Evidence That Intragenic Recombination Contributes to Allelic Diversity of the S-RNase Gene at the Self-Incompatibility (S) Locus in Petunia inflata

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Abstract
For Solanaceae type self-incompatibility, discrimination between self and nonself pollen by the pistil is controlled by the highly polymorphic S-RNase gene. To date, the mechanism generating the allelic diversity of this gene is largely unknown. Natural populations offer a good opportunity to address this question because they likely contain different alleles that share recent common progenitors. We identified 19 S haplotypes from a natural population ofPetunia inflata in Argentina, used reverse transcriptase-polymerase chain reaction to obtain cDNAs for 15 alleles of the S-RNase gene, and sequenced all the cDNAs. Phylogenetic studies revealed that five of these alleles and two previously identified alleles form a major clade, and that the 5′ region ofS 19 allele was derived from an ancestor allele closely related to S 2, whereas its 3′ region was derived from an ancestor allele closely related to S 8. A similar evolutionary relationship was found among S 3,S 12, andS 15 alleles. These findings suggest that intragenic recombination contributed to the generation of the allelic diversity of the S-RNase gene. Two additional findings emerged from the sequence comparisons. First, the nucleotide sequence of theS 1 allele identified in this work is completely identical to that of the previously identifiedS 1 allele of a different origin. Second, in the two hypervariable regions HVa and HVb, thought to be involved in determining S allele specificity,S 6 andS 9 alleles differ only by four nucleotides, all in HVb, resulting in two amino acid differences. The implications of these findings are discussed.