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Li Y, Luo X, Peng X, Jin Y, Tan H, Wu L, Li J, Pei Y, Xu X, Zhang W. Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.). BMC Genomics 2023; 24:445. [PMID: 37553577 PMCID: PMC10408230 DOI: 10.1186/s12864-023-09528-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.). RESULTS In this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between 'YZH' and 'XHT'. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained. CONCLUSIONS The large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.
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Affiliation(s)
- Yadong Li
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Xiaobo Luo
- Guizhou Province Academy of Agricultural Sciences, Guizhou Institute of Biotechnology, Guiyang, 550003 China
| | - Xiao Peng
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Yueyue Jin
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Huping Tan
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Linjun Wu
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Jingwei Li
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Yun Pei
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Xiuhong Xu
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
| | - Wanping Zhang
- College of Agriculture, Guizhou University, Guiyang, 550003 China
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang, 550003 China
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Singh H, Sekhon BS, Kumar P, Dhall RK, Devi R, Dhillon TS, Sharma S, Khar A, Yadav RK, Tomar BS, Ntanasi T, Sabatino L, Ntatsi G. Genetic Mechanisms for Hybrid Breeding in Vegetable Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:2294. [PMID: 37375919 DOI: 10.3390/plants12122294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
To address the complex challenges faced by our planet such as rapidly changing climate patterns, food and nutritional insecurities, and the escalating world population, the development of hybrid vegetable crops is imperative. Vegetable hybrids could effectively mitigate the above-mentioned fundamental challenges in numerous countries. Utilizing genetic mechanisms to create hybrids not only reduces costs but also holds significant practical implications, particularly in streamlining hybrid seed production. These mechanisms encompass self-incompatibility (SI), male sterility, and gynoecism. The present comprehensive review is primarily focused on the elucidation of fundamental processes associated with floral characteristics, the genetic regulation of floral traits, pollen biology, and development. Specific attention is given to the mechanisms for masculinizing and feminizing cucurbits to facilitate hybrid seed production as well as the hybridization approaches used in the biofortification of vegetable crops. Furthermore, this review provides valuable insights into recent biotechnological advancements and their future utilization for developing the genetic systems of major vegetable crops.
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Affiliation(s)
- Hira Singh
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Bhallan Singh Sekhon
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Pradeep Kumar
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, India
| | - Rajinder Kumar Dhall
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Ruma Devi
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Tarsem Singh Dhillon
- Department of Vegetable Science, Punjab Agriculture University, Ludhiana 141004, India
| | - Suman Sharma
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
| | - Anil Khar
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | | | | | - Theodora Ntanasi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, IeraOdos 75, 11855 Athens, Greece
| | - Leo Sabatino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, IeraOdos 75, 11855 Athens, Greece
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Genomewide Identification and Characterization of the Genes Involved in the Flowering of Cotton. Int J Mol Sci 2022; 23:ijms23147940. [PMID: 35887288 PMCID: PMC9323069 DOI: 10.3390/ijms23147940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 01/27/2023] Open
Abstract
Flowering is a prerequisite for flowering plants to complete reproduction, and flowering time has an important effect on the high and stable yields of crops. However, there are limited reports on flowering-related genes at the genomic level in cotton. In this study, genomewide analysis of the evolutionary relationship of flowering-related genes in different cotton species shows that the numbers of flowering-related genes in the genomes of tetraploid cotton species Gossypium hirsutum and Gossypium barbadense were similar, and that these numbers were approximately twice as much as the number in diploid cotton species Gossypium arboretum. The classification of flowering-related genes shows that most of them belong to the photoperiod and circadian clock flowering pathway. The distribution of flowering-related genes on the chromosomes of the At and Dt subgenomes was similar, with no subgenomic preference detected. In addition, most of the flowering-related core genes in Arabidopsis thaliana had homologs in the cotton genome, but the copy numbers and expression patterns were disparate; moreover, flowering-related genes underwent purifying selection throughout the evolutionary and selection processes. Although the differentiation and reorganization of many key genes of the cotton flowering regulatory network occurred throughout the evolutionary and selection processes, most of them, especially those involved in the important flowering regulatory networks, have been relatively conserved and preferentially selected.
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Crosstalk between auxin and gibberellin during stalk elongation in flowering Chinese cabbage. Sci Rep 2021; 11:3976. [PMID: 33597591 PMCID: PMC7889655 DOI: 10.1038/s41598-021-83519-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 02/04/2021] [Indexed: 11/08/2022] Open
Abstract
Plant growth and development are tightly regulated by phytohormones. However, little is known about the interaction between auxin and gibberellin acid (GA) during flower stalk elongation and how it is directly related to organ formation. Therefore, the effects of indole acetic acid (IAA) and GA3 treatments and their interaction on flower stalk elongation in flowering Chinese cabbage were investigated. The growth of flowering Chinese cabbage is regulated by IAA and GA3, and the opposite results were observed after treatments with uniconazole (GA synthesis inhibitor) and N-1-naphthylphthalamic acid (NPA) (auxin transport inhibitor). Anatomical analysis of the pith region in stalks revealed that IAA promoted expansion via signal transduction and transport pathways. GA3 regulated the elongation of flower stalks by controlling GA synthesis and partially controlling the IAA signaling pathway. GA3 also had a stronger effect on stalk elongation than IAA. The results of qRT-PCR and histological analysis revealed that GA3 and IAA induced the expansion of cell walls by activating the expression of genes encoding cell wall structural proteins such as Expansin (EXP). These findings provide new insights into the mechanism of stalk formation regulated by the combination of IAA and GA3.
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Akter A, Itabashi E, Kakizaki T, Okazaki K, Dennis ES, Fujimoto R. Genome Triplication Leads to Transcriptional Divergence of FLOWERING LOCUS C Genes During Vernalization in the Genus Brassica. FRONTIERS IN PLANT SCIENCE 2020; 11:619417. [PMID: 33633752 PMCID: PMC7900002 DOI: 10.3389/fpls.2020.619417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/29/2020] [Indexed: 05/17/2023]
Abstract
The genus Brassica includes oil crops, vegetables, condiments, fodder crops, and ornamental plants. Brassica species underwent a whole genome triplication event after speciation between ancestral species of Brassica and closely related genera including Arabidopsis thaliana. Diploid species such as Brassica rapa and Brassica oleracea have three copies of genes orthologous to each A. thaliana gene, although deletion in one or two of the three homologs has occurred in some genes. The floral transition is one of the crucial events in a plant's life history, and time of flowering is an important agricultural trait. There is a variation in flowering time within species of the genus Brassica, and this variation is largely dependent on a difference in vernalization requirements. In Brassica, like in A. thaliana, the key gene of vernalization is FLOWERING LOCUS C (FLC). In Brassica species, the vernalization response including the repression of FLC expression by cold treatment and the enrichment of the repressive histone modification tri-methylated histone H3 lysine 27 (H3K27me3) at the FLC locus is similar to A. thaliana. B. rapa and B. oleracea each have four paralogs of FLC, and the allotetraploid species, Brassica napus, has nine paralogs. The increased number of paralogs makes the role of FLC in vernalization more complicated; in a single plant, paralogs vary in the expression level of FLC before and after vernalization. There is also variation in FLC expression levels between accessions. In this review, we focus on the regulatory circuits of the vernalization response of FLC expression in the genus Brassica.
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Affiliation(s)
- Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Department of Horticulture, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Tsu, Japan
| | - Tomohiro Kakizaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Tsu, Japan
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- School of Life Sciences, Faculty of Science, University of Technology, Sydney, Broadway, NSW, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- *Correspondence: Ryo Fujimoto,
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Transcriptional Structure of Petunia Clock in Leaves and Petals. Genes (Basel) 2019; 10:genes10110860. [PMID: 31671570 PMCID: PMC6895785 DOI: 10.3390/genes10110860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/20/2023] Open
Abstract
The plant circadian clock coordinates environmental signals with internal processes including secondary metabolism, growth, flowering, and volatile emission. Plant tissues are specialized in different functions, and petals conceal the sexual organs while attracting pollinators. Here we analyzed the transcriptional structure of the petunia (Petunia x hybrida) circadian clock in leaves and petals. We recorded the expression of 13 clock genes in petunia under light:dark (LD) and constant darkness (DD). Under light:dark conditions, clock genes reached maximum expression during the light phase in leaves and the dark period in petals. Under free running conditions of constant darkness, maximum expression was delayed, especially in petals. Interestingly, the rhythmic expression pattern of PhLHY persisted in leaves and petals in LD and DD. Gene expression variability differed among leaves and petals, time of day and photoperiod. The transcriptional noise was higher especially in leaves under constant darkness. We found that PhPRR7, PhPRR5, and PhGI paralogs showed changes in gene structure including exon number and deletions of CCT domain of the PRR family. Our results revealed that petunia petals presented a specialized clock.
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The role of FRIGIDA and FLOWERING LOCUS C genes in flowering time of Brassica rapa leafy vegetables. Sci Rep 2019; 9:13843. [PMID: 31554847 PMCID: PMC6761103 DOI: 10.1038/s41598-019-50122-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/03/2019] [Indexed: 02/01/2023] Open
Abstract
There is a wide variation of flowering time among lines of Brassica rapa L. Most B. rapa leafy (Chinese cabbage etc.) or root (turnip) vegetables require prolonged cold exposure for flowering, known as vernalization. Premature bolting caused by low temperature leads to a reduction in the yield/quality of these B. rapa vegetables. Therefore, high bolting resistance is an important breeding trait, and understanding the molecular mechanism of vernalization is necessary to achieve this goal. In this study, we demonstrated that BrFRIb functions as an activator of BrFLC in B. rapa. We showed a positive correlation between the steady state expression levels of the sum of the BrFLC paralogs and the days to flowering after four weeks of cold treatment, suggesting that this is an indicator of the vernalization requirement. We indicate that BrFLCs are repressed by the accumulation of H3K27me3 and that the spreading of H3K27me3 promotes stable FLC repression. However, there was no clear relationship between the level of H3K27me3 in the BrFLC and the vernalization requirement. We also showed that if there was a high vernalization requirement, the rate of repression of BrFLC1 expression following prolonged cold treatments was lower.
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Kim J, Manivannan A, Kim DS, Lee ES, Lee HE. Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering in Raphanus sativus in-bred lines for marker-assisted backcross breeding. HORTICULTURE RESEARCH 2019; 6:120. [PMID: 31700647 PMCID: PMC6823433 DOI: 10.1038/s41438-019-0200-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/08/2023]
Abstract
The sequencing of radish genome aids in the better understanding and tailoring of traits associated with economic importance. In order to accelerate the genomics assisted breeding and genetic selection, transcriptomes of 33 radish inbred lines with diverse traits were sequenced for the development of single nucleotide polymorphic (SNP) markers. The sequence reads ranged from 2,560,543,741 bp to 20,039,688,139 bp with the GC (%) of 47.80-49.34 and phred quality score (Q30) of 96.47-97.54%. A total of 4951 polymorphic SNPs were identified among the accessions after stringent filtering and 298 SNPs with efficient marker assisted backcross breeding (MAB) markers were generated from the polymorphic SNPs. Further, functional annotations of SNPs revealed the effects and importance of the SNPs identified in the flowering process. The SNPs were predominantly associated with the four major flowering related transcription factors such as MYB, MADS box (AG), AP2/EREB, and bHLH. In addition, SNPs in the vital flowering integrator gene (FT) and floral repressors (EMBRYONIC FLOWER 1, 2, and FRIGIDA) were identified among the radish inbred lines. Further, 50 SNPs were randomly selected from 298 SNPs and validated using Kompetitive Allele Specific PCR genotyping system (KASP) in 102 radish inbred lines. The homozygosity of the inbred lines varied from 56 to 96% and the phylogenetic analysis resulted in the clustering of inbred lines into three subgroups. Taken together, the SNP markers identified in the present study can be utilized for the discrimination, seed purity test, and adjusting parental combinations for breeding in radish.
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Affiliation(s)
- Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Eun-Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
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Li H, Fan Y, Yu J, Chai L, Zhang J, Jiang J, Cui C, Zheng B, Jiang L, Lu K. Genome-Wide Identification of Flowering-Time Genes in Brassica Species and Reveals a Correlation between Selective Pressure and Expression Patterns of Vernalization-Pathway Genes in Brassica napus. Int J Mol Sci 2018; 19:E3632. [PMID: 30453667 PMCID: PMC6274771 DOI: 10.3390/ijms19113632] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/11/2018] [Accepted: 11/14/2018] [Indexed: 12/28/2022] Open
Abstract
Flowering time is a key agronomic trait, directly influencing crop yield and quality. Many flowering-time genes have been identified and characterized in the model plant Arabidopsis thaliana; however, these genes remain uncharacterized in many agronomically important Brassica crops. In this study, we identified 1064, 510, and 524 putative orthologs of A. thaliana flowering-time genes from Brassica napus, Brassica rapa, and Brassica oleracea, respectively, and found that genes involved in the aging and ambient temperature pathways were fewer than those in other flowering pathways. Flowering-time genes were distributed mostly on chromosome C03 in B. napus and B. oleracea, and on chromosome A09 in B. rapa. Calculation of non-synonymous (Ka)/synonymous substitution (Ks) ratios suggested that flowering-time genes in vernalization pathways experienced higher selection pressure than those in other pathways. Expression analysis showed that most vernalization-pathway genes were expressed in flowering organs. Approximately 40% of these genes were highly expressed in the anther, whereas flowering-time integrator genes were expressed in a highly organ-specific manner. Evolutionary selection pressures were negatively correlated with the breadth and expression levels of vernalization-pathway genes. These findings provide an integrated framework of flowering-time genes in these three Brassica crops and provide a foundation for deciphering the relationship between gene expression patterns and their evolutionary selection pressures in Brassica napus.
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Affiliation(s)
- Haojie Li
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Liang Chai
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Jingfang Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Jun Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Benchuan Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Liangcai Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
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