DNA variation in the wild plant Arabidopsis thaliana revealed by amplifiedfragment length polymorphism analysis

To investigate the level and pattern of DNA variation of Arabidopsis thalia na 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 f or 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 (F1-3) with a large number of unique bands. Linkage disequilibrium between polymorphic AFLPs w as tested. The proportion of significant linkage disequilibria was close to random expectation after neglecting the ecotype F1-3. This result indicate s that the effect of recombination could not be ignored in this selfing spe cies. A neighbor-joining tree was constructed on the basis of the AFLP vari ation. This tree has a star-like topology and shows no clear association be tween ecotype and geographic origin, suggesting a recent spread of this pla nt species and limited migration between its habitats.