Abstract
Efficient and consistent chromosome identification is the foundation for successful cytogenetic studies. Fluorescent in situ hybridization (FISH) has been the most popular technique for chromosome identification in plants. Large insert genomic DNA clones, such as bacterial artificial chromosome (BAC) clones, and repetitive DNA sequences have been the most commonly used DNA probes for FISH. However, most of such traditional probes can only be used to identify a single chromosome or are too polymorphic to consistently identify the same chromosome in the target species. In contrast, FISH using oligonucleotide (oligo)-based probes is highly versatile. In this procedure, a large number of oligos specific to a chromosomal region, to an entire chromosome, or to multiple chromosomes are computationally identified, synthesized in parallel, and labeled as probes. In addition, each oligo probe can be used for thousands of FISH experiments and represents an infinite resource. In this chapter we describe a detailed protocol for amplification and labeling of oligo-based probes, relevant chromosome preparation, and FISH procedures.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Jiang JM, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068
McClintock B (1929) Chromosome morphology in Zea mays. Science 69:629
Jiang JM, Gill BS, Wang GL et al (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci U S A 92(10):4487–4491
Lysak MA, Fransz PF, Ali HBM et al (2001) Chromosome painting in Arabidopsis thaliana. Plant J 28:689–697
Mukai Y, Yumiko N, Maki Y (1993) Simultaneous discrimination of the three genomes in hexaploid wheat by multicolor fluorescence in situ hybridization using total genomic and highly repeated DNA probes. Genome 36:489–494
Kato A, Lamb JC, Birchler JA (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci U S A 101:13554–13559
Lamb JC, Danilova T, Bauer MJ et al (2007) Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 175:1047–1058
Danilova TV, Friebe B, Gill BS (2012) Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Chromosoma 121(6):597–611
Beliveau BJ, Joyce EF, Apostolopoulos N et al (2012) Versatile design and synthesis platform for visualizing genomes with oligopaint FISH probes. Proc Natl Acad Sci U S A 109:21301–21306
Han YH, Zhang T, Thammapichai P et al (2015) Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics 200:771–779
Jiang JM (2019) Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res 27. https://doi.org/10.1007/s10577-019-09607-z
Braz GT, He L, Zhao H et al (2018) Comparative Oligo-FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics 208:513–523
He L, Braz GT, Torres GA et al (2018) Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species. Chromosoma 127:505–513
Qu MM, Li K, Han Y et al (2017) Integrated karyotyping of woodland strawberry (Fragaria vesca) with oligopaint FISH probes. Cytogenet Genome Res 153:158–164
Hou LL, Xu M, Zhang T et al (2018) Chromosome painting and its applications in cultivated and wild rice. BMC Plant Biol 18:110
Meng Z, Zhang Z, Yan T et al (2018) Comprehensively characterizing the cytological features of Saccharum spontaneum by the development of a complete set of chromosome-specific oligo probes. Front Plant Sci 9:1624
Albert PS, Zhang T, Semrau K et al (2019) Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. Proc Natl Acad Sci U S A 116:1679–1685
Murgha YE, Rouillard J-M, Gulari E (2014) Methods for the preparation of large quantities of complex single-stranded oligonucleotide libraries. PLoS One 9:e94752
De Carvalho CR, Saraiva LS (1993) An Air Drying Technique for Maize Chromosomes without Enzymatic Maceration. Biotech Histochem 68:142–145
Schubert I, Fransz PF, Fuchs J, de Jong JH (2001) Chromosome painting in plants. Methods Cell Sci 23:57–69
Ross KJ, Fransz P, Jones GH (1996) A light microscopic atlas of meiosis in Arabidopsis thaliana. Chromosom Res 4:507–516
Acknowledgments
This work was supported by National Science Foundation (NSF) grants MCB-1412948 and IOS-1444514 to J.J.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Braz, G.T., Yu, F., do Vale Martins, L., Jiang, J. (2020). Fluorescent In Situ Hybridization Using Oligonucleotide-Based Probes. In: Nielsen, B.S., Jones, J. (eds) In Situ Hybridization Protocols . Methods in Molecular Biology, vol 2148. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0623-0_4
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0623-0_4
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0622-3
Online ISBN: 978-1-0716-0623-0
eBook Packages: Springer Protocols