NUCLEOTIDE POLYMORPHISM IN THE ACIDIC CHITINASE FOCUS (CHIA) REGION OF THE WILD PLANT ARABIDOPSIS-THALIANA

To investigate DNA variation in natural plant populations, a 1.8-kb re gion of the acidic chitinase locus (ChiA) was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Jap an. As in the Adh region, dimorphism was detected throughout the inves tigated ChiA region, suggesting the possibility that dimorphic DNA var iation exists in the entire nuclear genome of A. thaliana. The ChiA re gion was divided into two blocks by an intragenic recombination betwee n two parental sequence types, which diverged 7.4 MYA under the assump tion that nucleotide mutation rate per site per year is mu = 10(-9.) N ucleotide diversity in the entire ChiA region was 0.0104. Tajima's tes t was significantly negative for both nucleotide and indel variations, which was manifested as an excess of unique polymorphisms. However, t he level and pattern of polymorphism in the ChiA region were inconsist ent with simple theoretical explanations. The HKA test detected no dif ference in the levels of intra- and interspecific variations between t he ChiA and Adh regions. In the ChiA coding region, no difference in t he patterns of synonymous and replacement variation was found in intra - and interspecific comparisons by the MK test. Although it was diffic ult to determine the exact genetic mechanism acting on the ChiA locus, these results suggested that the ChiA locus region was under the same genetic mechanism before and after the establishment of A. thaliana a s a species.