Fat element-a new marker for chromosome and genome analysis in the Triticeae

Chromosome Research

Volumn 18, Issue 6, 2010, Pages 697-709

  Badaeva, Ekaterina D ^a   Zoshchuk, Svyatoslav A ^a   Paux, Etienne ^b   Gay, Georges ^b   Zoshchuk, Natalia V ^a   Roger, Delphine ^b   Zelenin, Alexander V ^a   Bernard, Michel ^b   Feuillet, Catherine ^b  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b Diversity and Ecophysiology of Cereals   (France)

Author keywords

cereal; chromosome; evolution; Fat sequence; Fluorescence in situ hybridisation (FISH); genome

Indexed keywords

AGROPYRON; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BARLEY; BIOINFORMATICS; CEREAL; CHROMOSOME 3; CHROMOSOME ANALYSIS; CHROMOSOME IDENTIFICATION; CLONE; CROP; ELYMUS; FLUORESCENCE IN SITU HYBRIDIZATION; GENOME ANALYSIS; GENUS; HORDEUM CHILENSE; HORDEUM GENICULATUM; HORDEUM SPONTANEUM; LAST COMMON ANCESTOR; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OAT; POACEAE; PRIORITY JOURNAL; RYE; SPECIES; TRITICALE; TRITICEAE; WHEAT;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; GENETIC MARKERS; GENOME, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; POACEAE; POLYPLOIDY; REPETITIVE SEQUENCES, NUCLEIC ACID;

AEGILOPS; AEGILOPS X TRITICUM; AGROPYRON; AVENA; BACTERIA (MICROORGANISMS); ELYMUS; HORDEUM; HORDEUM CHILENSE; HORDEUM MARINUM GUSSONIANUM; HORDEUM VULGARE; HORDEUM VULGARE SUBSP. SPONTANEUM; POACEAE; SECALE; TRITICEAE; TRITICOSECALE; TRITICUM; TRITICUM AESTIVUM;

EID: 77956918118     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-010-9151-x     Document Type: Article

References (65)

1. M Abubakar G Kimber 1982 Chromosome-pairing regulators in the former genus Aegilops Z Pflanzenzucht 89 130 138
2. EV Ananiev MI Vales RL Phillips HW Rines 2002 Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa Genome 45 431 441 1:CAS:528:DC%2BD38XjtlSnsbs%3D 10.1139/g01-148 11962640 (Pubitemid 34253917)
3. ED Badaeva B Friebe BS Gill 1996 Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosomes of diploid species Genome 39 293 306 1:CAS:528:DyaK28XjtVyjtbs%3D 10.1139/g96-040 18469894
4. ED Badaeva AV Amosova OV Muravenko, et al. 2002 Genome differentiation in Aegilops. 3. Evolution of the D-genome cluster Plant Syst Evol 231 163 190 1:CAS:528:DC%2BD38Xks1yis7c%3D 10.1007/s006060200018 (Pubitemid 34294012)
5. ED Badaeva AV Amosova TE Samatadze, et al. 2004 Genome differentiation in Aegilops. 4. Evolution of the U-genome cluster Plant Syst Evol 246 45 76 1:CAS:528:DC%2BD2cXjsFKqtr0%3D 10.1007/s00606-003-0072-4 (Pubitemid 38831273)
6. E Badaeva O Dedkova J Koenig S Bernard M Bernard 2008 Analysis of introgression of Aegilops ventricosa Tausch. genetic material in a common wheat background using C-banding Theor Appl Genet 117 803 811 1:CAS:528: DC%2BD1cXhtVSnsrjO 10.1007/s00122-008-0821-4 18597067
7. D Bardsley A Cuadrado P Jack, et al. 1999 Chromosome markers in the tetraploid wheat Aegilops ventricosa analysed by in situ hybridization Theor Appl Genet 99 300 304 10.1007/s001220051236 (Pubitemid 29373082)
8. RJ Bedbrook J Jones M O'Dell RJ Thompson RB Flavell 1980 A molecular description of telomeric heterochromatin in Secale species Cell 19 545 560 1:CAS:528:DyaL3cXhsVentr8%3D 10.1016/0092-8674(80)90529-2 6244112
9. A Belyayev O Raskina E Nevo 2001 Chromosomal distribution of reverse transcriptase-containing retroelements in two Triticeae species Chromosome Res 9 129 136 1:CAS:528:DC%2BD3MXislaqtbw%3D 10.1023/A:1009231019833 11321368 (Pubitemid 32269985)
10. A Belyayev O Raskina E Nevo 2005 Variability of the chromosomal distribution of Ty3-gypsy retrotransposons in the populations of two wild Triticeae species Cytogenet Genome Res 109 43 49 1:CAS:528:DC%2BD2MXitFeku7o%3D 10.1159/000082380 15753557 (Pubitemid 40470303)
11. A Cabrera B Friebe J Jiang BS Gill 1995 Characterization of Hordeum chilense chromosomes by C-banding and in situ hybridization using highly repeated DNA probes Genome 38 435 442 1:STN:280:DC%2BD1czgsl2rtg%3D%3D 18470181
12. M Charles H Belcram J Just, et al. 2008 Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat Genetics 180 1071 1086 1:CAS:528:DC%2BD1cXhtlWnurvM 10.1534/genetics.108.092304 18780739
13. Q Chen RL Conner A Laroche JB Thomas 1998 Genome analysis of Thinopyrum intermedium and Thinoryrum ponticum using genomic in situ hybridization Genome 41 580 586 1:CAS:528:DyaK1cXntlWks78%3D 10.1139/gen-41-4-580 9796107
14. A Cuadrado N Jouve 2002 Evolutionary trends of different repetitive DNA sequences during speciation in the genus Secale J Hered 93 339 345 1:CAS:528:DC%2BD3sXhtFyku70%3D 10.1093/jhered/93.5.339 12547922 (Pubitemid 36083968)
15. Dewey DR (1984) The genomic system of classification as a guide to intergeneric hybridization with the perennial Triticeae. In: Gustafson JP (ed) Gene manipulation in plant improvement. Plenum, New York, pp 209-280
16. J Dubkovsky J Dvořák 1994 Genome origin of Triticum cylindricum, Triticum triunciale, and Triticum ventricosum (Poaceae) inferred from variation in repeated nucleotide sequences: A methodological study Am J Bot 81 1327 1335 10.2307/2445408
17. J Dubkovsky J Dvořák 1995 Genome identification of the Triticum crassum complex (Poaceae) with the restriction patterns of repeated nucleotide sequences Am J Bot 182 131 140 10.2307/2445795
18. Dvořák J, Dubkovsky J (1996) Genome analysis of polyploid species employing variation in repeated nucleotide sequences. In: Jauhar PP (ed) Methods in genome analysis in plants. CRC, Boca Raton, pp 133-145
19. J Dvořák HB Zhang 1992 Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences Theor Appl Genet 84 419 429 10.1007/BF00229502
20. Feldman M (2001) Origin of cultivated wheat. In: Bonjean AP, Angus WJ (eds) The world wheat book: a history of wheat breeding. Intersept, London, pp 3-56
21. RB Flavell 1986 Repetitive DNA and chromosome evolution in plants Philos Trans R Soc Lond B Biol Sci 312 227 242 1:CAS:528:DyaL28XhvVWjsrk%3D 10.1098/rstb.1986.0004 2870519
22. RB Flavell MD Bennett JB Smith DB Smith 1974 Genome size and the proportion of repeated sequence DNA in plants Biochem Genet 12 257 269 1:CAS:528:DyaE2MXntVeguw%3D%3D 10.1007/BF00485947 4441361
23. RB Flavell J Rimpau DB Smith 1977 Repeated sequence DNA relationships in four cereal genomes Chromosoma 63 205 222 1:CAS:528:DyaE1cXjt1Sg 10.1007/BF00327450 (Pubitemid 8189388)
24. R Flavell M O'Dell D Smith 1979 Repeated sequence DNA comparisons between Triticum and Aegilops species Heredity 42 309 322 1:CAS:528:DyaL3cXjt12h 10.1038/hdy.1979.34
25. BR Friebe NA Tuleen BS Gill 1999 Development and identification of a complete set of Triticum aestivum-Aegilops geniculata chromosome addition lines Genome 42 374 380 10.1139/gen-42-3-374
26. WL Gerlach JR Bedbrook 1979 Cloning and characterization of ribosomal RNA genes from wheat and barley Nucleic Acids Res 7 1869 1885 1:CAS:528: DyaL3cXlsFamsQ%3D%3D 10.1093/nar/7.7.1869 537913
27. WL Gerlach TA Dyer 1980 Sequence organization of the repeated units in the nucleus of wheat which contains 5S-rRNA genes Nucleic Acids Res 8 4851 4865 1:CAS:528:DyaL3cXmtlGgs7s%3D 10.1093/nar/8.21.4851 7443527
28. SIS Grewal D Moazed 2003 Heterochromatin and epigenetic control of gene expression Science 301 798 802 1:CAS:528:DC%2BD3sXmtVGqsLk%3D 10.1126/science.1086887 12907790 (Pubitemid 36962612)
29. JS Heslop-Harrison 2000 Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes Plant Cell 12 617 636 1:CAS:528:DC%2BD3cXjvFyhur8%3D 10.1105/tpc.12.5.617 10810139 (Pubitemid 30343577)
30. S Huang A Sirikhachornkit X Su, et al. 2002 Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat Proc Natl Acad Sci USA 99 8133 8138 1:CAS:528:DC%2BD38XkvVGju78%3D 10.1073/pnas.072223799 12060759 (Pubitemid 34651018)
31. ML Irigoyen Y Loarce C Linares, et al. 2001 Discrimination of the closely related A and B genomes in AABB tetraploid species of Avena Theor Appl Genet 103 1160 1166 1:CAS:528:DC%2BD38XhtVyrsL8%3D 10.1007/s001220100723 (Pubitemid 34045649)
32. O Jaillon J-M Aury B Noel, et al. 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449 463 467 1:CAS:528:DC%2BD2sXhtV2is7%2FF 10.1038/nature06148 17721507 (Pubitemid 47509545)
33. J Jiang BS Gill G Wang PC Ronald DC Ward 1995 Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes Proc Natl Acad Sci USA 92 4487 4491 1:CAS:528: DyaK2MXls1aksL8%3D 10.1073/pnas.92.10.4487 7753830
34. JDG Jones RB Flavell 1982 The mapping of highly-repeated DNA families and their relationship to C-bands in chromosomes of Secale cereale Chromosoma 86 595 612 10.1007/BF00285606 (Pubitemid 13172111)
35. JDG Jones RB Flavell 1982 The structure, amount and chromosomal localisation of defined repeated DNA sequences in species of the genus Secale Chromosoma 86 613 641 1:CAS:528:DyaL3sXltVGluw%3D%3D 10.1007/BF00285607 (Pubitemid 13172112)
36. A Katsiotis T Schmidt JS Heslop-Harrison 1996 Chromosomal and genomic organization of Ty1-copia-like retrotransposon sequences in the genus Avena Genome 39 410 417 1:CAS:528:DyaK28XjtVyjurk%3D 10.1139/g96-052 8984007
37. G Kimber PJ Sallee MM Feiner 1988 The interspecific and evolutionary relationships of Triticum ovatum Genome 30 218 221 10.1139/g88-037
38. W Li P Zhang JP Fellers B Friebe BS Gill 2004 Sequence composition, organization, and evolution of the core Triticeae genome Plant J 40 500 511 1:CAS:528:DC%2BD2cXhtVyit7vJ 10.1111/j.1365-313X.2004.02228.x 15500466 (Pubitemid 39484170)
39. KY Lim R Matyasek A Kovarik J Fulnecek AR Leitch 2005 Molecular cytogenetics and tandem repeat sequence evolution in the allopolyploid Nicotiana rustica compared with diploid progenitors N. paniculata and N. undulata Cytogenet Genome Res 109 298 309 1:CAS:528:DC%2BD2MXitFersrk%3D 10.1159/000082413 15753590 (Pubitemid 40470336)
40. C Linares Y Loarce AAF Serna 2001 Isolation and characterization of two novel retrotransposons of the Ty1-copia group in oat genomes Chromosoma 110 115 123 1:CAS:528:DC%2BD3MXjsFKjtb0%3D 10.1007/s004120100138 11453554
41. G Linc BR Friebe RG Kynast, et al. 1999 Molecular cytogenetic analysis of Aegilops cylindrica Host Genome 42 497 503 1:STN:280:DyaK1MzhtFejtw%3D%3D 10.1139/gen-42-3-497 10382296
42. K Nagaki M Kishii H Tsujimoto T Sasakuma 1999 Tandem repetitive Afa-family sequences from Leymus racemosa and Psathyrostachys juncea (Poaceae) Genome 42 1258 1260 1:CAS:528:DC%2BD3cXpt12quw%3D%3D 10.1139/gen-42-6-1258 10659796
43. AH Paterson JE Bowers R Bruggmann, et al. 2009 The Sorghum bicolor genome and the diversification of grasses Nature 457 551 556 1:CAS:528: DC%2BD1MXhtFOmsb4%3D 10.1038/nature07723 19189423
44. E Paux D Roger E Badaeva, et al. 2006 Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B Plant J 48 463 474 1:CAS:528:DC%2BD28Xht1ahsLbN 10.1111/j.1365-313X.2006.02891.x 17010109 (Pubitemid 44571151)
45. E Paux P Sourdille J Salse, et al. 2008 A physical map of the 1-gigabase bread wheat chromosome 3B Science 322 101 104 1:CAS:528:DC%2BD1cXhtFyhurnK 10.1126/science.1161847 18832645
46. AL Rayburn BS Gill 1986 Isolation of a D-genome specific repeated DNA sequence from Aegilops squarrosa Plant Mol Biol Rep 4 104 109 10.1007/BF02732107
47. P Resta HB Zhang J Dubkovsky J Dvořák 1996 The origin of the genomes of Triticum biunciale, T. ovatum, T. neglectum, T. columnare, and T. rectum based on variation in repeated nucleotide sequences Am J Bot 83 1556 1565 1:CAS:528:DyaK2sXmtVCisA%3D%3D 10.2307/2445829
48. T Schmidt S Kubis JS Heslop-Harrison 1995 Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgaris L.): LINEs and Ty1-copia-like elements as major components of the genome Chromosome Res 3 335 345 1:CAS:528:DyaK2MXmvFCrtL0%3D 10.1007/BF00710014 7551548
49. PS Schnable D Ware RS Fulton, et al. 2009 The B73 maize genome: complexity, diversity, and dynamics Science 326 1112 1115 1:CAS:528: DC%2BD1MXhsVentLvL 10.1126/science.1178534 19965430
50. A Schneider G Linc M Molnar-Lang 2003 Fluorescence in situ hybridization polymorphism using two repetitive DNA clones in different cultivars of wheat Plant Breed 122 396 400 1:CAS:528:DC%2BD3sXpslGgtbk%3D 10.1046/j.1439-0523.2003. 00891.x (Pubitemid 37293151)
51. A Schneider I Molnár M Molnár-Láng 2008 Incorporation of Aegilops biuncialis chromosomes into wheat and their identification using fluorescent in situ hybridization Acta Biol Szeged 52 133 137
52. Sequencing Project International Rice G 2005 The map-based sequence of the rice genome Nature 436 793 800 10.1038/nature03895 (Pubitemid 41160631)
53. S Sharma SN Raina 2005 Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes Cytogenet Genome Res 109 15 26 1:CAS:528:DC%2BD2MXitFeku74%3D 10.1159/000082377 15753554 (Pubitemid 40470300)
54. R Solano G Hueros A Fominaya E Ferrer 1992 Organization of repeated sequences in species of the genus Avena Theor Appl Genet 83 602 607 10.1007/BF00226904
55. SE Staton MC Ungerer RC Moore 2009 The genomic organization of Ty3/gypsy-like retrotransposons in Helianthus (Asteraceae) homoploid hybrid species Am J Bot 96 1646 1655 1:CAS:528:DC%2BD1MXhtF2jtLvP 10.3732/ajb.0800337
56. GL Sun T Daley Y Ni 2007 Molecular evolution and genome divergence at RPB2 gene of the St and H genomes in Elymus species Plant Mol Biol 64 645 655 1:CAS:528:DC%2BD2sXntlajsLs%3D 10.1007/s11103-007-9183-6 17551673 (Pubitemid 47036782)
57. S Taketa H Ando K Takeda GE Harrison JS Heslop-Harrison 2000 The distribution, organization and evolution of two abundant and widespread repetitive DNA sequences in the genus Hordeum Theor Appl Genet 100 169 176 1:CAS:528:DC%2BD3cXhs1Gmsbo%3D 10.1007/s001220050023
58. The Arabidopsis Genome Initiative 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 796 815 10.1038/35048692 (Pubitemid 32016083)
59. W Thomas T Stefan H Andreas, et al. 2009 A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley Plant J 59 712 722 10.1111/j.1365-313X.2009.03874.x
60. AV Vershinin T Schwarzacher JS Heslop-Harrison 1995 The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes Plant Cell 7 1823 1833 1:CAS:528:DyaK2MXpslOns7k%3D 10.1105/tpc.7.11.1823 8535136 (Pubitemid 3019798)
61. Y Yen G Kimber 1990 The U genome in Triticum ovatum from Turkey Cereal Res Commun 18 13 19
62. Y Yen G Kimber 1992 Genomic relationships on N-genome Triticum species Genome 35 962 966
63. HB Zhang J Dvorak 1992 The genome origin and evolution of hexaploid Triticum crassum and Triticum syriacum determined from variation in repeated nucleotide sequences Genome 35 806 814 1:CAS:528:DyaK3sXls1equw%3D%3D
64. H-B Zhang J Dvořák JG Waines 1992 Diploid ancestry and evolution of Triticum kotschyi and T. peregrinum examined using variation in repeated nucleotide sequences Genome 35 182 191 1:CAS:528:DyaK38XkvVCntL4%3D
65. P Zhang W Li J Fellers B Friebe BS Gill 2004 BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements Chromosoma 112 288 299 1:CAS:528:DC%2BD2cXisV2isb0%3D 10.1007/s00412-004-0273-9 14986017 (Pubitemid 38477258)