Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants
Fluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis,...
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| Format: | Article |
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MDPI AG
2023-07-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/15/2816 |
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| author | Arrashid Harun Hui Liu Shipeng Song Sumeera Asghar Xiaopeng Wen Zhongming Fang Chunli Chen |
| author_facet | Arrashid Harun Hui Liu Shipeng Song Sumeera Asghar Xiaopeng Wen Zhongming Fang Chunli Chen |
| author_sort | Arrashid Harun |
| collection | DOAJ |
| description | Fluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis, low sensitivity, cross-hybridization, and limited resolution. In contrast, oligo-based FISH represents a more efficient method for chromosomal studies in plants. Oligo probes are computationally designed and synthesized for any plant species with a sequenced genome and are suitable for single and repetitive DNA sequences, entire chromosomes, or chromosomal segments. Furthermore, oligo probes used in the FISH experiment provide high specificity, resolution, and multiplexing. Moreover, oligo probes made from one species are applicable for studying other genetically and taxonomically related species whose genome has not been sequenced yet, facilitating molecular cytogenetic studies of non-model plants. However, there are some limitations of oligo probes that should be considered, such as requiring prior knowledge of the probe design process and FISH signal issues with shorter probes of background noises during oligo-FISH experiments. This review comprehensively discusses de novo oligo probe synthesis with more focus on single-copy DNA sequences, preparation, improvement, and factors that affect oligo-FISH efficiency. Furthermore, this review highlights recent applications of oligo-FISH in a wide range of plant chromosomal studies. |
| first_indexed | 2024-03-11T00:18:19Z |
| format | Article |
| id | doaj.art-4f7aa12984a84938810afa80f6687c81 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T00:18:19Z |
| publishDate | 2023-07-01 |
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| record_format | Article |
| series | Plants |
| spelling | doaj.art-4f7aa12984a84938810afa80f6687c812023-11-18T23:26:17ZengMDPI AGPlants2223-77472023-07-011215281610.3390/plants12152816Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in PlantsArrashid Harun0Hui Liu1Shipeng Song2Sumeera Asghar3Xiaopeng Wen4Zhongming Fang5Chunli Chen6Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, ChinaNational Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, ChinaNational Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, ChinaKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, ChinaKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, ChinaKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, ChinaKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, ChinaFluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis, low sensitivity, cross-hybridization, and limited resolution. In contrast, oligo-based FISH represents a more efficient method for chromosomal studies in plants. Oligo probes are computationally designed and synthesized for any plant species with a sequenced genome and are suitable for single and repetitive DNA sequences, entire chromosomes, or chromosomal segments. Furthermore, oligo probes used in the FISH experiment provide high specificity, resolution, and multiplexing. Moreover, oligo probes made from one species are applicable for studying other genetically and taxonomically related species whose genome has not been sequenced yet, facilitating molecular cytogenetic studies of non-model plants. However, there are some limitations of oligo probes that should be considered, such as requiring prior knowledge of the probe design process and FISH signal issues with shorter probes of background noises during oligo-FISH experiments. This review comprehensively discusses de novo oligo probe synthesis with more focus on single-copy DNA sequences, preparation, improvement, and factors that affect oligo-FISH efficiency. Furthermore, this review highlights recent applications of oligo-FISH in a wide range of plant chromosomal studies.https://www.mdpi.com/2223-7747/12/15/2816oligo-FISHsingle-copyrepetitive sequenceprobe labelingoligonucleotide synthesistraditional FISH |
| spellingShingle | Arrashid Harun Hui Liu Shipeng Song Sumeera Asghar Xiaopeng Wen Zhongming Fang Chunli Chen Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants Plants oligo-FISH single-copy repetitive sequence probe labeling oligonucleotide synthesis traditional FISH |
| title | Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants |
| title_full | Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants |
| title_fullStr | Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants |
| title_full_unstemmed | Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants |
| title_short | Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants |
| title_sort | oligonucleotide fluorescence in situ hybridization an efficient chromosome painting method in plants |
| topic | oligo-FISH single-copy repetitive sequence probe labeling oligonucleotide synthesis traditional FISH |
| url | https://www.mdpi.com/2223-7747/12/15/2816 |
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