Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques

Molecular Genetics and Genomics

Volumn 269, Issue 4, 2003, Pages 464-474

  Leigh, F ^a   Kalendar, R ^b   Lea, V ^a   Lee, D ^a   Donini, P ^a   Schulman, A H ^b,c  

^a NATIONAL INSTITUTE OF AGRICULTURAL BOTANY   (United Kingdom)

^b UNIVERSITY OF HELSINKI   (Finland)

^c FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

Barley DNA fingerprinting Inter retrotransposon amplified polymorphism (IRAP); Retrotransposon insertional polymorphism; Retrotransposon microsatellite amplified polymorphism (REMAP); Sequence specific amplified polymorphism (S SAP) markers

Indexed keywords

MICROSATELLITE DNA; MOLECULAR MARKER; PRIMER DNA;

ARTICLE; BARLEY; DNA FINGERPRINTING; DNA POLYMORPHISM; DNA TRANSPOSITION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE INSERTION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETIC VARIABILITY; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; RETROPOSON;

DNA FINGERPRINTING; DNA PRIMERS; GENETIC MARKERS; HORDEUM; RETROELEMENTS;

EMBRYOPHYTA; HORDEUM; HORDEUM VULGARE; HORDEUM VULGARE SUBSP. VULGARE; INSERTION SEQUENCES;

EID: 0043124416     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-003-0850-2     Document Type: Article

References (27)

1. Boeke JD, Corces VG (1989) Transcription and reverse transcription of retrotransposons. Annu Rev Microbiol 43:403-434
2. Boeke JD, Garfinkel DJ, Styles CA, Fink GR (1985) Ty elements transpose through an RNA intermediate. Cell 40:491-500
3. Boyko E, Kalendar R, Korzun V, Korol A, Schulman AH, Gill BS (2002) A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defence related genes: insights into cereal chromosome structure and function. Plant Mol Biol 48:767-790
4. Ellis THN, Poyser SJ, Knox MR, Vershinin AV, Ambrose MJ (1998) Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol Gen Genet 260:9-19
5. Fedoroff N (2000) Transposons and genome evolution in plants. Proc Natl Acad Sci USA 97:7002-7007
6. Gribbon BM, Pearce SR, Kalendar R, Schulman AH, Paulin L, Jack PL, Kumar A, Flavell AJ (1999) Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Mol Gen Genet 261:883-891
7. Jääskeläinen M, Mykkänen A-H, Arna T, Vicient C, Suoniemi A, Kalendar R, Savilahti H, Schulman AH (1999) Retrotransposon BARE -1: expression of encoded proteins and formation of virus-like particles in barley cells. Plant J 20:413-422
8. Jackson JA, Matthews D (2000) A modified inter-SSR PCR protocol for use in conjunction with the LI-COR Gene ReadIR 4200 DNA analyser. Biotechniques 28:914-920
9. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor App Gen 98:704-711
10. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE -1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603-6607
11. Kumar A, Bennetzen J (1999) Plant retrotransposons. Annu Rev Genet 33:479-532
12. Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison JS, Waugh R, Flavell AJ (1997) The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. Genetica 100:205-217
13. Lee D, Ellis THN, Turner L, Hellens RP, Cleary WG (1990) A copia-like element in Pisum demonstrates the uses of dispersed repeated sequences in genetic analysis. Plant Mol Biol 15:707-722
14. Manninen I, Schulman AH (1993) BARE -1, a copia -like retroelement in barley (Hordeum vulgare L.). Plant Mol Biol 22:829-846.
15. Manninen O, Kalendar R, Robinson J, Schulman AH (2000) Application of BARE -1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley. Mol Gen Genet 264:325-334
16. Panstruga R, Büschges R, Piffanelli P, Schulze-Lefert P (1999) A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res 26:1056-1062
17. Porceddu A, Albertini E, Baracaccia G, Marconi, G, Bertoli FB, Veronesi, F (2002) Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L. Mol Gen Genet 267:107-114
18. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768
19. Shirasu K, Schulman AS, Lahaye T, Schulze-Lefert P (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10:908-915
20. Suoniemi A, Narvanto A, Schulman AH (1996) The BARE -1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol Biol 31:295-306
21. Suoniemi A, Schmidt D, Schulman, AH (1997) BARE -1 insertion site preferences and evolutionary conservation of RNA and cDNA processing sites. Genetica 100:219-230
22. Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH (1999) Retrotransposon BARE -1 and its role in genome evolution in the genus Hordeum. Plant Cell 11:1769-1784
23. Vicient CM, Kalendar R, Schulman AH (2001) Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Res 11:2041-2049
24. Vos P, Hogers R, Bleeker M, Reijans M, van der Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
25. Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W (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
26. Wei F, Wing RA, Wise RP (2002) Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 14:1903-1917
27. Xiong Y, Eickbush TH (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9:3353-3362