Fluorescence in situ hybridization (FISH) has been an efficient way for integrating physical and genetic maps of various small genomes like rice, sorghum and Brachypodium; whereas in the large genomes like barley, the repetitive nature of the genome complicates the generation and detection of single-copy FISH probes. Here, we used exemplarily physical map contigs of a defined interval of the long arm of barley chromosome 2H to evaluate the potential of FISH-based mapping as a supportive means for genetic anchoring of the physical map and to resolve the linear order of contigs along the respective chromosome. Repeat-free FISH probes corresponding to 8 previously anchored BAC contigs were specifically allocated to chromosome 2H. This represented an almost 90% success rate in single-copy FISH probe development. FISH mapping of contigs located in the subtelomeric region revealed an over-performance of genetic mapping over FISH for physical map anchoring.

1.
Anderson LK, Doyle GG, Brigham B, Carter J, Hooker KD, et al: High-resolution crossover maps for each bivalent of Zea mays using recombination nodules. Genetics 165:849-865 (2003).
2.
Cheng Z, Buell CR, Wing RA, Gu M, Jiang J: Toward a cytological characterization of the rice genome. Genome Res 11:2133-2141 (2001).
3.
Drouaud J, Camilleri C, Bourguignon PY, Canaguier A, Berard A, et al: Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination ‘hot spots'. Genome Res 16:106-114 (2006).
4.
Fukui K, Kamisugi Y, Sakai F: Physical mapping of 5S rDNA loci by direct-cloned biotinylated probes in barley chromosomes. Genome 37:105-111 (1994).
5.
Hasterok R, Marasek A, Donnison IS, Armstead I, Thomas A, et al: Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 173:349-362 (2006).
6.
International Barley Genome Sequencing Consortium: A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711-716 (2012).
7.
Jensen-Seaman MI, Furey TS, Payseur BA, Lu YT, Roskin KM, et al: Comparative recombination rates in the rat, mouse, and human genomes. Genome Res 14:528-538 (2004).
8.
Karafiatova M, Bartos J, Kopecky D, Ma L, Sato K, et al: Mapping nonrecombining regions in barley using multicolor FISH. Chromosome Res 21:739-751 (2013).
9.
Kato A: High-density fluorescence in situ hybridization signal detection on barley (Hordeum vulgare L.) chromosomes with improved probe screening and reprobing procedures. Genome 54:151-159 (2011).
10.
Kato A, Albert PS, Vega JM, Birchler JA: Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotech Histochem 81:71-78 (2006).
11.
Kim JS, Islam-Faridi MN, Klein PE, Stelly DM, Price HJ, et al: Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171:1963-1976 (2005).
12.
Lapitan NLV, Brown SE, Kennard W, Stephens JL, Knudson DL: FISH physical mapping with barley BAC clones. Plant J 11:149-156 (1997).
13.
Leitch IJ, Heslop-Harrison JS: Physical mapping of the 18S-5.8S-26S ribosomal-RNA genes in barley by in situ hybridization. Genome 35:1013-1018 (1992).
14.
Leitch IJ, Heslop-Harrison JS: 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 (1993).
15.
Ma L, Vu GTH, Schubert V, Watanabe K, Stein N, et al: Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res 18:841-850 (2010).
16.
Phillips D, Nibau C, Ramsay L, Waugh R, Jenkins G: Development of a molecular cytogenetic recombination assay for barley. Cytogenet Genome Res 129:154-161 (2010).
17.
Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, et al: Potential of synteny-based anchoring of the barley genome physical map. Funct Integr Genomics 13:339-350 (2013).
18.
Sadder MT, Weber G: Karyotype of maize (Zea mays L.) mitotic metaphase chromosomes as revealed by fluorescence in situ hybridization (FISH) with cytogenetic DNA markers. Plant Mol Biol Rep 19:117-123 (2001).
19.
Sadder MT, Ponelies N, Born U, Weber G: Physical localization of single-copy sequences on pachytene chromosomes in maize (Zea mays L.) by chromosome in situ suppression hybridization. Genome 43:1081-1083 (2000).
20.
Schmutzer T, Ma L, Pousarebani N, Bull F, Stein N, et al: Kmasker - a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare. Cytogenet Genome Res 142:66-78 (2014).
21.
Stephens JL, Brown SE, Lapitan NLV, Knudson DL: Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 47:179-189 (2004).
22.
Szinay D, Chang SB, Khrustaleva L, Peters S, Schijlen E, et al: High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. Plant J 56:627-637 (2008).
23.
Valarik M, Bartos J, Kovarova P, Kubalakova M, de Jong H, Dolezel J: High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 37:940-950 (2004).
24.
Wang K, Guo W, Zhang T: Detection and mapping of homologous and homoeologous segments in homoeologous groups of allotetraploid cotton by BAC-FISH. BMC Genomics 8:178 (2007).
25.
Wicker T, Matthews DE, Keller B: TREP: a database for Triticeae repetitive elements. Trends Plant Sci 7:561-562 (2002).
26.
Wu JZ, Mizuno H, Hayashi-Tsugane M, Ito Y, Chiden Y, et al: Physical maps and recombination frequency of six rice chromosomes. Plant J 36:720-730 (2003).
27.
You FM, Huo NX, Gu YQ, Luo MC, Ma YQ, et al: BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinform 9:253 (2008).
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