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Abstract
Fluorescent in situ hybridization (FISH) is a powerful cytogenetic technique for identifying chromosomes and mapping specific genes and DNA sequences on individual chromosomes. Genomic in situ hybridization (GISH) and multicolor FISH (mc-FISH) represent two special types of FISH techniques. Both GISH and mc-FISH experiments have general steps and features of FISH, including chromosome preparation, probe labeling, blocking DNA preparation, target-probe DNA hybridization, post-hybridization washes, and hybridization signal detection. Specifically, GISH uses total genomic DNA from two species as probe and blocking DNA, respectively, and it can differentiate chromosomes from different genomes. The mc-FISH takes advantage of simultaneous hybridization of several DNA probes labeled by different fluorochromes to different targets on the same chromosome sample. Hybridization signals from different probes are detected using different fluorescence filter sets. Multicolor FISH can provide more structural details for target chromosomes than single-color FISH. In this chapter, we present the general experimental procedures for these two techniques with specific details in the critical steps we have modified in our laboratories.
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Affiliation(s)
- Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102, USA.
| | - Zhao Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Zhixia Niu
- USDA-ARS, Cereal Crops Research Unit, Northern Crop Science Laboratory, 1605 Albrecht Blvd. North, Fargo, ND, 58102, USA
| | - Chao-Chien Jan
- USDA-ARS, Sunflower and Plant Biology Research Unit, Northern Crop Science Laboratory, Fargo, ND, 58102, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
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Yu G, Klindworth DL, Friesen TL, Faris JD, Zhong S, Rasmussen JB, Xu SS. Development of a diagnostic co-dominant marker for stem rust resistance gene Sr47 introgressed from Aegilops speltoides into durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2367-2374. [PMID: 26260850 DOI: 10.1007/s00122-015-2590-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
A robust and diagnostic STS marker for stem rust resistance gene Sr47 was developed and validated for marker-assisted selection. Stem rust (caused by Puccinia graminis f. sp. tritici, Pgt) resistance gene Sr47, originally transferred from Aegilops speltoides to durum wheat (Triticum turgidum subsp. durum) line DAS15, confers a high level of resistance to Pgt race TTKSK (Ug99). Recently, the durum Rusty 5D(5B) substitution line was used to reduce the Ae. speltoides segment, and the resulting lines had Sr47 on small Ae. speltoides segments on wheat chromosome arm 2BL. The objective of this study was to develop a robust marker for marker-assisted selection of Sr47. A 200-kb segment of the Brachypodium distachyon genome syntenic with the Sr47 region was used to identify wheat expressed sequence tags (ESTs) homologous to the B. distachyon genes. The wheat EST sequences were then used to develop sequence-tagged site (STS) markers. By analyzing the markers for polymorphism between Rusty and DAS15, we identified a co-dominant STS marker, designated as Xrwgs38, which amplified 175 and 187 bp fragments from wheat chromosome 2B and Ae. speltoides chromosome 2S segments, respectively. The marker co-segregated with the Ae. speltoides segments carrying Sr47 in the families from four BC2F1 plants, including the parent plants for durum lines RWG35 and RWG36 with the pedigree of Rusty/3/Rusty 5D(5B)/DAS15//47-1 5D(5B). Analysis of 62 durum and common wheat cultivars/lines lacking the Sr47 segment indicated that they all possessed the 175-bp allele of Xrwgs38, indicating that it was diagnostic for the small Ae. speltoides segment carrying Sr47. This study demonstrated that Xrwgs38 will facilitate the selection of Sr47 in durum and common wheat breeding.
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Affiliation(s)
- Guotai Yu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Daryl L Klindworth
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, USDA-ARS, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Timothy L Friesen
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, USDA-ARS, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Justin D Faris
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, USDA-ARS, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Jack B Rasmussen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Steven S Xu
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, USDA-ARS, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.
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Pirseyedi SM, Somo M, Poudel RS, Cai X, McCallum B, Saville B, Fetch T, Chao S, Marais F. Characterization of recombinants of the Aegilops peregrina-derived Lr59 translocation of common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2403-14. [PMID: 26239411 DOI: 10.1007/s00122-015-2594-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/23/2015] [Indexed: 05/26/2023]
Abstract
A compensating, recombined Lr59 translocation with greatly reduced alien chromatin was identified. Microsatellite locus Xdupw217 occurs within the remaining segment and can be used as a co-dominant marker for Lr59. In earlier studies, leaf rust (caused by Puccinia triticina Eriks.) resistance gene Lr59 was transferred from Aegilops peregrina (Hackel) Maire et Weiler to chromosome arm 1AL of common wheat (Triticum aestivum L.). The resistance gene was then genetically mapped on the translocated chromosome segment following homoeologous pairing induction. Eight recombinants that retained the least alien chromatin apparently resulted from crossover within a terminal region of the translocation that was structurally different from 1AL. These recombinants could not be differentiated by size, and it was not clear whether they were compensating in nature. The present study determined that the distal part of the original translocation has group 6 chromosome homoeology and a 6BS telomere (with the constitution of the full translocation chromosome being 1AS·1L(P)·6S(P) ·6BS). During the allosyndetic pairing induction experiment to map and shorten the full size translocation, a low frequency of quadrivalents involving 1A, the 1A translocation, and two 6B chromosomes was likely formed. Crossover within such quadrivalents apparently produced comparatively small compensating alien chromatin inserts within the 6BS satellite region on chromosome 6B of seven of the eight recombinants. It appears that the Gli-B2 storage protein locus on 6BS has not been affected by the recombination events, and the translocations are therefore not expected to affect baking quality. Simple sequence repeat marker results showed that Lr59-151 is the shortest recombinant, and it will therefore be used in breeding. Marker DUPW217 detects a homoeo-allele within the remaining alien chromatin that can be used for marker-assisted selection of Lr59.
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Affiliation(s)
| | - Mohamed Somo
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Roshan Sharma Poudel
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | | | - Barry Saville
- Trent University, Peterborough, ON, K9J 7B8C, Canada
| | | | - Shiaoman Chao
- Agricultural Research Service Biosciences Research Laboratory, US Department of Agriculture, Fargo, ND, 58102, USA
| | - Francois Marais
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
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Kielsmeier-Cook J, Danilova TV, Friebe B, Rouse MN. Resistance to the Ug99 Race Group of Puccinia graminis f. sp. tritici in Wheat-Intra/intergeneric Hybrid Derivatives. PLANT DISEASE 2015; 99:1317-1325. [PMID: 30690994 DOI: 10.1094/pdis-09-14-0922-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
New races of Puccinia graminis f. sp. tritici, the causal agent of stem rust, threaten global wheat production. In particular, races belonging to the Ug99 race group significantly contribute to yield loss in several African nations. Genetic resistance remains the most effective means of controlling this disease. A collection of 546 wheat-intra- and intergeneric hybrids developed by W. J. Sando (United States Department of Agriculture, Beltsville, MD) was screened with eight races of P. graminis f. sp. tritici, including races TTKSK, TTKST, TTTSK, TRTTF, TTTTF, TPMKC, RKQQC, and QTHJC. There were 152 accessions resistant to one or more races and 29 accessions resistant to TTKSK, TTKST, and TTTSK. Of these 29 accessions, 9 were resistant to all races, 14 had infection type patterns that were indistinguishable from cultivars possessing Sr9h and Sr42, 2 were indistinguishable from accessions with SrTmp, and 4 did not display resistant patterns of accessions with any known Sr gene. Three accessions (604981, 605286, and 611932) characterized cytogenetically were disomic substitution lines, each with a single Thinopyrum ponticum chromosome pair. One accession (606057) was a disomic substitution or addition line with two pairs of T. ponticum chromosomes. In total, seven accessions are postulated to contain novel stem rust resistance genes. This research indicates the value of extant collections of wheat-intergeneric hybrids as sources of disease resistance genes.
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Affiliation(s)
| | - Tatiana V Danilova
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan 66506
| | - Bernd Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan 66506
| | - Matthew N Rouse
- Cereal Disease Laboratory, United States Department of Agriculture, St. Paul, MN and Department of Plant Pathology, University of Minnesota, St. Paul
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Goutam U, Kukreja S, Yadav R, Salaria N, Thakur K, Goyal AK. Recent trends and perspectives of molecular markers against fungal diseases in wheat. Front Microbiol 2015; 6:861. [PMID: 26379639 PMCID: PMC4548237 DOI: 10.3389/fmicb.2015.00861] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/06/2015] [Indexed: 01/24/2023] Open
Abstract
Wheat accounts for 19% of the total production of major cereal crops in the world. In view of ever increasing population and demand for global food production, there is an imperative need of 40-60% increase in wheat production to meet the requirement of developing world in coming 40 years. However, both biotic and abiotic stresses are major hurdles for attaining the goal. Among the most important diseases in wheat, fungal diseases pose serious threat for widening the gap between actual and attainable yield. Fungal disease management, mainly, depends on the pathogen detection, genetic and pathological variability in population, development of resistant cultivars and deployment of effective resistant genes in different epidemiological regions. Wheat protection and breeding of resistant cultivars using conventional methods are time-consuming, intricate and slow processes. Molecular markers offer an excellent alternative in development of improved disease resistant cultivars that would lead to increase in crop yield. They are employed for tagging the important disease resistance genes and provide valuable assistance in increasing selection efficiency for valuable traits via marker assisted selection (MAS). Plant breeding strategies with known molecular markers for resistance and functional genomics enable a breeder for developing resistant cultivars of wheat against different fungal diseases.
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Affiliation(s)
- Umesh Goutam
- Department of Biotechnology, Lovely Professional University, PhagwaraPunjab, India
| | - Sarvjeet Kukreja
- Department of Biotechnology, Lovely Professional University, PhagwaraPunjab, India
| | - Rakesh Yadav
- Department of Bio and Nano technology, Guru Jambheshwar University of Science and TechnologyHisar, India
| | - Neha Salaria
- Department of Biotechnology, Lovely Professional University, PhagwaraPunjab, India
| | - Kajal Thakur
- Department of Biotechnology, Lovely Professional University, PhagwaraPunjab, India
| | - Aakash K. Goyal
- International Center for Agriculture Research in the Dry Areas (ICARDA)Morocco
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Ye X, Lu Y, Liu W, Chen G, Han H, Zhang J, Yang X, Li X, Gao A, Li L. The effects of chromosome 6P on fertile tiller number of wheat as revealed in wheat-Agropyron cristatum chromosome 5A/6P translocation lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:797-811. [PMID: 25656149 DOI: 10.1007/s00122-015-2466-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/17/2015] [Indexed: 05/12/2023]
Abstract
This study explored the genetic constitutions of several wheat- A. cristatum translocation lines and determined the effects of A. cristatum 6P chromosome segments on fertile tiller number in wheat. Progress in wheat breeding is hampered by a relatively narrow range of genetic variation. To overcome this hurdle, wild relatives of common wheat with superior agronomic traits are often used as donors of desirable genes in wheat-breeding programs. One of the successfully utilized wheat wild relatives is Agropyron cristatum (L.) Gaertn (2n = 4x = 28; genomes PPPP). We previously reported that WAT31-13 was a wheat-A. cristatum 5A-6P reciprocal translocation line with higher fertile tiller number and grain number per spike compared to common wheat. However, WAT31-13 was genetically unstable. In this study, we analyzed the 43 genetically stable progenies from WAT31-13 using genomic in situ hybridization, dual-color fluorescence in situ hybridization, and molecular markers. We classified them into three translocation types (TrS, TrL and TrA) and seven subtypes, and also pinpointed the translocation breakpoint. The genotypic data, combined with the phenotypes of each translocation type, enabled us to physically map agronomic traits to specific A. cristatum 6P chromosome arms or segments. Our results indicated that A. cristatum chromosome 6P played an important role in regulating fertile tiller number, and that positive and negative regulators of fertile tiller number existed on the A. cristatum chromosome arm 6PS and 6PL, respectively. By exploring the relationship between fertile tiller number and A. cristatum chromosome segment, this study presented a number of feasible approaches for creation, analysis, and utilization of wheat-alien chromosome translocation lines in genetic improvement of wheat.
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Affiliation(s)
- Xueling Ye
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Yu G, Zhang Q, Friesen TL, Rouse MN, Jin Y, Zhong S, Rasmussen JB, Lagudah ES, Xu SS. Identification and mapping of Sr46 from Aegilops tauschii accession CIae 25 conferring resistance to race TTKSK (Ug99) of wheat stem rust pathogen. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:431-43. [PMID: 25523501 DOI: 10.1007/s00122-014-2442-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 12/06/2014] [Indexed: 05/28/2023]
Abstract
Mapping studies confirm that resistance to Ug99 race of stem rust pathogen in Aegilops tauschii accession Clae 25 is conditioned by Sr46 and markers linked to the gene were developed for marker-assisted selection. The race TTKSK (Ug99) of Puccinia graminis f. sp. tritici, the causal pathogen for wheat stem rust, is considered as a major threat to global wheat production. To address this threat, researchers across the world have been devoted to identifying TTKSK-resistant genes. Here, we report the identification and mapping of a stem rust resistance gene in Aegilops tauschii accession CIae 25 that confers resistance to TTKSK and the development of molecular markers for the gene. An F2 population of 710 plants from an Ae. tauschii cross CIae 25 × AL8/78 were first evaluated against race TPMKC. A set of 14 resistant and 116 susceptible F2:3 families from the F2 plants were then evaluated for their reactions to TTKSK. Based on the tests, 179 homozygous susceptible F2 plants were selected as the mapping population to identify the simple sequence repeat (SSR) and sequence tagged site (STS) markers linked to the gene by bulk segregant analysis. A dominant stem rust resistance gene was identified and mapped with 16 SSR and five new STS markers to the deletion bin 2DS5-0.47-1.00 of chromosome arm 2DS in which Sr46 was located. Molecular marker and stem rust tests on CIae 25 and two Ae. tauschii accessions carrying Sr46 confirmed that the gene in CIae 25 is Sr46. This study also demonstrated that Sr46 is temperature-sensitive being less effective at low temperatures. The marker validation indicated that two closely linked markers Xgwm210 and Xwmc111 can be used for marker-assisted selection of Sr46 in wheat breeding programs.
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Affiliation(s)
- Guotai Yu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
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Tian HL, Wang FG, Zhao JR, Yi HM, Wang L, Wang R, Yang Y, Song W. Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015. [PMID: 26052247 DOI: 10.1007/s11032-015-0202-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the maize (Zea mays L.) genome. SNPs have several advantages over simple sequence repeats, such as ease of data comparison and integration, high-throughput processing of loci, and identification of associated phenotypes. SNPs are thus ideal for DNA fingerprinting, genetic diversity analysis, and marker-assisted breeding. Here, we developed a high-throughput and compatible SNP array, maizeSNP3072, containing 3072 SNPs developed from the maizeSNP50 array. To improve genotyping efficiency, a high-quality cluster file, maizeSNP3072_GT.egt, was constructed. All 3072 SNP loci were localized within different genes, where they were distributed in exons (43 %), promoters (21 %), 3' untranslated regions (UTRs; 22 %), 5' UTRs (9 %), and introns (5 %). The average genotyping failure rate using these SNPs was only 6 %, or 3 % using the cluster file to call genotypes. The genotype consistency of repeat sample analysis on Illumina GoldenGate versus Infinium platforms exceeded 96.4 %. The minor allele frequency (MAF) of the SNPs averaged 0.37 based on data from 309 inbred lines. The 3072 SNPs were highly effective for distinguishing among 276 examined hybrids. Comparative analysis using Chinese varieties revealed that the 3072SNP array showed a better marker success rate and higher average MAF values, evaluation scores, and variety-distinguishing efficiency than the maizeSNP50K array. The maizeSNP3072 array thus can be successfully used in DNA fingerprinting identification of Chinese maize varieties and shows potential as a useful tool for germplasm resource evaluation and molecular marker-assisted breeding.
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Affiliation(s)
- Hong-Li Tian
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Feng-Ge Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Jiu-Ran Zhao
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Hong-Mei Yi
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Lu Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Rui Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Yang Yang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Wei Song
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
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Li GR, Zhao JM, Li DH, Yang EN, Huang YF, Liu C, Yang ZJ. A Novel Wheat- Dasypyrum breviaristatum Substitution Line with Stripe Rust Resistance. Cytogenet Genome Res 2014; 143:280-7. [DOI: 10.1159/000366051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2014] [Indexed: 11/19/2022] Open
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