FISH, which allows the mapping of DNA sequences directly onto chromosomes, has revolutionized plant molecular cytogenetics research since it was first adapted from mammalian research. Repetitive DNA sequences can generate unique FISH patterns on individual chromosomes for karyotyping (chromosome identification) and phylogenetic/evolution analyses. FISH and/or genomic in situ hybridization (GISH) on meiotic metaphase chromosomes provide more information on chromosome pairing than traditional pairing analysis. FISH on meiotic pachytene chromosomes coupled with digital imaging systems has become an efficient method for developing physical maps in plant species, especially those with small genomes. FISH-based physical mapping provides a valuable complementary approach to genome sequencing and map-based cloning research, and it will continue to play an important role in relating DNA sequence information to chromosome biology. In addition, FISH using RNA probes and FISH with immunoassays are becoming increasingly important techniques in studies of chromosome structure and functions that control gene expression and regulation.
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References
Bass HW, Marshall WF, Sedat JW, Agard DA, Cande WZ (1997) Telomeres cluster de novo before the initiation of synapsis: a three-dimensional spatial analysis of telomere positions before and during meiotic prophase. J Cell Biol 137:5–18
Feng Q, Zhang YJ, Hao P, Wang SY, Fu G, Huang YC, et al. (2002) Sequence and analysis of rice chromosome 4. Nature 420:316–320
Fransz PF, Alonso-Blanco C, Liharska TB, Peeters AJM, Zabel P, de Jong JH (1996a) High-resolution physical mapping inArabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J 9:421–430
Fransz PF, Stam M, Montijn B, Hoopen RT, Weigant J, Kooter JM, Oud O, Nanninga N (1996b) Detection of single-copy genes and chromosome rearrangements in Petunia hybrida by fluorescence in situ hybridisation. Plant J 9:767–774
Friebe B, Kynast RG, Zhang P, Qi L, Dhar M, Gill BS (2001) Chromosome healing by addition of telomeric repeats in wheat occurs during the first mitotic divisions of the sporophyte and is a gradual process. Chromosome Res 9:137–146
Heslop-Harrison JS, Leitch AR, Schwarzacher T, Anamthawat-Jonsson K (1990) Detection and characterization of 1B/1R translocations in hexaploid wheat. Heredity 65:385–392
Jackson SA, Wang M, Goodman H, Jiang J (1998) Fiber-FISH analysis of repetitive DNA elements in Arabidopsis thaliana. Genome 41:566–572
Jackson SA, Cheng Z, Wang M-L, Goodman HM, Jiang J (2000) Comparative FISH mapping of a 431-kb Arabidopsis thaliana BAC contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome. Genetics 156:833–838
Jackson SA, Zhang P, Chen WP, Phillips RL, Friebe B, Muthukrishnan S, Gill BS (2001) High-resolution structural analysis of biolistic transgene integration into the nuclear genome of wheat. Theor Appl Genet 103:56–62
Le HT, Armstrong KC, Miki B (1989) Detection of rye DNA in wheat-rye hybrids and wheat translocation stocks using total genomic DNA as a probe. Plant Mol Biol Rep 7:150–158
Leitch IJ, Heslop-Harrison JS (1992) Physical mapping of the 18S-5.8S-26S rRNA genes in barley by in situ hybridization. Genome 35:1013–1018
Leitch IJ, Heslop-Harrison JS (1993) Physical mapping of four sites of 5S rDNA sequences and one site of the alpha-amylase-2 gene in barley (Hordeum vulgare). Genome 36:517–523
Leitch IJ, Leitch AR, Heslop-Harrison JS (1991) Physical mapping of plant DNA sequences by simultaneous in situ hybridization of two differently fluorescent probes. Genome 34:329–333
Leitch AR, Schwarzacher T, Jackson D, Leitch IJ (1994) In situ hybridization: a practical guide. BIOS Scientific, Oxford, UK
Lysak MA, Fransz PF, Ali HBM, Schubert I (2001) Chromosome painting in Arabidopsis thaliana. Plant J 28:689–697
Mukai Y, Nakahara Y, Yamamoto M (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
Parra I, Windle B (1993) High resolution visual mapping of stretched DNA by fluorescent hybridisation. Nature Genet 5:17–21
Rigby PWJ, Dieckmann M, Rhodes C, Berg P (1977) Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol 113:237–251
Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, et al. (2002) The genome sequence and structure of rice chromosome 1. Nature (London) 420:312–316
Schubert I, Fransz PF, Fuchs J, de Jong JH (2001) Chromosome painting in plants. Methods Cell Sci 23:57–69
Schwarzacher T, Leitch AR, Bennett MD, Heslop-Harrison JS (1989) In situ localization of parental genomes in a wide hybrid. Ann Bot 64:315–324
Walling JG, Pires JC, Jackson SA (2005) Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods. Methods Enzymol 395:443–460
Wiegant J, Ried T, Nederlof PM, van der Ploeg M, Tanke HJ, Rapp AK (1991) In situ hybridization with fluoresceinated DNA. Nucleic Acids Res 19:3237–3241
Zhang P, Friebe B, Lukaszewski AJ, Gill BS (2001) The centromere structure in Robertsonian wheat-rye translocation chromosomes indicates that centric breakage-fusion can occur at different positions within the primary constriction. Chromosoma 110:335–344
Zhong X-B, Fransz PF, Wennekes-van Eden J, Zabel P, van Kammen A, de Jong JH (1996) High-resolution mapping on pachytene chromosomes and extended DNA fibres by fluorescence in-situ hybridization. Plant Mol Biol Rep 14:232–242
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Zhang, P., Friebe, B. (2009). FISH on Plant Chromosomes. In: Liehr, T. (eds) Fluorescence In Situ Hybridization (FISH) — Application Guide. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70581-9_32
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DOI: https://doi.org/10.1007/978-3-540-70581-9_32
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