Genome constitution and classification using retrotransposon-based markers in the orphan crop banana

Journal of Plant Biology

Volumn 48, Issue 1, 2005, Pages 96-105

  Chee, How Teo ^a,d   Siang, Hee Tan ^b   Chai, Ling Ho ^a   Faridah, Qamaruz Zaman ^a   Othman, Yasmin Rofina ^c   Heslop Harrison, John Seymour ^d   Kalendar, Ruslan ^e   Schulman, Alan Howard ^e,f  

^a UNIVERSITY PUTRA MALAYSIA   (Malaysia)

^b Sime Darby Berhad   (Malaysia)

^c UNIVERSITY OF MALAYA   (Malaysia)

^d UNIVERSITY OF LEICESTER   (United Kingdom)

^e UNIVERSITY OF HELSINKI   (Finland)

^f FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

Genome constitution; Inter Retrotransposon Amplified Polymorphism; Long terminal repeat; Musa; Phylogenetic analysis; Retrotransposon

Indexed keywords

MUSA; MUSA ACUMINATA; MUSA BALBISIANA;

EID: 20744449042     PISSN: 12269239     EISSN: None     Source Type: Journal    
DOI: 10.1007/bf03030568     Document Type: Article

References (28)

1. Baumel A, Ainouche M, Kalendar R, Schulman AH (2002) Inter- retrotransposon amplified polymorphism (IRAP), and retotransposon-microsatellite amplified polymorphism (REMAP) in populations of the young allopolyploid species Spartina angelica Hubbard (Poaceae). Mol Biol Evol 19: 1218-1227
2. Boyko E, Kalendar R, Korzun V, Gill B, Schulman AH (2002) Combined mapping of Aegilops tauschii by retrotransposon, microsatellite, and gene markers. Plant Mol Biol 48: 767-790
3. Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucl Acids Res 20: 3639-3644
4. Flavell AJ, Knox MR, Pearce SR, Ellis THN (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16: 643-650
5. Grandbastien M-A, Spielmann A, Caboche M (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337: 376-380
6. Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture. EMBO J 12: 2521-2528
7. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93: 7783-7788
8. Horry JP, Ortiz R, Arnaud E, Crouch JH, Ferris RSB, Jones DR, Mateo N, Picq C, Vuylsteke (1997) Banana and plantain. In D Fuccillo, L Sears, P Stapleton, eds, Biodiversity in Trust. (Conservation and Use of Plant Genetic Resources in CGIAR Centres), Cambridge University, London, pp 67-81
9. Iwamoto M, Nagashima H, Nagamine T, Higo T, Higo K (1999) p-SINE1-like intron of the CatA catalase homologs and phylogenetic relationships among AA-genome Oryza and related species. Theor Appl Genet 98: 853-861
10. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman AH (1999) IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98: 704-711
11. 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
12. Kumar A, Bennetzen J (1999) Plant retrotransposons. Ann Rev Genet 33: 479-532
13. 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
14. Nakayashiki H, Ikeda K, Hashimota Y, Tosa Y, Mayama S (2001) Methylation is not the main force repressing the retrotransposon MAGGY in Magnaporthe grisea. Nucl Acids Res 29: 1278-1284
15. Pearce SR, Harrison G, Li D, Heslop-Harrison JS, Kumar A, Flavell AJ (1996) The Ty1-copia group of retrotransposons in Vicia species: Copy number, sequence heterogeneity and chromosomal localisation. Mol Gen Genet 205: 305-315
16. Pearce SR, Knox M, Ellis THN, Flavell AJ, Kumar A (2000) Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum. Mol Gen Genet 263: 898-907
17. Pearce SR, Stuart-Rogers C, Knox MR, Kumar A, Ellis THN, Flavell AJ (1999) Rapid isolation of plant Ty1-copia group retrotransposon LTR sequences for molecular marker studies. Plant J 19: 711-717
18. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
19. 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
20. Shimamura M, Yasue H, Ohshima K, Abe H, Kato H, Kishiro T, Goto M, Munechika I, Okada N (1997) Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388: 666-670
21. Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P (2000) A contiguous 66 kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10: 908-915
22. Stover P, Simmonds NW (1987) Bananas, Ed 3. Longman, London
23. Tatout C, Warwick S, Lenoir A, Deragon JM (1999) Sine insertions as clade markers for wild Crucifer species. Mol Biol Evol 16: 1614-1621
24. Teo CH, Tan SH, Othman YR, Schwarzacher T (2002) The cloning of Ty1-copia-like retrotransposons from 10 varieties of banana (Musa sp.). J Biochem Mol Biol Biophys 6: 193-201
25. Vicient CM, Jääskeläinen M, Kalendar R, Schulman AH (2001) Active retrotransposons are a common feature of grass genomes. Plant Physiol 125: 1283-1292
26. Vicient CM, Schulman AH (2002) Copia-like retrotransposons in the rice genome: few and assorted. Genome Lett 1: 35-47
27. Voytas DF, Cummings MP, Konieczny AK, Ausubel FM, Rodermel SR (1992) Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89: 7124-7128
28. 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