Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana

To investigate DNA variation in natural plant populations, a 1.8-kb regionof the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes ofArabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As inthe Adh region, dimorphism was detected throughout the investigated ChiAregion, suggesting the possibility that dimorphic DNA variation exists inthe entire nuclear genome of A. thaliana. The ChiA region was divided intotwo blocks by an intragenic recombination between two parental sequencetypes, which diverged 7.4 MYA under the assumption that nucleotide mutationrate per site per year is mu = 10(- 9). Nucleotide diversity in the entireChiA region was 0.0104. Tajima's test was significantly negative for bothnucleotide and indel variations, which was manifested as an excess ofunique polymorphisms. However, the level and pattern of polymorphism in theChiA region were inconsistent with simple theoretical explanations. The HKAtest detected no difference in the levels of intra- and interspecificvariations between the ChiA and Adh regions. In the ChiA coding region, nodifference in the patterns of synonymous and replacement variation wasfound in intra- and interspecific comparisons by the MK test. Although itwas difficult to determine the exact genetic mechanism acting on the ChAlocus, these results suggested that the ChA locus region was under the samegenetic mechanism before and after the establishment of A. thaliana as aspecies.