Evidence that intragenic recombination contributes to allelic diversity of the S-RNASE gene at the self-incompatibility (S) locus in Petunia inflata

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 of Petunia 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 of S₁₉ allele was derived from an ancestor allele closely related to S₂, whereas its 3′ region was derived from an ancestor allele closely related to S₈. A similar evolutionary relationship was found among S₃, S₁₂, and S₁₅ 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 the S₁ allele identified in this work is completely identical to that of the previously identified S₁ allele of a different origin. Second, in the two hypervariable regions HVa and HVb, thought to be involved in determining S allele specificity, S₆ and S₉ alleles differ only by four nucleotides, all in HVb, resulting in two amino acid differences. The implications of these findings are discussed.