Nucleotide sequence variation at two genes of the phenylpropanoid pathway,the FAH1 and F3H genes, in Arabidopsis thaliana

The FAH1 and F3H genes encode ferulate-5-hydroxylase and flavanone-3-hydrox ylase, which are enzymes in the pathways leading to the synthesis of sinapi c acid esters and flavonoids, respectively. Nucleotide variation at these g enes was surveyed by sequencing a sample of 20 worldwide Arabidopsis thalia na ecotypes and one Arabidopsis lyrata spp, petraea stock. In contrast with most previously studied genes, the percentage of singletons was rather low in both the FAH1 and the F3H gene regions. There was, therefore, no footpr int of a recent species expansion in the pattern of nucleotide variation in these regions. In both FAH1 and F3H, nucleotide variation was structured i nto two major highly differentiated haplotypes. In both genes, there was a peak of silent polymorphism in the 5' part of the coding region without a p arallel increase in silent divergence. In FAH1, the peak was centered at th e beginning of the second exon. In F3H, nucleotide diversity was highest at the beginning of the gene. The observed pattern of variation in both FAH1 and F3H, although suggestive of balancing selection, was compatible with a neutral model with no recombination.