DNA Variation in the Wild Plant Arabidopsis thaliana Revealed by Amplified Fragment Length Polymorphism Analysis

Corresponding author: Naohiko T. Miyashita, Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan., arabis{at}kais.kyoto-u.ac.jp (E-mail)

Communicating editor: J. A. BIRCHLER

To investigate the level and pattern of DNA variation of Arabidopsis thaliana at the entire genome level, AFLP analysis was conducted for 38 ecotypes distributed throughout the world. Ten pairs of selective primers were used to detect a total of 472 bands, of which 374 (79.2%) were polymorphic. The frequency distribution of polymorphic bands was skewed toward an excess of singleton variation. On the basis of AFLP variation, nucleotide diversity for the entire genome was estimated to be 0.0106, which was within the range reported previously for specific nuclear genes. The frequency distribution of pairwise distance was bimodal because of an ecotype (Fl-3) with a large number of unique bands. Linkage disequilibrium between polymorphic AFLPs was tested. The proportion of significant linkage disequilibria was close to random expectation after neglecting the ecotype Fl-3. This result indicates that the effect of recombination could not be ignored in this selfing species. A neighbor-joining tree was constructed on the basis of the AFLP variation. This tree has a star-like topology and shows no clear association between ecotype and geographic origin, suggesting a recent spread of this plant species and limited migration between its habitats.

This article has been cited by other articles:

				N. Scarcelli, J. M. Cheverud, B. A. Schaal, and P. X. Kover Antagonistic pleiotropic effects reduce the potential adaptive value of the FRIGIDA locus PNAS, October 23, 2007; 104(43): 16986 - 16991. [Abstract] [Full Text] [PDF]

				J. O. Borevitz, S. P. Hazen, T. P. Michael, G. P. Morris, I. R. Baxter, T. T. Hu, H. Chen, J. D. Werner, M. Nordborg, D. E. Salt, et al. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana PNAS, July 17, 2007; 104(29): 12057 - 12062. [Abstract] [Full Text] [PDF]

				C. Shindo, G. Bernasconi, and C. S. Hardtke Natural Genetic Variation in Arabidopsis: Tools, Traits and Prospects for Evolutionary Ecology Ann. Bot., June 1, 2007; 99(6): 1043 - 1054. [Abstract] [Full Text] [PDF]

				E. M. Goss, M. Kreitman, and J. Bergelson Genetic Diversity, Recombination and Cryptic Clades in Pseudomonas viridiflava Infecting Natural Populations of Arabidopsis thaliana Genetics, January 1, 2005; 169(1): 21 - 35. [Abstract] [Full Text] [PDF]

				A. Basu, M. Ghosh, R. Meyer, W. Powell, S. L. Basak, and S. K. Sen Analysis of Genetic Diversity in Cultivated Jute Determined by Means of SSR Markers and AFLP Profiling Crop Sci., March 1, 2004; 44(2): 678 - 685. [Abstract] [Full Text] [PDF]

				T. P. Michael, P. A. Salome, H. J. Yu, T. R. Spencer, E. L. Sharp, M. A. McPeek, J. M. Alonso, J. R. Ecker, and C. R. McClung Enhanced Fitness Conferred by Naturally Occurring Variation in the Circadian Clock Science, November 7, 2003; 302(5647): 1049 - 1053. [Abstract] [Full Text] [PDF]

				O. Pontes, R. J. Lawrence, N. Neves, M. Silva, J.-H. Lee, Z. J. Chen, W. Viegas, and C. S. Pikaard Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis PNAS, September 30, 2003; 100(20): 11418 - 11423. [Abstract] [Full Text] [PDF]

				T. Kado, H. Yoshimaru, Y. Tsumura, and H. Tachida DNA Variation in a Conifer, Cryptomeria japonica (Cupressaceae sensu lato) Genetics, August 1, 2003; 164(4): 1547 - 1559. [Abstract] [Full Text] [PDF]

				K. J. Schmid, T. R. Sorensen, R. Stracke, O. Torjek, T. Altmann, T. Mitchell-Olds, and B. Weisshaar Large-Scale Identification and Analysis of Genome-Wide Single-Nucleotide Polymorphisms for Mapping in Arabidopsis thaliana Genome Res., June 1, 2003; 13(6): 1250 - 1257. [Abstract] [Full Text] [PDF]

				J. O. Borevitz and M. Nordborg The Impact of Genomics on the Study of Natural Variation in Arabidopsis Plant Physiology, June 1, 2003; 132(2): 718 - 725. [Full Text] [PDF]

				H. Kuittinen, D. Salguero, and M. Aguade Parallel Patterns of Sequence Variation Within and Between Populations at Three Loci of Arabidopsis thaliana Mol. Biol. Evol., November 1, 2002; 19(11): 2030 - 2034. [Full Text] [PDF]

				H. K. Stenoien, C. B. Fenster, H. Kuittinen, and O. Savolainen Quantifying latitudinal clines to light responses in natural populations of Arabidopsis thaliana (Brassicaceae) Am. J. Botany, October 1, 2002; 89(10): 1604 - 1608. [Abstract] [Full Text] [PDF]

				D. Tian, H. Araki, E. Stahl, J. Bergelson, and M. Kreitman Signature of balancing selection in Arabidopsis PNAS, August 20, 2002; 99(17): 11525 - 11530. [Abstract] [Full Text] [PDF]

				V. Le Corre, F. Roux, and X. Reboud DNA Polymorphism at the FRIGIDA Gene in Arabidopsis thaliana: Extensive Nonsynonymous Variation Is Consistent with Local Selection for Flowering Time Mol. Biol. Evol., August 1, 2002; 19(8): 1261 - 1271. [Abstract] [Full Text] [PDF]

				B. Haubold, J. Kroymann, A. Ratzka, T. Mitchell-Olds, and T. Wiehe Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana Genetics, July 1, 2002; 161(3): 1269 - 1278. [Abstract] [Full Text] [PDF]

				M. Iizuka, H. Tachida, and H. Matsuda A Neutral Model With Fluctuating Population Size and Its Effective Size Genetics, May 1, 2002; 161(1): 381 - 388. [Abstract] [Full Text] [PDF]

				A. Kawabe, K. Yamane, and N. T. Miyashita DNA Polymorphism at the Cytosolic Phosphoglucose Isomerase (PgiC) Locus of the Wild Plant Arabidopsis thaliana Genetics, November 1, 2000; 156(3): 1339 - 1347. [Abstract] [Full Text]

				H. Kuittinen and M. Aguadé Nucleotide Variation at the CHALCONE ISOMERASE Locus in Arabidopsis thaliana Genetics, June 1, 2000; 155(2): 863 - 872. [Abstract] [Full Text]