DNA polymorphism in the blast disease resistance gene Pita of the wild rice Oryza rufipogon and its related species

Intra-and interspecific DNA variations in the blast resistance gene Pita in wild rice (Oryza rufipogon), cultivated rice (O. sativa), and two other related wild rice species (O. meridionalis and O. officinalis) were analyzed to elucidate the nucleotide polymorphism maintenance mechanisms and evolution of Pita in these species. Nucleotide diversity at silent sites of O. rufipogon Pita was 0.0101, an intermediate value relative to other O. rufipogon nuclear genes. A dimorphic pattern of nucleotide polymorphism was detected in the O. rufipogon Pita region. Inoculation of the blast fungus Magnaporthe oryzae verified that the O. rufipogon Pita gene resides in a dimorphic sequence type. The resistance Pita allele had lower levels of variation than the susceptibility pita allele. A hypothesis of evolutionary relationships indicated that the amino acid mutation in the O. rufipogon Pita protein responsible for the difference between resistance and susceptibility occurred relatively recently. These results suggested that the resistance Pita originated from the susceptibility pita. Nucleotide diversity at replacement sites of the leucine-rich domain (LRD) of both the resistance and susceptibility O. rufipogon pita was low. In tests of neutrality, significantly negative values were detected for the LRD of O. rufipogon susceptibility pita. The low nucleotide diversity at replacement sites of the LRD of the susceptibility pita could be explained by purifying selection. Comparison of Pita between O. rufipogon and O. officinalis revealed an excess of nonconservative amino acid substitutions in the LRD, which could be related to the host-pathogen interaction.