Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana

An similar to 1.9-kb region encompassing the CHI-gene, which encodes chalco ne isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thalian a (L.) Heynh. and in 1 ecotype of A. lyrata ssp, petraea. There was no evid ence for dimorphism at the CHI region. A minimum of three recombination eve nts was inferred in the history of the sampled ecotypes of the highly selfi ng A. thaliana. The estimated nucleotide diversity (theta(TOTAL) = 0.004, t heta(SIL) = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum to ward an excess of low-frequency polymorphisms, together with the bell-shape d distribution of painwise nucleotide differences at CHI suggests that A. t haliana has recently experienced a rapid population growth. Although this p attern could also be explained by a recent selective sweep at the studied r egion, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and div ergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the la tter regions.