Tubulin-based polymorphism (TBP): A new tool, based on functionally relevant sequences, to assess genetic diversity in plant species

Genome

Volumn 47, Issue 2, 2004, Pages 281-291

  Bardini, Mauro ^a   Lee, David ^b   Donini, Paolo ^b   Mariani, Anna ^c,d   Gianì, Silvia ^d   Toschi, Marcello ^d   Lowe, Chris ^b   Breviario, Diego ^d  

^a UNIVERSITY OF MILAN   (Italy)

^b NATIONAL INSTITUTE OF AGRICULTURAL BOTANY   (United Kingdom)

^c Ist Ric Miglioramento Genetico P   (Italy)

^d CNR   (Italy)

Author keywords

Brassica napus; Coffea; Lotus; SSRs; tubulin

Indexed keywords

BRASSICA; BRASSICA NAPUS; COFFEA; EMBRYOPHYTA; LOTUS; SINAPIS ARVENSIS;

EID: 2542505841     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g03-132     Document Type: Article

References (40)

1. Anthony, F., Combes, M.C., Astorga, C., Bertrand, B., Graziosi, G., and Lashermes, P. 2002. The origin of cultivated Coffea arabica L. varieties revealed by AFLP and SSR markers. Theor. Appl. Genet. 104: 894-900.
2. Ball, P.W., and Chrtkova-Zertova, A. 1968. Lotus corniculatus group. In Flora Europea. Vol. 2. Edited by T.G. Tutin et al. University Press, Cambridge, U.K. pp. 173-176.
3. Campos, L.P., Raelson, J.V., and Grant, W.F. 1994. Genome relationships among Lotus species based on random amplified polymorphic DNA (RAPD). Theor. Appl. Genet. 88: 417-422.
4. Gaut, B.S., Peek, A.S., Morton, B.R., and Clegg, M.T. 1999. Patterns of genetic diversification within the Adh gene family in grasses (Poaceae). Mol. Biol. Evol. 16: 1086-1097.
5. Geuna, F., Hartings, H., and Scienza, A. 1997. Discrimination between cultivars of Vitis vinifera based on molecular variability concerning 5′ untranslated regions of the StSy-CHS genes. Theor. Appl. Genet. 95: 375-383.
6. Gianì, S., and Breviario, D. 1996. Rice β-tubulin mRNA levels are modulated during flower development and in response to external stimuli. Plant Sci. 116: 147-157.
7. Gianì, S., Morello, L., Bardini, M., and Breviario, D. 2003. Tubulin intron sequences: multi-functional tools. Cell Biol. Int. 27: 203-205.
8. Grivet, D., Jeandroz, S., and Favre, J.M. 1999. Nad1 b/c intron polymorphism reveals maternal inheritance of the mitochondrial genome in Picea abies. Theor. Appl. Genet. 99: 346-349.
9. Herrera, J.C., Combes, M.C., Anthony, F., Charrier, A., and Lashermes, P. 2002. Introgression into the allotetraploid coffee (Coffea arabica L.): segregation and recombination of the C. canephora genome in the tetraploid interspecific hybrid (C. arabica x C. canephora). Theor. Appl. Genet. 104: 661-668.
10. Hongtrakul, V., Huestis, G.M., and Knapp, S.J. 1997. Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: genetic diversity among oilseed inbred lines. Theor. Appl. Genet. 95: 400-407.
11. Jackson, J.A., and Matthews, D. 2000. A modified inter-SSR protocol for use in conjunction with the LI-COR Gene ReadIR 4200 DNA analyser. Biotechniques, 28: 914-920.
12. Jeon, J.S., Lee, S., Jung, K.H., Jun, S.J., Kim, C., and An, G. 2000. Tissue-preferential expression of a rice α-tubulin gene, OsTubA1, mediated by the first intron. Plant Physiol. 123: 1005-1014.
13. Karp, A., Peter, G., Ingram, I., and Ingram, D. 1998. Molecular tools for screening biodiversity. Chapman and Hall, London, U.K.
14. Kelchner, S.A. 2002. Group II introns as phylogenetic tools: structure, function, and evolutionary constraints. Am. J. Bot. 89: 1651-1669.
15. Koebner, R.M.D., Powell, W., and Donini, P. 2001. Contributions of DNA molecular marker technologies to the genetics and breeding of wheat and barley. Plant Breed. Rev. 21: 181-220.
16. Laroche, J., and Bousquet, J. 1999. Evolution of the mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron1. Mol. Biol. Evol. 16: 441-452.
17. Lashermes, P., Combes, M.C., Robert, J., Trouslot, P., D'Hort, A., Anthony, F., and Charrier, A. 1999. Molecular characterization and origin of the Coffea arabica L. genome. Mol. Gen. Genet. 261: 259-266.
18. Liaud, M.F., Brinkmann, H., and Cerff, R. 1992. The beta-tubulin gene family of pea: primary structure, genomic organization and intron-dependent evolution of genes. Plant Mol. Biol. 18: 639-651.
19. Morello, L., Bardini, M., Sala, F., and Breviario, D. 2002. A long leader intron of the OsTub16 rice beta-tubulin gene is required for high level gene expression and can autonomously promote transcription both in vivo and in vitro. Plant J. 29: 33-44.
20. Morgante, M., and Olivieri, A.M. 1993. PCR-amplified microsatellites as markers in plant genetics. Plant J. 3: 175-182.
21. Nick, P. 1998. Signaling to the microtubular cytoskeleton in plants. Int. Rev Cytol. 184: 33-80.
22. Nogales, E. 2000. Structural insights into microtubule function. Annu. Rev. Biochem. 69: 277-302.
23. Ochs, G., Schock, G., Trischler, M., Kosemund, K., and Wild, A. 1999. Complexity and expression of the glutamine synthase multigene family in the amphidiploid crop Brassica napus. Plant Mol. Biol. 39: 395-405.
24. Peakall, R., and Smouse, P.E. 2001. GenAlEx: genetic analysis in Excel. Population genetic software for teaching and research. Australian National University, Canberra, Australia. Available from http://www.anu.edu.au/BoZo/ GenAlEx/ [accessed April 2003].
25. Pecchia, S., Mercatelli, E., and Vannacci, G. 1998. PCR amplification and characterization of the intergenic spacer region of the ribosomal DNA in Pyrenophora graminea. FEMS Microbiol. Lett. 166: 21-27.
26. Powell, W., Orozco-Castillo, C., Chalmers, K.J., Provan, J., and Waugh, R. 1995. Polymerase chain reaction-based assays for the characterization of plant genetic resources. Electrophoresis, 16: 1726-1730.
27. Rohlf, F.J. 1993. Numerical taxonomy and multivariate analysis system (NTSYS-pc). Exeter Software, Setauket, N.Y.
28. Roos, M.D., and Jones, W.T. 1985. The origin of Lotus corniculatus. Theor. Appl. Genet. 71: 284-288.
29. Rose, A.B. 2002. Requirements for intron-mediated enhancement of gene expression in Arabidopsis. RNA, 8: 1444-1453.
30. Sallares, R., and Brown, T.A. 1999. PCR-based analysis of the intergenic spacers of the Nor loci on the A genomes of Triticum diploids and polyploids. Genome, 42: 116-128.
31. Sasanuma, T., and Miyashita, N.T. 1998. Subfamily divergence in the multigene family of ribulose-1,5-biphosphate carboxylase/oxygenase (rbcS) in Triticae and its relative. Genes Genet. Syst. 73: 297-309.
32. Small, R.I., Ryburn, J.A., and Wendel, J.F. 1999. Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton. Mol. Biol. Evol. 16: 491-501.
33. Snustad, D.P., Haos, N.A., Kopczack, S.D., and Silflow, C.D. 1992. The small genome of Arabidopsis contains at least nine expressed β-tubulin genes. Plant Cell, 4: 549-556.
34. Soranzo, N., Provan, J., and Powell, W. 1999. An example of microsatellite length variation in the mitochondrial genome of conifers. Genome, 42: 158-161.
35. Steiner, J.J. 1999. Birdsfoot trefoil origins and germplasm diversity. In Trefoil: the science and technology of the Lotus. Edited by P.R. Beuselinck. CSSA Special Publications No. 28.
36. Thitamadee, S., Tuchihara, K., and Hashimoto, T. 2002. Microtubule basis for left-handed helical growth in Arabidopsis. Nature (London), 417: 193-196.
37. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
38. Tommasini, L., Batley, J., Arnold, G.M., Cooke, R.J., Donini, P., Lee, D., Law, J.R., Lowe, C., Moule, C., Trick, M., and Edwards, K.J. 2003. The development of multiplex simple sequence repeat (SSR) markers to complement distinctness, uniformity and stability testing of rape (Brassica napus L.) varieties. Theor. Appl. Genet. 106: 1091-1101.
39. Turner, L., Hellens, R.P., Lee, D., and Ellis, T.H.N. 1993 Genetic aspects of the organisation of legumin genes in pea. Plant Mol. Biol. 22: 101-112.
40. Wang, R.I., Stec, A., Hey, J., Lukens, L., and Doebley, J. 1999. The limits of selection during maize domestication. Nature (London), 398: 236-239.