ARS | Publication request: Evolutionary dynamics of the genomic region around the blast resistance gene Pi-ta in AA genome Oryza species

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 3, 2009
Publication Date: December 1, 2009
Citation: Lee, S., Costanzo, S., Jia, Y., Olsen, K.M., Caicedo, A.L. 2009. Evolutionary dynamics of the genomic region around the blast resistance gene Pi-ta in AA genome Oryza species. Genetics. 183:1315-1325.

Interpretive Summary: Blast disease of rice is one of the most serious threats to stable rice production. The Pi-ta gene in rice has been effectively used to prevent blast disease for several decades worldwide. Understanding of origin and evolution of Pi-ta should benefit a sustainable introduction and utilization of resistance (R) genes for crop improvement. In the present study, we analyzed DNA sequences at 8 megabase regions around the Pi-ta gene in 159 accessions of seven AA genome oryza species O. sativa, O. rufipogon, O. nivara, O. meridionalis, O. glaberrima, O. barthii, and O. glumaepatula to gain insights on evolutionary dynamics at the Pi-ta locus. A 3364 bp fragment encoding a predicted transposon was found at the proximity of the Pi-ta promoter region associated with the resistance phenotype. In addition, 33 new Pi-ta DNA haplotypes and 18 new Pi-ta amino acid variants were identified. The Pi-ta haplotypes in O. sativa was predicted to be originated from O. rufipogon. In O. rufipogon, patterns of nucleotide variation in the Pi-ta genomic region suggest that recent directional selection significantly deviates from neutral evolution had occurred. However, recent directional selection was not found in all O. sativa groups. Results of sequence variation in flanking regions around Pi-ta in O. sativa suggest that the size of the Pi-ta introgression was at least 5 Mb in all elite resistant cultivars, but not in the cultivars without Pi-ta. These findings demonstrate that Pi-ta has evolved under extensive selection pressure, and the role of transposon and additional plant modifiers in Pi-ta mediated disease resistance are implicated.

Technical Abstract: The Pi-ta gene in rice has been predicted to directly detect the pathogen signaling molecule in preventing blast disease. The resistance Pi-ta allale (alanine at 918) has been introgressed between cultivated rice to confer blast resistance. To understand the evolutionary dynamics present of Pi-ta, we examined sequences of the Pi-ta locus and its flanking regions in 159 accessions composed of seven AA genome Oryza species: O. sativa, O. rufipogon, O. nivara, O. meridionalis, O. glaberrima, O. barthii, and O. glumaepatula. A 3364 bp fragment encoding a predicted transposon was consistently found at the proximity of the Pi-ta promoter region associated with the resistance phenotype. In addition, the present study identified 33 new Pi-ta haplotypes and 18 new Pi-ta amino acid variants. Haplotype network analysis demonstrated that the Pi-ta haplotypes in O. sativa originated from O. rufipogon. In O. rufipogon, patterns of nucleotide variation in the Pi-ta genomic region suggest recent directional selection, while significant deviation from neutral evolution was not found in all O. sativa groups. Results of sequence variation in flanking regions around Pi-ta in O. sativa suggest that the size of the Pi-ta introgression was at least 5 Mb in all elite resistant cultivars, but not in the cultivars without Pi-ta. These findings demonstrate that Pi-ta evolved under extensive selection pressure, and the role of transposon and additional plant modifiers in Pi-ta mediated disease resistance are implicated.