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22 pages, 7224 KiB

Open AccessFeature PaperArticle

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

by Tania Kartseva, Vladimir Aleksandrov, Ahmad M. Alqudah, Mian Abdur Rehman Arif, Konstantina Kocheva, Dilyana Doneva, Katelina Prokopova, Andreas Börner and Svetlana Misheva

Plants 2024, 13(8), 1084; https://doi.org/10.3390/plants13081084 - 12 Apr 2024

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Abstract

Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits—grain protein content (GPC) and thousand kernel weight (TKW)—across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. [...] Read more.

Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits—grain protein content (GPC) and thousand kernel weight (TKW)—across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, and genotypic data from the 25K Infinium iSelect array. As a result, we detected 16 quantitative trait nucleotides (QTNs) associated with GPC and 15 associated with TKW, all of which passed the false discovery rate threshold. Seven loci favorably influenced GPC, resulting in an increase of 1.4% to 8.1%, while four loci had a positive impact on TKW with increases ranging from 1.9% to 8.4%. While some loci confirmed previously published associations, four QTNs linked to GPC on chromosomes 2A, 7A, and 7B, as well as two QTNs related to TKW on chromosomes 1B and 6A, may represent novel associations. Annotations for proteins involved in the senescence-associated nutrient remobilization and in the following buildup of resources required for seed germination have been found for selected putative candidate genes. These include genes coding for storage proteins, cysteine proteases, cellulose-synthase, alpha-amylase, transcriptional regulators, and F-box and RWP-RK family proteins. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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13 pages, 7376 KiB

Open AccessArticle

Evaluation of Grain-Filling-Related Traits Using Taichung 65 x DV85 Chromosome Segment Substitution Lines (TD-CSSLs) of Rice

by Abebaw Dessie Mabreja, Vincent Pamugas Reyes, Than Kutay Soe, Kodai Shimakawa, Daigo Makihara, Shunsaku Nishiuchi and Kazuyuki Doi

Plants 2024, 13(2), 289; https://doi.org/10.3390/plants13020289 - 18 Jan 2024

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Abstract

Grain yield of rice consists of sink capacity and grain filling. There are some genes known to contribute to sink capacity, but few genes associated with grain filling are known. We conducted a genetic analysis on yield-related traits by using a chromosome segment [...] Read more.

Grain yield of rice consists of sink capacity and grain filling. There are some genes known to contribute to sink capacity, but few genes associated with grain filling are known. We conducted a genetic analysis on yield-related traits by using a chromosome segment substitution line population that have introgression from DV85, an aus variety of rice, in the background of T65, a japonica variety. Refined whole-genome genotypes of the 43 TD-CSSLs were obtained by genotyping-by-sequencing. The effects of previously detected quantitative trait loci (QTLs), qNSC1 and qNSC2, were confirmed by the amount of non-structural carbohydrate (NSC) at 5 days after heading (DAH). The CSSL for qSWTR11, the QTL for decrease in shoot weight during the maturity stage, showed the highest NSC at 5 DAH and lowest at 35 DAH. The brown rice yield of these lines were not stably significant. Most of the sink-related traits correlated between the 2 tested years, but most of the grain-filling traits did not show correlation between the 2 years. Correlation analysis revealed that the sink capacity is stable and primarily determines the yield, and grain filling is more affected by the environment. In addition, biomass production before heading and during the maturity stage contributes to higher yield in TD-CSSLs, and the amount of translocation of stem reserve does not affect much to the yield. We conclude that higher NSC at the heading stage and rapid decrease in shoot biomass during the maturity stage did not directly contribute to the yield formation in the japonica genetic background. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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14 pages, 4966 KiB

Open AccessArticle

The Small Auxin-Up RNA SAUR10 Is Involved in the Promotion of Seedling Growth in Rice

by Xiaolong Huang, Zhanhua Lu, Lisheng Zhai, Na Li and Huiqing Yan

Plants 2023, 12(22), 3880; https://doi.org/10.3390/plants12223880 - 17 Nov 2023

Cited by 1 | Viewed by 975

Abstract

Small auxin-up-regulated RNAs (SAURs) are genes rapidly activated in response to auxin hormones, significantly affecting plant growth and development. However, there is limited information available about the specific functions of SAURs in rice due to the presence of extensive redundant genes. In this [...] Read more.

Small auxin-up-regulated RNAs (SAURs) are genes rapidly activated in response to auxin hormones, significantly affecting plant growth and development. However, there is limited information available about the specific functions of SAURs in rice due to the presence of extensive redundant genes. In this study, we found that OsSAUR10 contains a conserved downstream element in its 3′ untranslated region that causes its transcripts to be unstable, ultimately leading to the immediate degradation of the mRNA in rice. In our investigation, we discovered that OsSAUR10 is located in the plasma membrane, and its expression is regulated in a tissue-specific, developmental, and hormone-dependent manner. Additionally, we created ossaur10 mutants using the CRISPR/Cas9 method, which resulted in various developmental defects such as dwarfism, narrow internodes, reduced tillers, and lower yield. Moreover, histological observation comparing wild-type and two ossaur10 mutants revealed that OsSAUR10 was responsible for cell elongation. However, overexpression of OsSAUR10 resulted in similar phenotypes to the wild-type. Our research also indicated that OsSAUR10 plays a role in regulating the expression of two groups of genes involved in auxin biosynthesis (OsYUCCAs) and auxin polar transport (OsPINs) in rice. Thus, our findings suggest that OsSAUR10 acts as a positive plant growth regulator by contributing to auxin biosynthesis and polar transport. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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15 pages, 2347 KiB

Open AccessArticle

QTL Verification and Candidate Gene Screening of Fiber Quality and Lint Percentage in the Secondary Segregating Population of Gossypium hirsutum

by Ruixian Liu, Minghui Zhu, Yongqiang Shi, Junwen Li, Juwu Gong, Xianghui Xiao, Quanjia Chen, Youlu Yuan and Wankui Gong

Plants 2023, 12(21), 3737; https://doi.org/10.3390/plants12213737 - 31 Oct 2023

Viewed by 1081

Abstract

Fiber quality traits, especially fiber strength, length, and micronaire (FS, FL, and FM), have been recognized as critical fiber attributes in the textile industry, while the lint percentage (LP) was an important indicator to evaluate the cotton lint yield. So far, the genetic [...] Read more.

Fiber quality traits, especially fiber strength, length, and micronaire (FS, FL, and FM), have been recognized as critical fiber attributes in the textile industry, while the lint percentage (LP) was an important indicator to evaluate the cotton lint yield. So far, the genetic mechanism behind the formation of these traits is still unclear. Quantitative trait loci (QTL) identification and candidate gene validation provide an effective methodology to uncover the genetic and molecular basis of FL, FS, FM, and LP. A previous study identified three important QTL/QTL cluster loci, harboring at least one of the above traits on chromosomes A01, A07, and D12 via a recombinant inbred line (RIL) population derived from a cross of Lumianyan28 (L28) × Xinluzao24 (X24). A secondary segregating population (F₂) was developed from a cross between L28 and an RIL, RIL40 (L28 × RIL40). Based on the population, genetic linkage maps of the previous QTL cluster intervals on A01 (6.70–10.15 Mb), A07 (85.48–93.43 Mb), and D12 (0.40–1.43 Mb) were constructed, which span 12.25, 15.90, and 5.56 cM, with 2, 14, and 4 simple sequence repeat (SSR) and insertion/deletion (Indel) markers, respectively. QTLs of FL, FS, FM, and LP on these three intervals were verified by composite interval mapping (CIM) using WinQTL Cartographer 2.5 software via phenotyping of F₂ and its derived F_2:3 populations. The results validated the previous primary QTL identification of FL, FS, FM, and LP. Analysis of the RNA-seq data of the developing fibers of L28 and RIL40 at 10, 20, and 30 days post anthesis (DPA) identified seven differentially expressed genes (DEGs) as potential candidate genes. qRT-PCR verified that five of them were consistent with the RNA-seq result. These genes may be involved in regulating fiber development, leading to the formation of FL, FS, FM, and LP. This study provides an experimental foundation for further exploration of these functional genes to dissect the genetic mechanism of cotton fiber development. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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16 pages, 5901 KiB

Open AccessArticle

Metabolic Responses to Manganese Toxicity in Soybean Roots and Leaves

by Yanyan Wang, Jianyu Li, Yuhu Pan, Jingye Chen and Ying Liu

Plants 2023, 12(20), 3615; https://doi.org/10.3390/plants12203615 - 19 Oct 2023

Cited by 2 | Viewed by 1351

Abstract

Soybean is one of the most crucial beans in the world. Although Mn (manganese) is a kind of important nutritive element helpful to plant growth and health, excess Mn is harmful to crops. Nevertheless, the effect of Mn toxicity on soybean roots and [...] Read more.

Soybean is one of the most crucial beans in the world. Although Mn (manganese) is a kind of important nutritive element helpful to plant growth and health, excess Mn is harmful to crops. Nevertheless, the effect of Mn toxicity on soybean roots and leaves metabolism is still not clear. To explore this, water culture experiments were conducted on the development, activity of enzyme, and metabolic process of soybeans under varying levels of Mn treatment (5 and 100 μM). Compared with the control, the soybeans under Mn stress showed inhibited growth and development. Moreover, the activity of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX), and the soluble protein content in leaves and roots of soybean were all increased. However, soluble sugar and proline contents in soybean roots and leaves showed the opposite trend. In addition, the Mg (magnesium) and Fe (iron) ion contents in soybean leaves significantly decreased, and the Mn ion content greatly increased. In roots, the Mn and Fe ion content increased, whereas the Mg ion content decreased. Furthermore, the metabolomic analysis based on nontargeted liquid chromatography–mass spectrometry identified 136 and 164 differential metabolites (DMs) that responded to Mn toxicity in roots and leaves of soybean, respectively. These DMs might participate in five different primary metabolic pathways in soybean leaves and roots, suggesting that soybean leaves and roots demonstrate different kinds of reactions in response to Mn toxicity. These findings indicate that Mn toxicity will result in enzymes activity being changed and the metabolic pathway being seriously affected, hence inhibiting the development of soybean. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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15 pages, 4853 KiB

Open AccessArticle

Flavonoid Biosynthesis Pathway May Indirectly Affect Outcrossing Rate of Cytoplasmic Male–Sterile Lines of Soybean

by Chunjing Lin, Yuetong Duan, Rong Li, Pengnian Wang, Yanyan Sun, Xiaoyang Ding, Jingyong Zhang, Hao Yan, Wei Zhang, Bao Peng, Limei Zhao and Chunbao Zhang

Plants 2023, 12(19), 3461; https://doi.org/10.3390/plants12193461 - 01 Oct 2023

Viewed by 1460

Abstract

(1) Background: Cytoplasmic male sterility (CMS) is important for exploiting heterosis. Soybean (Glycine max L.) has a low outcrossing rate that is detrimental for breeding sterile lines and producing hybrid seeds. Therefore, the molecular mechanism controlling the outcrossing rate should be elucidated [...] Read more.

(1) Background: Cytoplasmic male sterility (CMS) is important for exploiting heterosis. Soybean (Glycine max L.) has a low outcrossing rate that is detrimental for breeding sterile lines and producing hybrid seeds. Therefore, the molecular mechanism controlling the outcrossing rate should be elucidated to increase the outcrossing rate of soybean CMS lines; (2) Methods: The male–sterile soybean lines JLCMS313A (with a high outcrossing rate; HL) and JLCMS226A (with a low outcrossing rate; LL) were used for a combined analysis of the transcriptome (RNA–seq) and the targeted phenol metabolome; (3) Results: The comparison between HL and LL detected 5946 differentially expressed genes (DEGs) and 81 phenolic metabolites. The analysis of the DEGs and differentially abundant phenolic metabolites identified only one common KEGG pathway related to flavonoid biosynthesis. The qRT–PCR expression for eight DEGs was almost consistent with the transcriptome data. The comparison of the cloned coding sequence (CDS) regions of the SUS, FLS, UGT, and F3H genes between HL and LL revealed seven single nucleotide polymorphisms (SNPs) only in the F3H CDS. Moreover, five significant differentially abundant phenolic metabolites between HL and LL were associated with flavonoid metabolic pathways. Finally, on the basis of the SNPs in the F3H CDS, one derived cleaved amplified polymorphic sequence (dCAPS) marker was developed to distinguish between HL and LL soybean lines; (4) Conclusions: The flavonoid biosynthesis pathway may indirectly affect the outcrossing rate of CMS sterile lines in soybean. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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16 pages, 3012 KiB

Open AccessArticle

A New Function of MbIAA19 Identified to Modulate Malus Plants Dwarfing Growth

by Jian Wang, Li Xue, Xiao Zhang, Yali Hou, Ke Zheng, Dongxu Fu and Wenxuan Dong

Plants 2023, 12(17), 3097; https://doi.org/10.3390/plants12173097 - 29 Aug 2023

Cited by 1 | Viewed by 926

Abstract

The primary determinants of apple (Malus) tree architecture include plant height and internode length, which are the significant criteria for evaluating apple dwarf rootstocks. Plant height and internode length are predominantly governed by phytohormones. In this study, we aimed to assess [...] Read more.

The primary determinants of apple (Malus) tree architecture include plant height and internode length, which are the significant criteria for evaluating apple dwarf rootstocks. Plant height and internode length are predominantly governed by phytohormones. In this study, we aimed to assess the mechanisms underlying dwarfism in a mutant of Malus baccata. M. baccata dwarf mutant (Dwf) was previously obtained through natural mutation. It has considerably reduced plant height and internode length. A comparative transcriptome analysis of wild-type (WT) and Dwf mutant was performed to identify and annotate the differentially expressed genes responsible for the Dwf phenotype using RNA-seq and GO and KEGG pathway enrichment analyses. Multiple DEGs involved in hormone signaling pathways, particularly auxin signaling pathways, were identified. Moreover, the levels of endogenous indole-3-acetic acid (IAA) were lower in Dwf mutant than in WT. The Aux/IAA transcription factor gene MbIAA19 was downregulated in Dwf mutant due to a single nucleotide sequence change in its promoter. Genetic transformation assay demonstrated strong association between MbIAA19 and the dwarf phenotype. RNAi-IAA19 lines clearly exhibited reduced plant height, internode length, and endogenous IAA levels. Our study revealed that MbIAA19 plays a role in the regulation of dwarfism and endogenous IAA levels in M. baccata. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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16 pages, 3088 KiB

Open AccessArticle

Supplementing the Nuclear-Encoded PSII Subunit D1 Induces Dramatic Metabolic Reprogramming in Flag Leaves during Grain Filling in Rice

by Ai-Zhen Sun, Juan-Hua Chen, Xue-Qi Jin, Han Li and Fang-Qing Guo

Plants 2023, 12(16), 3009; https://doi.org/10.3390/plants12163009 - 21 Aug 2023

Viewed by 914

Abstract

Our previous study has demonstrated that the nuclear-origin supplementation of the PSII core subunit D1 protein stimulates growth and increases grain yields in transgenic rice plants by enhancing photosynthetic efficiency. In this study, the underlying mechanisms have been explored regarding how the enhanced [...] Read more.

Our previous study has demonstrated that the nuclear-origin supplementation of the PSII core subunit D1 protein stimulates growth and increases grain yields in transgenic rice plants by enhancing photosynthetic efficiency. In this study, the underlying mechanisms have been explored regarding how the enhanced photosynthetic capacity affects metabolic activities in the transgenic plants of rice harboring the integrated transgene RbcS^PTP-OspsbA cDNA, cloned from rice, under control of the AtHsfA2 promoter and N-terminal fused with the plastid-transit peptide sequence (PTP) cloned from the AtRbcS. Here, a comparative metabolomic analysis was performed using LC-MS in flag leaves of the transgenic rice plants during the grain-filling stage. Critically, the dramatic reduction in the quantities of nucleotides and certain free amino acids was detected, suggesting that the increased photosynthetic assimilation and grain yield in the transgenic plants correlates with the reduced contents of free nucleotides and the amino acids such as glutamine and glutamic acid, which are cellular nitrogen sources. These results suggest that enhanced photosynthesis needs consuming more free nucleotides and nitrogen sources to support the increase in biomass and yields, as exhibited in transgenic rice plants. Unexpectedly, dramatic changes were measured in the contents of flavonoids in the flag leaves, suggesting that a tight and coordinated relationship exists between increasing photosynthetic assimilation and flavonoid biosynthesis. Consistent with the enhanced photosynthetic efficiency, the substantial increase was measured in the content of starch, which is the primary product of the Calvin–Benson cycle, in the transgenic rice plants under field growth conditions. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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17 pages, 4355 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the VILLIN Gene Family in Soybean

by Yueqiong Zhou, Liangliang He, Shaoli Zhou, Qing Wu, Xuan Zhou, Yawen Mao, Baolin Zhao, Dongfa Wang, Weiyue Zhao, Ruoruo Wang, Huabin Hu and Jianghua Chen

Plants 2023, 12(11), 2101; https://doi.org/10.3390/plants12112101 - 25 May 2023

Cited by 2 | Viewed by 1370

Abstract

The VILLIN (VLN) protein is an important regulator of the actin cytoskeleton, which orchestrates many developmental processes and participates in various biotic and abiotic responses in plants. Although the VLN gene family and their potential functions have been analyzed in several plants, knowledge [...] Read more.

The VILLIN (VLN) protein is an important regulator of the actin cytoskeleton, which orchestrates many developmental processes and participates in various biotic and abiotic responses in plants. Although the VLN gene family and their potential functions have been analyzed in several plants, knowledge of VLN genes in soybeans and legumes remains rather limited. In this study, a total of 35 VLNs were characterized from soybean and five related legumes. Combining with the VLN sequences from other nine land plants, we categorized the VLN gene family into three groups according to phylogenetic relationships. Further detailed analysis of the soybean VLNs indicated that the ten GmVLNs were distributed on 10 of the 20 chromosomes, and their gene structures and protein motifs showed high group specificities. The expression pattern analysis suggested that most GmVLNs are widely expressed in various tissues, but three members have a very high level in seeds. Moreover, we observed that the cis−elements enriched in the promoters of GmVLNs are mainly related to abiotic stresses, hormone signals, and developmental processes. The largest number of cis−elements were associated with light responses, and two GmVLNs, GmVLN5a, and GmVLN5b were significantly increased under the long light condition. This study not only provides some basic information about the VLN gene family but also provides a good reference for further characterizing the diverse functions of VLN genes in soybeans. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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Review

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14 pages, 1848 KiB

Open AccessReview

Advancements in Rice Leaf Development Research

by Xiaoting Gong, Jian Chen, Yanxin Chen, Ying He and Dagang Jiang

Plants 2024, 13(6), 904; https://doi.org/10.3390/plants13060904 - 21 Mar 2024

Viewed by 653

Abstract

Rice leaf morphology is a pivotal component of the ideal plant architecture, significantly impacting rice yield. The process of leaf development unfolds through three distinct stages: the initiation of leaf primordia, the establishment and maintenance of polarity, and leaf expansion. Genes regulating leaf [...] Read more.

Rice leaf morphology is a pivotal component of the ideal plant architecture, significantly impacting rice yield. The process of leaf development unfolds through three distinct stages: the initiation of leaf primordia, the establishment and maintenance of polarity, and leaf expansion. Genes regulating leaf morphology encompass transcription factors, hormones, and miRNAs. An in-depth synthesis and categorization of genes associated with leaf development, particularly those successfully cloned, hold paramount importance in unraveling the complexity of rice leaf development. Furthermore, it provides valuable insights into the potential for molecular-level manipulation of rice leaf types. This comprehensive review consolidates the stages of rice leaf development, the genes involved, molecular regulatory pathways, and the influence of plant hormones. Its objective is to establish a foundational understanding of the creation of ideal rice leaf forms and their practical application in molecular breeding. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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22 pages, 4374 KiB

Open AccessSystematic Review

Plant Serpins: Potential Inhibitors of Serine and Cysteine Proteases with Multiple Functions

by Monaliza Macêdo Ferreira, Ariana Silva Santos, Adriadna Souza Santos, Maria Zugaib and Carlos Priminho Pirovani

Plants 2023, 12(20), 3619; https://doi.org/10.3390/plants12203619 - 19 Oct 2023

Cited by 2 | Viewed by 1086

Abstract

Plant serpins are a superfamily of protein inhibitors that have been continuously studied in different species and have great biotechnological potential. However, despite ongoing studies with these inhibitors, the biological role of this family in the plant kingdom has not yet been fully [...] Read more.

Plant serpins are a superfamily of protein inhibitors that have been continuously studied in different species and have great biotechnological potential. However, despite ongoing studies with these inhibitors, the biological role of this family in the plant kingdom has not yet been fully clarified. In order to obtain new insights into the potential of plant serpins, this study presents the first systematic review of the topic, whose main objective was to scrutinize the published literature to increase knowledge about this superfamily. Using keywords and the eligibility criteria defined in the protocol, we selected studies from the Scopus, PubMed, and Web of Science databases. According to the eligible studies, serpins inhibit different serine and non-serine proteases from plants, animals, and pathogens, and their expression is affected by biotic and abiotic stresses. Moreover, serpins like AtSerpin1, OSP-LRS, MtSer6, AtSRP4, AtSRP5, and MtPiI4, act in resistance and are involved in stress-induced cell death in the plant. Also, the system biology analysis demonstrates that serpins are related to proteolysis control, cell regulation, pollen development, catabolism, and protein dephosphorylation. The information systematized here contributes to the design of new studies of plant serpins, especially those aimed at exploring their biotechnological potential. Full article

(This article belongs to the Special Issue Crop Breeding: Molecular Genetics and Genomics)

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