Protocals for Oligonucleotide Fluorescence in situ Hybridization in Plants
Received date: 2022-11-20
Accepted date: 2023-01-10
Online published: 2023-01-10
Oligonucleotide fluorescence in situ hybridization (Oligo-FISH) is a new technology that integrates bioinformatics analysis, high throughput DNA synthesis and fluorescence in situ hybridization experiments. It is applicable to plant species with a reference genome. Oligo probes are able design to a chromosomal region, an entire chromosome, and a set of chromosomes according to researchers’ requirements. Oligo-FISH has been successfully applied to studies on karyotyping, chromosome variation, population evolution, homologous chromosome pairing, haplotype analysis, and heteropolyploid identification in several plant species. Here, we introduce the concrete operational processes of oligonucleotide-based probe design, amplification and labeling, chromosomes preparation, and fluorescence in situ hybridization in plants, so as to facilitate Oligo-FISH application in the cytogenetics research in the future.
Fanfan Zhang, Xinying Xing, Wenqing Shi, Yi Shen, Zhukuan Cheng . Protocals for Oligonucleotide Fluorescence in situ Hybridization in Plants[J]. Chinese Bulletin of Botany, 2023 , 58(2) : 274 -284 . DOI: 10.11983/CBB22265
| [1] | 程新杰, 于恒秀, 程祝宽 (2019). 水稻减数分裂染色体分析方法. 植物学报 54, 503-508. |
| [2] | Albert PS, Zhang T, Semrau K, Rouillard JM, Kao YH, Wang CJR, Danilova TV, Jiang JM, Birchler JA (2019). Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. Proc Natl Acad Sci USA 116, 1679-1685. |
| [3] | Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang YM, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT (2012). Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci USA 109, 21301-21306. |
| [4] | Boyle S, Rodesch MJ, Halvensleben HA, Jeddeloh JA, Bickmore WA (2011). Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Chromosome Res 19, 901-909. |
| [5] | Braz GT, do Vale Martins L, Zhang T, Albert PS, Birchler JA, Jiang JM (2020). A universal chromosome identification system for maize and wild Zea species. Chromosome Res 28, 183-194. |
| [6] | Braz GT, He L, Zhao HN, Zhang T, Semrau K, Rouillard JM, Torres GA, Jiang JM (2018). Comparative Oligo- FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics 208, 513-523. |
| [7] | Cheng ZK, Buell CR, Wing RA, Jiang JM (2002). Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 10, 379-387. |
| [8] | Do Vale Martins L, de Oliveira Bustamante F, da Silva Oliveira AR, da Costa AF, de Lima Feitoza L, Liang QH, Zhao HN, Benko-Iseppon AM, Mu?oz-Amatriaín M, Pedrosa-Harand A, Jiang JM, Brasileiro-Vidal AC(2021). BAC- and Oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris. Chromosoma 130, 133-147. |
| [9] | Do Vale Martins L, Yu F, Zhao HN, Dennison T, Lauter N, Wang HY, Deng ZH, Thompson A, Semrau K, Rouillard JM, Birchler JA, Jiang JM (2019). Meiotic crossovers characterized by haplotype-specific chromosome painting in maize. Nat Commun 10, 4604. |
| [10] | Han YH, Zhang T, Thammapichai P, Weng YQ, Jiang JM (2015). Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics 200, 771-779. |
| [11] | He L, Braz GT, Torres GA, Jiang JM (2018). Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species. Chromosoma 127, 505-513. |
| [12] | Hou LL, Xu M, Zhang T, Xu ZH, Wang WY, Zhang JX, Yu MM, Ji W, Zhu CW, Gong ZY, Gu MH, Jiang JM, Yu HX (2018). Chromosome painting and its applications in cultivated and wild rice. BMC Plant Biol 18, 110. |
| [13] | Idziak D, Betekhtin A, Wolny E, Lesniewska K, Wright J, Febrer M, Bevan MW, Jenkins G, Hasterok R (2011). Painting the chromosomes of Brachypodium: current status and future prospects. Chromosoma 120, 469-479. |
| [14] | Jiang JM (2019). Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res 27, 153-165. |
| [15] | Jiang JM, Gill BS (2006). Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49, 1057-1068. |
| [16] | Liu GQ, Zhang T (2021). Single copy oligonucleotide fluorescence in situ hybridization probe design platforms: development, application and evaluation. Int J Mol Sci 22, 7124. |
| [17] | Liu XY, Sun S, Wu Y, Zhou Y, Gu SW, Yu HX, Yi CD, Gu MH, Jiang JM, Liu B, Zhang T, Gong ZY (2020). Dual-color Oligo-FISH can reveal chromosomal variations and evolution in Oryza species. Plant J 101, 112-121. |
| [18] | Lou QF, Zhang YX, He YH, Li J, Jia L, Cheng CY, Guan W, Yang SQ, Chen JF (2014). Single-copy gene-based chromosome painting in cucumber and its application for chromosome rearrangement analysis in Cucumis. Plant J 78, 169-179. |
| [19] | Lysak MA, Fransz PF, Ali HBM, Schubert I (2001). Chromosome painting in Arabidopsis thaliana. Plant J 28, 689-697. |
| [20] | Meng Z, Zhang ZL, Yan TY, Lin QF, Wang Y, Huang WY, Huang YJ, Li ZJ, Yu QY, Wang JP, Wang K (2018). Comprehensively characterizing the cytological features of Saccharum spontaneum by the development of a comp- lete set of chromosome-specific Oligo probes. Front Plant Sci 9, 1624. |
| [21] | Qu MM, Li KP, Han YL, Chen L, Li ZY, Han YH (2017). Integrated karyotyping of woodland strawberry (Fragaria vesca) with Oligopaint FISH probes. Cytogenet Genome Res 153, 158-164. |
| [22] | Shi PY, Sun HJ, Liu GQ, Zhang X, Zhou JW, Song RR, Xiao J, Yuan CX, Sun L, Wang ZK, Lou QF, Jiang JM, Wang XE, Wang HY (2022). Chromosome painting reveals inter-chromosomal rearrangements and evolution of subgenome D of wheat. Plant J 112, 55-67. |
| [23] | Xin HY, Zhang T, Han YH, Wu YF, Shi JS, Xi ML, Jiang JM (2018). Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides. Chromosoma 127, 313-321. |
| [24] | Yamada NA, Rector LS, Tsang P, Carr E, Scheffer A, Sederberg MC, Aston ME, Ach RA, Tsalenko A, Sampas N, Peter B, Bruhn L, Brothman AR (2011). Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH. Cytogenet Genome Res 132, 248-254. |
| [25] | Yu F, Zhao XW, Chai J, Ding XE, Li XT, Huang YJ, Wang XH, Wu JY, Zhang MQ, Yang QH, Deng ZH, Jiang JM (2022). Chromosome-specific painting unveils chromosomal fusions and distinct allopolyploid species in the Saccharum complex. New Phytol 233, 1953-1965. |
| [26] | Zhang FF, Shen Y, Miao CB, Cao YW, Shi WQ, Du GJ, Tang D, Li YF, Luo Q, Cheng ZK (2020). OsRAD51D promotes homologous pairing and recombination by preventing nonhomologous interactions in rice meiosis. New Phytol 227, 824-839. |
| [27] | Zhang FF, Tang D, Shen Y, Xue ZH, Shi WQ, Ren LJ, Du GJ, Li YF, Cheng ZK (2017). The F-box protein ZYGO1 mediates bouquet formation to promote homologous pairing, synapsis, and recombination in rice meiosis. Plant Cell 29, 2597-2609. |
| [28] | Zhang T, Liu GQ, Zhao HN, Braz GT, Jiang JM (2021). Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization. Plant Biotechnol J 19, 1967-1978. |
/
| 〈 |
|
〉 |
Home