The nucleotide sequence of a gene, Hf1, encoding the flavonoid 3′,5′-hydroxylase in commercial petunias was compared to those in natural species to reconstruct historical events that occurred at the Hf1 locus in commercial petunias in the course of breeding since the 1830s. Intact Hf1 genes of any natural species so far studied were not detectable in 84 commercial petunias examined and were considered to have been removed by breeders. The dominant Hf1 alleles isolated from 14 Hf1 Hf1 cultivars

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... howed an identical open reading frame (ORF) sequence and were considered to result from inter-allelic recombination between Hf1 of Petunia axillaris subsp. axillaris or subsp. parodii and Hf1 of P. integrifolia subsp. integrifolia or P. inflata, which were recorded as or assumed to be the historical parents of commercial petunias. Recessive hf1-3 was considered to be a mutant allele of the recombined Hf1 associated with the insertion of a retrotransposable element (rTph1) into exon III. The recessive hf1-2 allele showed a sequence identical to that of Hf1 of P. integrifolia subsp. integrifolia and P. inflata, except for a transposable element (dTph9) inserted into exon III and a target site duplication. We analyzed the potential causes of the recombination that occurred at the Hf1 locus and of the removal of dominant Hf1 genes of natural species from commercial petunias.