ARS | Publication request: Molecular evolution and strong selective sweep at the rice blast resistance gene Pi-ta during crop domestication

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 1, 2009
Publication Date: January 10, 2009
Citation: Lee, S., Jia, Y. 2009. Molecular evolution and strong selective sweep at the rice blast resistance gene Pi-ta during crop domestication. In: Proceedings Plant and Animal Genome XVII Conference, January 10-14, 2009, San Diego,CA. P243.

Technical Abstract: The Pi-ta gene in rice has been effectively deployed worldwide to prevent the infection by the blast fungus Magnaporthe oryzae in a gene for gene specificity. The genomic region spanning Pi-ta and six flanking genes in 157 rice accessions composed of seven Oryza species including US and Asian cultivars and red rice biotypes were sequenced to understand the evolutionary process at the Pi-ta locus. The genome wide SSR markers were used to analyze 16 selected accessions to examine Pi-ta introgression during domestication. Five major clades of the Pi-ta alleles were identified among 157 accessions. Based on amino acid sequences 25 Pi-ta variants were predicted in six Oryza species. High degrees of nucleotide variation in the 5’UTR, 3’UTR, and the intron were observed to distinguish Pi-ta variants. A 219 bp Indel was consistently found in the 5’UTR in 46 accessions that contains Pi-ta. Additional Indels ranging from 243 to 530 bp were identified in the 3’UTR and the intron in 24 accessions of O. sativa, O. rufipogon, O. nivara, O. barthii, O. glaberima and O. glumaepatula. Nucleotide diversity at the Pi-ta locus was low in both US and Asian cultivars, but Tajima’s D value was significantly higher in the Pi-ta in US cultivars. Alignments of DNA sequences of Pi-ta, flanking genes, and SSR markers revealed convincing evidence for a strong selective sweep at the Pi-ta locus and its surrounding regions in US cultivars. The Pi-ta alleles in the US red rice accessions were more similar to Asian cultivars than to US cultivars and wild rice relatives. Furthermore, the evidence of Pi-ta migration through gene flow between cultivated and red rice will be presented.