Development of new marker methods - An example from oil palm

Plant Genetic Resources: Characterisation and Utilisation

Volumn 1, Issue 2-3, 2003, Pages 103-113

  Price, Zuzana ^a   Schulman, Alan H ^b,c   Mayes, Sean ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF HELSINKI   (Finland)

^c FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

Cocos nucifera; Copia like retrotransposons; Diversity; Elaeis guineensis; Elaeis oleifera

Indexed keywords

ARECACEAE; COCOEAE; COCOS NUCIFERA; ELAEIS; ELAEIS GUINEENSIS; ELAEIS OLEIFERA; EMBRYOPHYTA; TRANSPOSONS;

EID: 2642518248     PISSN: 14792621     EISSN: None     Source Type: Journal    
DOI: 10.1079/pgr200317     Document Type: Review

References (64)

1. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
2. Balint-Kurti PJ, Clendennen SK, Dolezelova M, Valarik M, Dolezel J, Beetham PR and May GD (2000) Molecular Genetics and Genomics 263: 908-915.
3. Baumel A, Ainouche M, Kalendar R and Schulman AH (2002) Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae). Molecular Biology and Evolution 19: 1218-1227.
4. Bhattacharyya MK, Gonzales RA, Kraft M and Buzzll RI (1997) A copia-like retrotransposon Tgmr closely linked to the R K allele that confers race specific resistance to soybean to Phytophthora sojae. Plant Molecular Biology 34: 255-264.
5. Boyko E, Kalendar R, Korzun V, Fellers J, Korol A, Sculman AH and 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 Molecular Biology 48: 767-790.
6. Breto MP, Ruiz C, Pina JA and Asins MJ (2001) The diversification of Citrus clementina Hort. Ex Tan., a vegetatively propagated crop species. Molecular Phylogenetics and Evolution 21: 285-293.
7. Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresiwich S and Wessler SR (2000) The MITE family Heartbreaker (Hbr): molecular markers in maize. Proceedings of the National Academy of Science USA 97: 10083-10089.
8. Castilho A, Vershinin A and Heslop-Harrison JS (2000) Repetitive DNA and the chromosomes in the genome of oil palm (Elaeis guineensis). Annals of Botany 85: 837-844.
9. Chang RY, O'Donoughue LS and Bureau TE (2001) Inter-MITE polymorphisms (IMP): a high throughput transposon-based genome mapping and fingerprinting approach. Theoretical and Applied Genetics 102: 773-781.
10. Ellis THN, Poyser IJ, Knox MR, Vershinin AV and Ambrose MJ (1998) Ty1 copia class retrotransposon insertion site polymorphism for linkage and diversity analysis in pea. Molecular Genetics and Genomics 260: 9-19.
11. Feschotte C, Jiang N and Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nature Reviews 3: 329-341.
12. Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R and Kumar A (1992) Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Research 20: 3639-3644.
13. Gabriel A and Mules EH (1999) Fidelity of retrotransposon replication. Annals of the New York Academy of Science 870: 108-118.
14. Gribbon BM, Pearce SR, Kalendar R, Schulman AH, Paulin L, Jack P, Kumar A and Flavell AJ (1999) Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes. Molecular Genetics and Genomics 261: 883-891.
15. Hirochika H (2001) Contribution of the Tos17 retrotransposon to rice functional genomics. Current Opinions in Plant Biology 4: 118-122.
16. Iwamoto M, Nagashima H, Nagamine T, Hogo H and Higo K (1999) p-SINE1-like intron of the CatA catalase homologs and phylogenetic relationships among AA-genome Oryza and related species. Theoretical and Applied Genetics 98: 853-861.
17. Jääskeläinen M, Mykkänen TA, Vicient CM, Suoniemi A, Kalendar R, Savilahti H and Schulman AH (1999) Retrotransposonn BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. Plant Journal 20: 413-422.
18. Jones DL (1994) Palms Throughout the World. Australia: Reed New Holland Publishers.
19. Kalendar R, Grob T, Regina M, Suoniemi A and Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics 98: 704-711.
20. Kalendar R, Tanskanen J, Immonen S, Nevo E and Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by Bare-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proceedings of the National Academy of Science USA 97: 6603-6607.
21. Kenward KD, Bai D, Ban MR and Brandle JE (1998) Isolation and characterization of Tnd-1, a retrotransposon marker linked to black rot resistance in tobacco. Theoretical and Applied Genetics 198: 387-395.
22. Kubis S, Schmidt T and Heslop-Harrison JS (1998) Repetitive DNA elements as a major component of plant genomes. Annals of Botany 82: 45-48.
23. Kumar A and Bennetzen JL (1999) Plant retrotransposons. Annual Review of Genetics 33: 479-532.
24. Kumar A and Hirochika H (2001) Applications of retrotransposons as genetic tools in plant biology. Trends in Plant Science 6: 127-133.
25. Kumar A, Pearce SR, McLean K, Harrison G, Heslop-Harrison JS, Waugh R and Flavell AJ (1997) The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution and use as molecular markers. Genetica 100: 205-217.
26. Lee DL, Ellis THN, Turner L, Hellens RP and Cleary WG (1990) A copia-like element in Pisum demonstrates the uses of dispersed repeated sequences in genetic analysis. Plant Molecular Biology 15: 707-722.
27. Lee SJ, Jeung JU, Cho SK, Um BY, Chung WI, Bae JM and Shin JS (2002) Diversity and varietal classification of Hibiscus syriacus L with the heterogeneity within retrotransposon-like elements. Molecular Cells 30: 362-368.
28. Manninen O, Kalendar R, Robinson J and Schulman AH (2000) Application of BARE-1 retrotransposon markers to the mapping of major resistance gene for net blotch in barley. Molecular Genetics and Genomics 264: 325-334.
29. Matsuoka Y and Tsunewaki K (1999) Evolutionary dynamics of Ty1-copia group retrotransposons in grass shown by reverse transcriptase domain analysis. Molecular Biology and Evolution 16: 208-217.
30. Melayah D, Bonnivard E, Chalhoub B, Audeon C and Grandbastien MA (2001) The mobility of the Tobacco Tnt1 retrotransposon correlates with its transcriptional activation by fungal factors. Plant Journal 28: 159-168.
31. Mhiri C and Grandbastien MA (2001) Analysis of Solanaceae biodiversity using Tnt1-related retrotransposons. In: Proceedings of the 1st ESF Meeting on 'Retrotransposons; Their Impact on Organisms, Genomes, and Biodiversity'.
32. Okamoto H and Hirochika H (2000) Efficient insertion mutagenesis of arabidopsis by tissue culture-induced activation of the tobacco retrotransposon Tto1. Plant Journal 23: 291-304.
33. Panstruga R, Blschges R, Piffanelli P and Schulze-Lefert P (1998) A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Research 26: 1056-1062.
34. Pearce SR, Harrison G, Li D, Heslop-Harison JS, Kumar A and Flavell AJ (1996) The Ty1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation. Molecular Genetics and Genomics 250: 305-315.
35. Pearce SR, Harrison G and Heslop-Harrison JS (1997) Characterization and genomic organization of Ty1-copia retrotransposon in rye (Secale cereale). Genome 40: 617-625.
36. Pearce SR, Stuart-Rogers C, Knox MR, Kumar A, Ellis THN and Flavell A (1999) Rapid isolation of plant Ty1-copia retrotransposon sequences for molecular marker studies. Plant Journal 19: 711-717.
37. Pearce SR, Knox M, Ellis TNH, Flavell AJ and Kumar A (2000) Pea Ty1-copia group retrotransposons: transitional activity and use as markers to study genetic diversity in Pisum. Molecular Genetics and Genomics 203: 898-907.
38. Pelcy F and Merdinoglu D (2002) Development of grape molecular markers based on retrotransposons. Poster at Plant, Animal and Microbe Genome X, San Diego.
39. Porceddu A, Albertini E, Barcaccia G, Marconi G, Bertoli FB and Veronesi F (2002) Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L. Molecular Genetics and Genomics 267: 107-114.
40. Posada D and Crandall KA (1998) MODEL TEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
41. Presting GG, Malysheva L, Fuchs J and Schubert I (1998) A Ty3/ gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant Journal 16: 721-728.
42. Price Z (2003) Investigation of copia-like retrotransposons and their application in oil palm. PhD Thesis, Cambridge University, UK.
43. Price Z, Dumortier F and Mayes S (2002a) Development of an application of IRAP (Inter Retrotransposon Amplified Polymorphism) based on copia-like retrotransposons in African oil palm (Elaeis guineensis Jacq.). Poster at Plant, Animal and Microbe Genome X, San Diego.
44. Price Z, Dumortier F, MacDonald DW and Mayes S (2002b) Characterisation of copia-like retrotransposons in oil palm (Elaeis guineensis Jacq.). Theoretical and Applied Genetics 104: 860-867.
45. Ramsay L, Macaulay M, Cardle L, Morgante M, Degli Ivanissevich S, Maestri E, Powell W and Waugh R (1999) Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant Journal 17: 415-425.
46. Rosenquist E-A (1985) The genetic base of oil palm breeding populations. Proceedings of the Palm Oil Research Institute, Malaysia 10: 10-27.
47. Sambrook J and Russell DW (2001) Molecular Cloning, a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
48. San Miguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berlan A, Springer PS, Edwards KJ, Lee M, Avramova Z and Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
49. Sato Y, Sentoku N, Miura Y, Hirochika H, Kitano H and Matsuoka M (1999) Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants. EMBO Journal 18: 992-1002.
50. Schneider A, Walker SA, Poyser S, Sagan M, Ellis TH and Downie J (1999) Genetic mapping and functional analysis of a nodulation-defective mutant (sym19) of pea (Pisum sativum L.). Molecular Genetics and Genomics 262: 1-11.
51. Shirasu K, Schulman AH, Lahaye T and Schulze-Lefert P (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Research 10: 908-915.
52. Swofford DL (2001) PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), Version 4.0b10. Sunderland, MA: Sinauer Associates.
53. Takano M, Kanegae H, Shinomura T, Miyao A, Hirochika H and Furuya M (2001) Isolation and characterization of rice phytochome A mutants. Plant Cell 13: 521-534.
54. Tatout C, Warwick S, Lenoir A and Deragon JM (1999) SINE insertion as clade markers for wild crucifer species. Molecular Biology and Evolution 16: 1614-1021.
55. Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
56. Vershinin AV and Ellis THN (1999) Heterogeneity of the internal structure of PDR1, a family of Ty1 copia-like retrotransposons. Molecular Genetics and Genomics 262: 703-713.
57. Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, Nevo E and Schulman AH (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11: 1769-1784.
58. Vicient CM, Jääskeläinen M, Kalendar R and Schulman AH (2001) Active retrotransposons are a common feature of grass genomes. Plant Physiology 125: 1283-1292.
59. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M and Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407-4414.
60. Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT and Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequences-specific amplification polymorphisms (S-SAP). Molecular Genetics and Genomics 253: 687-694.
61. Wei F, Gobelman-Werner K, Moroll SM, Kurth J, Mao L, Wing RA, Leister D, Schulze-Lefert P and Wise R (1999) The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR families and suppressed recombination within a 240kb DNA interval on chromosome 5S (1HS) of barley. Genetics 153: 1929-1948.
62. Wei F, Wing RA and Wise R (2002) Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 14: 1903-1917.
63. Yamazaki M, Tsugawa H, Miyao A, Yano M, Wu J, Yamamoto S, Matsumoto T, Sasaki T and Hirochika H (2001) The rice retrotransposon Tos17 prefers low-copy-number sequences as integration targets. Molecular Genetics and Genomics 265: 336-344.
64. Yu GX and Wise RP (2000) An anchored AFLP- and retrotransposon-based map of diploid Avena. Genome 43: 736-749.