Mapping nonrecombining regions in barley using multicolor FISH

Chromosome Research

Volumn 21, Issue 8, 2013, Pages 739-751

  Karafiatova M ^a   Bartos J ^a   Kopecky D ^a   Ma, L ^b   Sato, K ^c   Houben, A ^b   Stein, N ^b   Dolezel J ^a  

^a INSTITUTE OF EXPERIMENTAL BOTANY   (Czech Republic)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^c OKAYAMA UNIVERSITY   (Japan)

Author keywords

cDNA; genetic mapping; low copy FISH; multicolor FISH; nonrecombining regions; physical mapping

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; BARLEY; CHROMOSOME; CHROMOSOME 7H; CHROMOSOME MAP; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LOCATION; GENE MAPPING; GENE REARRANGEMENT; GENOME ANALYSIS; METAPHASE CHROMOSOME; PRIORITY JOURNAL;

BACTERIA (MICROORGANISMS); HORDEUM;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; CLONING, MOLECULAR; CONTIG MAPPING; DNA, PLANT; GENETIC MARKERS; GENOME, PLANT; HORDEUM; IN SITU HYBRIDIZATION, FLUORESCENCE; NUCLEIC ACID HYBRIDIZATION; SEQUENCE ANALYSIS, DNA;

EID: 84891836111     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-013-9380-x     Document Type: Article

References (59)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Birnbiom HC (1983) A rapid alkaline extraction method for the isolation of plasmid DNA. Methods Enzymol 100:243-255
3. Cai W, Ling J, Irvin B, Ohler L, Rose E et al (1998) High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping. Proc Natl Acad Sci U S A 95:3390-3395
4. Cao M, Sleper DA, Dong F, Jiang J (2000) Genomic in situ hybridization (GISH) reveals high chromosome pairing affinity between Lolium perenne and Festuca mairei. Genome 43:398-403
5. Cheng Z, Presting GG, Buell CR, Wing RA, Jiang J (2001) High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosomes 10 of rice. Genetics 157:1749-1757
6. de Jong JH, Fransz P, Zabel P (1999) High resolution FISH in plants - techniques and applications. Trends Plant Sci 4:258-263
7. Devos KM, Gale MD (1993) Extended genetic maps of the homeologous group-3 chromosomes of wheat, rye and barley. Theor Appl Genet 85:649-652
8. Doležel J, Greilhuber J, Lucretti S, Meister A, Lysak MA, Nardi L, Obermayer R (1998) Plant genome size estimation by flow-cytometry: inter-laboratory comparison. Ann Bot 82:17-26
9. Endo TR (1990) Gametocidal chromosomes and their induction of chromosome mutation in wheat. Jpn J Genet 65:135-152
10. Endo TR (2007) The gametocidal chromosomes as a tool for chromosome manipulation in wheat. Chromosome Res 15:67-75
11. Farré A, Cuadrado A, Lacasa-Benito I, Cistué L, Schubert I, Comadran J, Jansen J, Romagosa I (2012) Genetic characterization of a reciprocal translocation present in a widely grown barley variety. Mol Breed 30:1109-1119
12. Fischer JA, Favreau MB (1991) Plasmid purification by phenol extraction from guanidinium thiocyanate solution: development of an automated protocol. Anal Biochem 194:309-315
13. Fuchs J, Schubert I (1995) Localization of seed protein genes on metaphase chromosomes of Vicia faba via fluorescence in situ hybridization. Chromosome Res 3:94-100
14. Fukui K, Kamisugi Y, Sakai F (1994) Physical mapping of 5S rDNA loci by direct-cloned biotinylated probes in barley chromosomes. Genome 37:105-117
15. Gamborg OL, Wetter LR (1975) Plant tissue culture methods. National Research Council of Canada, Saskatoon
16. Giacalone J, Delobette V, Gibaja L, Ni L, Skidas Y et al (2000) Optical mapping of BAC clones from the human Y chromosome DAZ locus. Genome Res 10:1421-1429
17. Harwood WA, Bilham LJ, Travella S, Salvo-Garrido H, Snape JW (2005) Fluorescence in situ hybridization to localize transgenes in plant chromosomes. Methods Mol Biol 286:327-340
18. Heng HH, Tsui LC (1998) High resolution free chromatin/DNA fiber fluorescent in situ hybridization. J Chromatogr 86:219-229
19. Janda J, Šafář J, Kubaláková M, Bartoš J, Kovářová P, Suchánková P, Pateyron S, Číhalíková J, Sourdille P, Šimková H, Faivre-Rampant P, Hřibová E, Bernard M, Lukaszewski A, Doležel J, Chalhoub B (2006) Advanced resources for plant genomics: BAC library specific for the short arm of wheat chromosome 1B. Plant J 47:977-986
20. Joshi GP, Nasuda S, Endo TR (2011) Dissection and cytological mapping of barley chromosome 2H in the genetic background of common wheat. Genes Genet Syst 86:231-248
21. Kato A (2011) 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
22. Kato A, Vega JM, Han FP, Lamb JC, Birchler JA (2005) Advances in plant chromosome identification and cytogenetic techniques. Curr Opin Plant Biol 8:148-154
23. Kato A, Albert PS, Vega JM, Bichler JA (2006) Sensitive fluorescence in situ hybridization signal detection in maize using directly labelled probes produced by high concentration DNA polymerase nick translation. Biotech Histochem 81:71-78
24. 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
25. Kumar A, Simons K, Iqbal MJ, de Jiménez MM, Bassi FM, Ghavami F, Al-Azzam O, Drader T, Wang Y, Luo MC, Gu YQ, Denton A, Lazo GR, Xu SS, Dvorak J, Kianian PM, Kianian SF (2012) Physical mapping resources for large plant genomes: radiation hybrids for wheat d-genome progenitor Aegilops tauschii. BMC Genomics 13:597
26. Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397-412
27. Leicht IJ, Heslop-Harrison JS (1992) Physical mapping of 18S-5,8S-26S rRNA genes in barley by in situ hybridization. Genome 35:1013-1018
28. Leicht IJ, Heslop-Harrison JS (1993) Physical mapping of 4 sites of 5S rDNA sequences and one site of the aplha-amylase-2 gene in barley (Hordeum vulgare). Genome 36:517-523
29. Linde-Laursen IB (1978) Giemsa C-banding of barley chromosomes; II. Banding patterns of trisomics and telotrisomics. Hereditas 89:37-41
30. Lysák MA, Číhalíková J, Kubaláková M, Šimková H, Künzel G, Doležel J (1999) Flow karyotyping and sorting of mitotic chromosomes of barley (Hordeum vulgare L.). Chromosome Res 7:431-444
31. Ma L, Vu GTH, Schubert V, Watanabe K, Stein N, Houben A, Schubert I (2010) Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res 18:841-850
32. Masoudi-Nejad A, Nasuda S, McIntosh RA, Endo TR (2002) Transfer of rye chromosome segments to wheat by gametocidal system. Chromosome Res 10:349-357
33. Mayer KFX, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steurnagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Slase J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249-1263
34. Meyers BC, Scalabrin S, Morgante M (2004) Mapping and sequencing complex genomes: let's get physical! Nat Rev Genet 5:578-588
35. Michalak de Jimenez MK, Bassi FM, Ghavami F, Simons K, Dizon R, Seetan RI, Alnemer LM, Denton AM, DoǧramacI M, Šimková H, Doležel J, Seth K, Luo MC, Dvorak J, Gu YQ, Kianian SF (2013) A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus. Funct Integr Genomics 13:19-32
36. Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Bergès H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101-104
37. Pérez R, de Bustos A, Cuadrado Á (2009) Localization of Rad50, a single-copy gene, on group 5 chromosomes of beat, using a FISH protocol employing tyramide for signal amplification (Tyr-FISH). Cytogenet Genome Res 125:321-328
38. Peterson DG, Lapitan NLV, Stack SM (1999) Localization of single- and low-copy sequences on tomato synaptonemal complex spreads using fluorescence in situ hybridization (FISH). Genetics 152:427-439
39. Phillips D, Nibau C, Wnetrzak J, Jenkins G (2012) High resolution analysis of meiotic chromosome structure and behaviour in barley (Hordeum vulgare L.). PLoS One 7:e39539
40. Riera-Lizarazu O, Vales MI, Kianian SF (2008) Radiation hybrid (PH) and happy mapping in plants. Cytogenet Genome Res 120:233-240
41. Sakai K, Nasuda S, Sato K, Endo TR (2009) Dissection of barley chromosome 3H in common wheat and comparison of 3H physical and genetic maps. Genes Genet Syst 84:25-34
42. Sato K, Shin-I T, Seki M, Shinozaki K, Yoshida H, Takeda K, Yamanaki Y, Conte M, Kohara Y (2009) Development of 5006 full-length CDNAs in barley: a tool for accessing cereal genomics resources. DNA Res 16:81-89
43. Schnabel E, Kulikova O, Penmetsa RV, Bisseling T, Cook DR, Frugoli J (2003) An integrated physical, genetic and cytogenetic map around the sunn locus of Medicago truncatula. Genome 46:665-672
44. Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262:110-114
45. Singh RJ, Tsuchiya T (1982) An improved Giemsa N-banding technique for the identification of barley chromosomes. J Hered 73:227-229
46. Tang X, Szinay D, Lang C, Ramanna MS, van der Vossen EAG, Datema E, Lankhorst RK, de Boer J, Peters SA, Bachem C, Stiekema W, VisserR GF, de Jong H, Bai Y (2008) Cross-species bacterial artificial chromosome-fluorescence in situ hybridization painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements. Genetics 180:1319-1328
47. Tang X, de Boer JM, van Eck HJ, Bachem CH, Visser RGF, de Jong H (2009) Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology. Chromosome Res 17:399-915
48. The International Barley Genome Sequencing Consortium (2012) A physical, genetical and functional sequence assembly of the barley genome. Nature 491:711-716
49. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763-768
50. Tjio JH, Hagberg A (1951) Cytological studies on some X-ray mutants of barley. Ann Aula Dei 2:149-167
51. Tomato Genome Consortium (2012) The tomato genome sequence provides the insight into fleshy fruit evolution. Nature 485:635-641
52. Tsujimoto H, Mukai Y, Keisuke A, Nagaki K, Fujigaki J, Yamamoto M, Sasakuma T (1997) Identification of individual barley chromosomes based on repetitive sequences: conservative distribution of Afa-family repetitive sequences on the chromosome of barley and wheat. Genes Genet Syst 72:303-309
53. Valárik M, Bartoš J, Kovářová P, Kubaláková M, de Jong JH, Doležel J (2004) High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 37:940-950
54. Wang CH-JR, Harper L, Cande WZ (2006) High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18:529-544
55. Wardrop J, Sape J, Powell W, Machray GC (2002) Constructing plant radiation hybrids panel. Plant J 31:223-228
56. Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Doležel J, Keller B, Stein N (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23:1706-1718
57. Yang K, Zhang H, Converse R, Wang Y, Rong X, Wu Z, Luo B, Yue L, Jian L, Zhu L, Wang X (2011) Fluorescence in situ hybridization on plant extended chromatin DNA fibres for single-copy and repetitive DNA sequences. Plant Cell Rep 30:1779-1786
58. Zhou S, Bechner MC, Place M, Churas CP, Pape L, Leong SA, Runnheim R, Forrest D, Goldstein S, Livny M, Schwartz DC (2007) Validation of rice genome sequence by optical mapping. BMC Genomics 8:278
59. Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstain S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC (2009) A single molecule scaffold for the maize genome. PLoS Genet 5:e1000711