cancer prevention. So, it is widely planted around the world. However, in the production of cabbage, the property of head-splitting not only reduces the appearance quality and commercial value of cabbage but also easily infects the area with head-splitting by germs, resulting in yield reduction, even no yield, and economic losses. For the head-splitting of cabbage, this paper introduced the causes, evaluation methods and indexes, and anatomic properties and reviewed some QTLs that have been obtained. But the cabbage molecular research of head-splitting is still in its infancy compared with other vegetable plants. Head-splitting is greatly affected by water. Although the cultivation and management methods can reduce the head-splitting rate, genetic improvement of head-splitting is still the most economic and efficient way in the long run. Therefore, the changes in the substances regulating cell water potential, the development of cell wall, ductility and toughness, calcium ion-regulated pectinase and cellulase activities, expansin genes, and even the ETH and ABA pathways related to maturation and abscission can provide ideas and directions for future gene mining and mechanism analysis for head-splitting tolerance, and thus accelerate the molecular breeding process. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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12 pages, 1135 KiB  
Review
Pectin, Lignin and Disease Resistance in Brassica napus L.: An Update
by Duoduo Wang, Qianhui Lu, Shunda Jin, Xiangyun Fan and Hui Ling
Horticulturae 2023, 9(1), 112; https://doi.org/10.3390/horticulturae9010112 - 14 Jan 2023
Cited by 4 | Viewed by 1949
Abstract
The plant cell wall is dynamically modified during host–pathogen interactions and acts as a crucial factor controlling plant immunity. In the context of recently revised models of plant primary cell walls (PCWs), pectin is considered to be important in determining the mechanical properties [...] Read more.
The plant cell wall is dynamically modified during host–pathogen interactions and acts as a crucial factor controlling plant immunity. In the context of recently revised models of plant primary cell walls (PCWs), pectin is considered to be important in determining the mechanical properties of PCWs. A secondary cell wall is present in some cell types and lignin is normally present and acts to strengthen wall rigidity. In this review, we summarize the recent advances in understanding cell-wall-mediated defense responses against pathogens in Brassica napus L. (B. napus). A major part of this response involves pectin and lignin, and these two major cell wall components contribute greatly to immune responses in B. napus. Crosstalk between pectin and lignin metabolism has been detected in B. napus upon pathogen infection, suggesting a synergistic action of pectin and lignin metabolism in regulating cell wall integrity as well as wall-mediated immunity. The transcriptional regulation of cell-wall-mediated immunity in B. napus along with that in Arabidopsis is discussed, and directions for future work are proposed for a better understanding of wall-mediated plant immunity in B. napus. Full article
(This article belongs to the Special Issue Advances in Brassica Crops Genomics and Breeding, 2nd Edition)
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