The flanking regions of two Petunia inflata S alleles are heterogeneous and contain repetitive sequences.

Genomic clones representing S1 and S3 alleles of the self-incompatibility locus (S locus) in Petunia inflata have been isolated and characterized. Extensive lengths of the flanking regions as well as the coding regions contained in both clones have been sequenced. Both alleles have a single, relatively short intron located within a region of high interallelic variability. Transcription start sites of both alleles have been determined by S1 nuclease mapping, and putative TATA boxes have been identified. Nucleotide sequence comparison of the two alleles shows a high level of diversity in the regions immediately flanking the coding region. Southern analysis demonstrates that this sequence diversity extends beyond the regions which have been sequenced, such that the two clones appear to be completely heterogeneous except for conserved sites within the coding regions of the two alleles. These analyses also reveal the presence of repetitive sequences which are very closely associated with the coding regions of both alleles. The influence of these characteristics on genetic recombination and the maintenance of allelic independence, as well as the organization of the S locus, are discussed.