Natural variation at the Pi-ta rice blast resistance locus

The resistance gene Pi-ta protect, rice crops against the fungal pathogen Magnaporthe grisea expressing the avirulence gene AVR-Pita in a gene-for-gene manner. Pi-ta, originally introgressed into japonica rice from indica origin, was previously isolated by positional cloning. In this study, we report the nucleotide sequence of a 5,113-base pair region containing a japonica susceptibility pi-ta allele, which has overall 99.6% nucleotide identity to the indica Pi-ta allele conferring resistance. The intron region shows the levels of sequence diversity that typically differentiate genes from indica and japonica rices, but the other gene regions show less diversity. Sequences of the Pi-to allele from resistant cultivars Katy and Drew from the southern United States are identical to the resistance Pi-ta sequence. Sequences from susceptible culfivars El Paso 144 and Cica 9 from Latin America define a third susceptibility haplotype. This brings the total number of Pi-ta haplotypes identified to four, including the resistance allele and three susceptibility alleles. The Pi-ta locus shows low levels of DNA polymorphism compared with other analyzed R genes. Understanding the natural diversity at the Pi-ta locus is important for designing specific markers for incorporation of this R gene into rice-breeding programs.