Molecular variation in plant cell populations evolving in vitro in different physiological contexts

Patrizia Bogani; Alessandra Simoni; Pietro Lio'; Angela Germinario; Marcello Buiatti

doi:10.1139/g01-033

journal article Aug 01, 2001

Molecular variation in plant cell populations evolving in vitro in different physiological contexts

Patrizia Bogani Alessandra Simoni Pietro Lio' Angela Germinario Marcello Buiatti

Genome Vol. 44 No. 4 pp. 549-558 · Canadian Science Publishing

View at Publisher Save 10.1139/g01-033

Abstract

Previous work has shown the fixation of context-specific random amplified polymorphic DNA (RAPD) patterns in tomato cell cultures grown for 2 years in different hormonal contexts. In this work, RAPD sequences were characterised and RAPD-derived molecular markers used for a further study of variation between and within auto- and auxo-trophic tomato cultures grown in different hormonal equilibria. Results were then compared with those obtained using microsatellite markers located in noncoding regions of differentiation- and hormone-related genes and with those obtained with the external transcribed spacer (ETS) from tomato rDNA. Hybridisation of RAPDs on a tomato genomic DNA bank, or on total DNA after enzymatic digestion, suggested that the markers were repetitive in nature. Sequence analysis, however, showed that the homology between different fragments was due mainly to the presence of homo-AT nucleotide stretches. Moreover, a series of computational methods, such as an information-theory algorithm coupled with ΔG estimates, suggested that the RAPD fragments isolated in our experiments are noncoding. The amplification of SSR-containing RAPD-derived markers, and of other SSRs located in noncoding regions of tomato functional genes, consistently showed polymorphism between auxo- and auto-trophic somaclones (the latter being either habituated or transgenic for Agrobacterium tumefaciens oncogenes) but not within these same clones. Differences were also found between auxotrophic clones and the differentiated tissue. These findings were confirmed by restriction fragment length polymorphism (RFLP) analysis with the REII repetitive element of the ETS from tomato rDNA, which was isolated during this study. The results obtained suggest a possible role for physiological context in the selection of RAPD patterns during the evolution of tomato cells with different endogenous hormonal equilibria. The results are discussed in terms of a possible role for variation in noncoding regions of hormone-related genes in the adaptation to different physiological contexts.Key words: Lycopersicon esculentum, RAPD, SSR, genetic variation, noncoding DNA, hormone control.

Topics

No keywords indexed for this article. Browse by subject →

References

28

[1]

Basic local alignment search tool

Stephen F. Altschul, Warren Gish, Webb Miller et al.

Journal of Molecular Biology 1990 10.1016/s0022-2836(05)80360-2

[2]

Bai D. Genome (1998) 10.1139/g98-028

[3]

Bogani P. Genome (1995) 10.1139/g95-119

[4]

Bogani P. Genome (1996) 10.1139/g96-107

[5]

Bogani P. Nicotiana. Mol. Phylogenet. Evol. (1997) 10.1006/mpev.1996.0356

[6]

Broun P. Mol. Gen. Genet. (1996) 10.1007/bf02191823

[7]

Charlesworth B. Nature (London) (1994) 10.1038/371215a0

[8]

Chen X. Proc. Natl. Acad. Sci. U.S.A. (1995) 10.1073/pnas.92.11.5199

[9]

Chen X. J. Biomol. Struct. Dyn. (1998) 10.1080/07391102.1998.10508989

[10]

Dean C. Rev. Plant. Physiol. Plant. Mol. Biol. (1995) 10.1146/annurev.pp.46.060195.002143

[11]

Edwards Y.J.K. J. Mol. Biol. (1998) 10.1006/jmbi.1998.1752

[12]

Interpreting correlations in biosequences

H Herzel, E.N Trifonov, O Weiss et al.

Physica A: Statistical Mechanics and its Applicati... 1998 10.1016/s0378-4371(97)00505-0

[13]

Klein-Lankhorst R.M. Theor. Appl. Genet. (1991) 10.1007/bf00229232

[14]

Mariappan S.V. Nucleic Acids Res. (1996) 10.1093/nar/24.4.775

[15]

Marky L.A. Biopolymer (1987) 10.1002/bip.360260911

[16]

Nadir E. Proc. Natl. Acad. Sci. U.S.A. (1996) 10.1073/pnas.93.13.6470

[17]

Ohmori T. Theor. Appl. Genet. (1996) 10.1007/bf00223369

[18]

Improved tools for biological sequence comparison.

W R Pearson, D J Lipman

Proceedings of the National Academy of Sciences 1988 10.1073/pnas.85.8.2444

[19]

Puget N. Cancer Res. (1999)

[20]

Richardson T. Nucleic Acids Res. (1995) 10.1093/nar/23.18.3798

[21]

Schimdt-Putcha W. Plant Mol. Biol. (1989) 10.1007/bf00016143

[22]

Smulders M.J.M. Theor. Appl. Genet. (1997) 10.1007/s001220050409

[23]

Detection of specific sequences among DNA fragments separated by gel electrophoresis

E.M. Southern

Journal of Molecular Biology 1975 10.1016/s0022-2836(75)80083-0

[24]

Storti E. Theor. Appl. Genet. (1994) 10.1007/bf00222399

[25]

Svitashev S. Genome (1998) 10.1139/g97-108

[26]

Weising K. PCR Meth. Appl. (1995) 10.1101/gr.4.5.249

[27]

Fingerprinting genomes using PCR with arbitrary primers

John Welsh, Michael McClelland

Nucleic Acids Research 1990 10.1093/nar/18.24.7213

[28]

DNA polymorphisms amplified by arbitrary primers are useful as genetic markers

John G.K. Williams, Anne R. Kubelik, Kenneth J. Livak et al.

Nucleic Acids Research 1990 10.1093/nar/18.22.6531

Metrics

8

Citations

28

References

Details

Published: Aug 01, 2001
Vol/Issue: 44(4)
Pages: 549-558
License: View

Authors

Cite This Article

Patrizia Bogani, Alessandra Simoni, Pietro Lio', et al. (2001). Molecular variation in plant cell populations evolving in vitro in different physiological contexts. Genome, 44(4), 549-558. https://doi.org/10.1139/g01-033

Molecular variation in plant cell populations evolving in vitro in different physiological contexts

You May Also Like