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Janíček T, Hobza R, Hudzieczek V. Laser Capture Microdissection: From Genomes to Chromosomes, from Complex Tissue to Single-Cell Analysis. Methods Mol Biol 2023; 2672:163-175. [PMID: 37335475 DOI: 10.1007/978-1-0716-3226-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Laser microdissection (LM) is a powerful tool for various molecular analyses providing pure samples for genomic, transcriptomic, and proteomic studies. Cell subgroups, individual cells, or even chromosomes can be separated via laser beam from complex tissues, visualized under the microscope, and used for subsequent molecular analyses. This technique provides information on nucleic acids and proteins, keeping their spatiotemporal information intact. In short, the slide with tissue is placed under the microscope, imaged by a camera onto a computer screen, where the operator selects cells/chromosomes based on morphology or staining and commands the laser beam to cut the specimen following the selected path. Samples are then collected in a tube and subjected to downstream molecular analysis, such as RT-PCR, next-generation sequencing, or immunoassay.
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Affiliation(s)
- Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
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Sheng M, Gao M, Wang L, Ren X. Chromosome Microdissection and Microcloning: Technique and Application in the Plant Sciences. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Maoyin Sheng
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science
- National Engineering Research Centre for Karst Rocky Desertification Control, Guizhou Normal University
- Guizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative Industry
| | - Mengdi Gao
- National Engineering Research Centre for Karst Rocky Desertification Control, Guizhou Normal University
- Guizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative Industry
| | - Linjiao Wang
- National Engineering Research Centre for Karst Rocky Desertification Control, Guizhou Normal University
- Guizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative Industry
| | - Xuelian Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science
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Wang L, Shi Q, Su H, Wang Y, Sha L, Fan X, Kang H, Zhang H, Zhou Y. St 2-80: a new FISH marker for St genome and genome analysis in Triticeae. Genome 2017; 60:553-563. [PMID: 28314114 DOI: 10.1139/gen-2016-0228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The St genome is one of the most fundamental genomes in Triticeae. Repetitive sequences are widely used to distinguish different genomes or species. The primary objectives of this study were to (i) screen a new sequence that could easily distinguish the chromosome of the St genome from those of other genomes by fluorescence in situ hybridization (FISH) and (ii) investigate the genome constitution of some species that remain uncertain and controversial. We used degenerated oligonucleotide primer PCR (Dop-PCR), Dot-blot, and FISH to screen for a new marker of the St genome and to test the efficiency of this marker in the detection of the St chromosome at different ploidy levels. Signals produced by a new FISH marker (denoted St2-80) were present on the entire arm of chromosomes of the St genome, except in the centromeric region. On the contrary, St2-80 signals were present in the terminal region of chromosomes of the E, H, P, and Y genomes. No signal was detected in the A and B genomes, and only weak signals were detected in the terminal region of chromosomes of the D genome. St2-80 signals were obvious and stable in chromosomes of different genomes, whether diploid or polyploid. Therefore, St2-80 is a potential and useful FISH marker that can be used to distinguish the St genome from those of other genomes in Triticeae.
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Affiliation(s)
- Long Wang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Qinghua Shi
- b State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China
| | - Handong Su
- b State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China
| | - Yi Wang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Lina Sha
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Xing Fan
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Houyang Kang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Haiqin Zhang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Yonghong Zhou
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.,c Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
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Han H, Liu W, Lu Y, Zhang J, Yang X, Li X, Hu Z, Li L. Isolation and application of P genome-specific DNA sequences of Agropyron Gaertn. in Triticeae. PLANTA 2017; 245:425-437. [PMID: 27832372 DOI: 10.1007/s00425-016-2616-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/31/2016] [Indexed: 05/21/2023]
Abstract
Different types of P genome sequences and markers were developed, which could be used to analyze the evolution of P genome in Triticeae and identify precisely wheat- A. cristatum introgression lines. P genome of Agropyron Gaertn. plays an important role in Triticeae and could provide many desirable genes conferring high yield, disease resistance, and stress tolerance for wheat genetic improvement. Therefore, it is significant to develop specific sequences and functional markers of P genome. In this study, 126 sequences were isolated from the degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) products of microdissected chromosome 6PS. Forty-eight sequences were identified as P genome-specific sequences by dot-blot hybridization and DNA sequences analysis. Among these sequences, 22 displayed the characteristics of retrotransposons, nine and one displayed the characteristics of DNA transposons and tandem repetitive sequence, respectively. Fourteen of 48 sequences were determined to distribute on different regions of P genome chromosomes by fluorescence in situ hybridization, and the distributing regions were as following: all over P genome chromosomes, centromeres, pericentromeric regions, distal regions, and terminal regions. We compared the P genome sequences with other genome sequences of Triticeae and found that the similar sequences of the P genome sequences were widespread in Triticeae, but differentiation occurred to various extents. Additionally, thirty-four molecular markers were developed from the P genome sequences, which could be used for analyzing the evolutionary relationship among 16 genomes of 18 species in Triticeae and identifying P genome chromatin in wheat-A. cristatum introgression lines. These results will not only facilitate the study of structure and evolution of P genome chromosomes, but also provide a rapid detecting tool for effective utilization of desirable genes of P genome in wheat improvement.
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Affiliation(s)
- Haiming Han
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuquan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zanmin Hu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic Improvement (NKCRI), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Abstract
Chromosome microdissection followed by microcloning is an efficient tool combining cytogenetics and molecular genetics that can be used for the construction of the high density molecular marker linkage map and fine physical map, the generation of probes for chromosome painting, and the localization and cloning of important genes. Here, we describe a modified technique to microdissect a single chromosome, paint individual chromosomes, and construct single-chromosome DNA libraries.
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Affiliation(s)
- Ying-Xin Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | | | - Zan-Min Hu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China.
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