Abstract
A growing number of international genome consortia have initiated large-scale sequencing projects for most of the major crop species. This huge amount of information not only boosted genetic and physical mapping research, but it also enabled novel applications on the level of chromosome biology including molecular cytogenetics that supports plant genetics, genomics, and breeding programs. The simultaneous detection of a large number of BAC-based probes by multicolor fluorescent in situ hybridization (FISH) can provide a rapid overview of super-contig and gap distribution on euchromatin chromosome areas and will display directly and precisely the positions of chromosome rearrangements. Furthermore, hybridizations of BACs on the chromosomes of related species can confirm genomic colinearity, or the occurrence of inversions and translocations events. This cross-species FISH together with meiotic pairing studies is a powerful source of information that elucidates the nature of genome rearrangements, and the consequences of such rearrangements for introgressive hybridizations. In this chapter we describe a general-purpose protocol for FISH on pachytene chromosomes.
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References
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183
Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524
Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M et al (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227–239
Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA et al (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30:83–89
Schubert I, Fransz PF, Fuchs J, de Jong JH (2001) Chromosome painting in plants. Methods Cell Sci 23:57–69
Sharma AK, Sharma A (2001) Chromosome painting—principles, strategies and scope. Methods Cell Sci 23:1–5
Kato A, Vega JM, Han F, Lamb JC, Birchler JA (2005) Advances in plant chromosome identification and cytogenetic techniques. Curr Opin Plant Biol 8:148–154
Jiang J, Gill BS (2006) Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068
De Jong JH, Fransz PF, Zabel P (1999) High resolution FISH in plants—techniques and applications. Trends Plant Sci 4:258–263
Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A et al (2002) Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 12:795–807
Yuan Y, San Miguel PJ, Bennetzen JL (2003) High-Cot sequence analysis of the maize genome. Plant J 34:249–255
Campell BR, Song YG, Posch TE, Cullis CA, Town CD (1992) Sequence and organization of 5s ribosomal RNA-encoding genes of Arabidopsis thaliana. Gene 112:225–228
Gerlach WL, Bedbrook JR (1979) Cloning and characterization of ribosomal-Rna genes from wheat and barley. Nucleic Acids Res 7: 1869–1885
Richards EJ, Ausubel FM (1988) Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell 53:127–136
Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15:8–15
Kulikova O, Gualtieri G, Geurts R, Kim D-J, Cook D, Huguet T, de Jong JH, Fransz PF, Bisseling T (2001) Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J 27:49–58
Woo SS, Jiang J, Gill BS, Paterson AH, Wing RA (1994) Construction and characterization of bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 22: 4922–4931
Zwick MS, Hanson RE, Islam-Faridi MN, Stelly DM, Wing RA, Price HJ, McKnight TD (1997) A rapid procedure for the isolation of Cot-1 DNA from plants. Genome 40:138–142
Zhong XB, de Jong JH, Zabel P (1996) Preparation of tomato meiotic pachytene and mitotic metaphase chromosomes suitable for fluorescence in situ hybridization (FISH). Chromosome Res 4:24–28
Kocsis E, Trus BL, Steer CJ, Bisher ME, Steven AC (1991) Image averaging of flexible fibrous macromolecules: the clathrin triskelion has an elastic proximal segment. J Struct Biol 107: 6–14
MandĂ¡kovĂ¡ T, Lysak MA (2008) Chromosomal phylogeny and karyotype evolution in x = 7 crucifer species (Brassicaceae). Plant Cell 20:2559–2570
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Geurts, R., de Jong, H. (2013). Fluorescent In Situ Hybridization (FISH) on Pachytene Chromosomes as a Tool for Genome Characterization. In: Rose, R. (eds) Legume Genomics. Methods in Molecular Biology, vol 1069. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-613-9_2
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DOI: https://doi.org/10.1007/978-1-62703-613-9_2
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