Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome

Molecular Genetics and Genomics

Volumn 280, Issue 4, 2008, Pages 275-285

  Lyons, Maura ^a   Cardle, Linda ^b   Rostoks, Nils ^b,c   Waugh, Robbie ^a   Flavell, Andrew J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^c UNIVERSITY OF LATVIA   (Latvia)

Author keywords

Barley; Genetic diversity; MITE; SSAP; Transposable element

Indexed keywords

ARTICLE; BARLEY; DNA POLYMORPHISM; DNA SEQUENCE; DNA STRUCTURE; GEL ELECTROPHORESIS; GENE IDENTIFICATION; GENE INSERTION; GENE ISOLATION; GENE NUMBER; GENETIC ANALYSIS; GENETIC VARIABILITY; GERMPLASM; INVERTED REPEAT; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; GENETIC MARKERS; GENOME, PLANT; HAPLOIDY; HORDEUM; INVERTED REPEAT SEQUENCES; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA;

ACARI; HORDEUM;

EID: 51349111169     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-008-0363-0     Document Type: Article

References (46)

1. A Badr K Muller R Schafer-Pregl H El Rabey S Effgen HH Ibrahim C Pozzi W Rohde F Salamini 2000 On the origin and domestication history of Barley (Hordeum vulgare) Mol Biol Evol 17 499 510
2. C Braquart V Royer H Bouhin 1999 DEC: a new miniature inverted-repeat transposable element from the genome of the beetle Tenebrio molitor Insect Mol Biol 8 571 574
3. B Bender N Kleckner 1986 Genetic evidence that Tn10 transposes by a nonreplicative mechanism Cell 45 801 815
4. BioEdit biological sequence alignment editor for Windows (1997) http://www.mbio.ncsu.edu/BioEdit/BioEdit.html
5. TE Bureau SR Wessler 1992 Tourist-a large family of small inverted repeat elements frequently associated with maize genes Plant Cell 4 1283 1294
6. TE Bureau SR Wessler 1994 Stowaway-a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants Plant Cell 6 907 916
7. TE Bureau SR Wessler 1994 Mobile inverted-repeat elements of the tourist family are associated with the genes of many cereal grasses Proc Natl Acad Sci USA 91 1411 1415
8. AM Casa C Brouwer A Nagel L Wang Q Zhang S Kresovich SR Wessler 2000 The MITE family heartbreaker (Hbr): molecular markers in maize Proc Natl Acad Sci USA 97 10083 10089
9. AM Casa SE Mitchell OS Smith JC Register III SR Wessler S Kresovich 2002 Evaluation of Hbr (MITE) markers for assessment of genetic relationships among maize (Zea mays L.) inbred lines Theor Appl Genet 104 104 110
10. RY Chang LS O'Donoughue TE Bureau 2001 Inter-MITE polymorphisms (IMP): a high throughput transposon- based genome mapping and fingerprinting approach Theor Appl Genet 102 773 781
11. Fedoroff N (1989) In: Howe M, Berg D (eds) Mobile DNA. Am Soc Microbiol, Washington, DC, pp 375-411
12. C Feschotte C Mouches 2000 Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon Mol Biol Evol 17 730 737
13. N Jiang SR Wessler 2001 Insertion preference of maize and rice miniature inverted repeat transposable elements as revealed by the analysis of nested elements Plant Cell 13 2553 2564
14. R Jing MR Knox JM Lee AV Vershinin MJ Ambrose THN Ellis AJ Flavell 2005 Insertional polymorphism and antiquity of PDR1 retrotransposon insertions in Pisum species Genetics 171 741 752
15. R Kalendar T Grob M Regina A Suoniemi A Schulman 1999 IRAP and REMAP: two new retrotransposon-based fingerprinting techniques Theoret Appl Genet 98 704 711
16. T Langdon G Jenkins R Hasterok R Neil Jones IP King 2003 A high-copy number CACTA family transposon in temperate grasses and cereals Genetics 163 1097 1108
17. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez JD Thompson TJ Gibson DG Higgins 2007 ClustalW and ClustalX version 2 Bioinformatics 23 2947 2948
18. H Le Quang S Wright ZH Yu T Bureau 2000 Transposon diversity in Arabidopsis thaliana Proc Nat Acad Sci USA 97 7376 7381
19. D Lepetit S Pasquet M Olive N Theze P Thiebaud 2000 Glider and vision: two new families of miniature inverted-repeat transposable elements in Xenopus laevis genome Genetica 108 163 169
20. K Madishetty P Condamine JT Svensson E Rodriguez TJ Close 2007 An improved method to identify BAC clones using pooled overgos Nucleic Acids Res 35 e5 e7
21. L Mao TC Wood Y Yu MA Budiman J Tomkins S Woo M Sasinowski G Presting D Frisch S Goff 2000 Rice transposable elements: a survey of 73, 000 sequence-tagged- connectors Genome Res 10 982 990
22. NCBI Expressed Sequence Tags Database (1993) http://www.ncbi.nlm.nih.gov/ projects/dbEST/
23. T Nakazaki Y Okumoto A Horibata S Yamahira M Teraishi H Nishida H Inoue T Tanisaka 2003 Mobilization of a transposon in the rice genome Nature 421 170 172
24. KC Park NH Kim YS Cho KH Kang JK Lee N-S Kim 2003 Genetic variations of AA genome Oryza species measured by MITE-AFLP Theor Appl Genet 107 2 203 209
25. Phylip phylogeny inference package (1980) http://evolution.genetics. washington.edu/phylip.html
26. P Rice I Longden A Bleasby 2000 EMBOSS: the European molecular biology open software suite Trends Genet 16 276 277
27. N Rostoks D Schmierer S Mudie T Drader R Brueggeman D Caldwell R Waugh A Kleinhofs 2006 Barley necrotic locus nec1 encodes the cyclic nucleotide-gated ion channel 4 homologous to the Arabidopsis HLM1 Mol Genet Genomics 275 159 168
28. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365-386
29. AH Schulman R Kalendar 2005 A movable feast: diverse retrotransposons and their contribution to barley genome dynamics Cytogenet Genome Res 110 598 605
30. J Shapiro 1979 A molecular model for the transposition and replication of bacteriophage Mu and other transposable elements Proc Nat Acad Sci USA 76 1933 1937
31. WY Song LY Pi TE Bureau PC Ronald 1998 Identification and characterization of 14 transposon-like elements in the noncoding regions of members of the Xa21 family of disease resistance genes in rice Mol Gen Genet 258 449 456
32. N Syed S Sundar M Wilkinson B Bhau J Cavalcanti AJ Flavell 2005 Ty1-copia retrotransposon-based SSAP marker development in Cashew (Anacardium occidentale L.) Theor Appl Genet 110 1195 1202
33. NH Syed AJ Flavell 2007 Sequence specific amplification polymorphisms (SSAP) - a multi-locus approach for analysing transposon insertions Nat Protoc 1 2746 2752
34. C Tatout S Warwick A Lenoir J-M Deragon 1999 SINE insertions as clade markers for wild crucifer species Mol Biol Evol 16 1614 1621
35. Triticeae Repeat Database (2000) In GrainGenes http://wheat.pw.usda.gov/ ggpages/oatCoP.html (17 Nov. 2000).
36. K Turcotte S Srinivasan T Bureau 2001 Survey of transposable elements from rice genomic sequences Plant J 25 169 179
37. KJF Verhoeven TK Vanhala A Biere E Nevo JMM Van Damme 2004 The genetic basis of adaptive population differentiation: a quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats Evolution 58 270 283
38. S Volis B Yakubov I Shulgina D Ward S Mendlinger 2005 Distinguishing adaptive from nonadaptive genetic differentiation: comparison of Qst and Fst at two spatial scales Heredity 95 466 475
39. P Vos R Hogers M Bleeker M Reijans T van de Lee M Hornes A Fritjers J Pot J Peleman M Kuiper M Zabeau 1995 AFLP: a new concept for DNA fingerprinting Nucleic Acid Res 23 4407 4414
40. R Waugh K McLean AJ Flavell SR Pcarce A Kumar BB Thomas W Powell 1997 Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP) Mol Gen Genet 253 687 694
41. T Wicker R Guyot N Yahiaoui B Keller 2003 CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements Plant Physiol 132 52 63
42. GJ Yang TC Hall 2003 MDM-1 and MDM-2: two mutator-derived MITE families in rice J Mol Evol 56 255 264
43. SR Yant L Meuse W Chiu Z Ivics Z Izsvak MA Kay 2000 Somatic integration and long-term transgene expression in normal and haemophilic mice using a DNA transposon system Nature Rev Genet 25 35 41
44. Y Yu JP Tomkins R Waugh DA Frisch D Kudrna A Kleinhofs RS Brueggeman GJ Muehlbauer RP Wise RA Wing 2000 A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes Theor Appl Genet 101 1093 1099
45. Q Zhang J Arbuckle SR Wessler 2000 Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize Proc Natl Acad Sci USA 97 1160 1165
46. X Zhang C Feschotte Q Zhang N Jiang WB Eggleston SR Wessler 2001 P instability factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases Proc Natl Acad Sci USA 98 12572 12577