Haplotype diversity and molecular evolution of the rice Pikm locus for blast resistance

Pikm-specific rice blast resistance is conferred by a combination of two genes that have a nucleotide-binding site and a leucine-rich repeat (LRR), Pikm1-TS and Pikm2-TS. To study the evolution of these genes, we investigated the allele diversity of their LRR regions in 16 elite rice cultivars and 35 landraces. Both phylogenetic trees were characterized by a deep bifurcation that separated two major clades of alleles. A high level of polymorphism was detected exclusively between these clades and not within each clade. This two-clade structure commonly observed for the two genes suggests that these genes have evolved together through bidirectional differentiation.