ARS | Publication request: Haplotype diversity at the Pi-ta locus in cultivated rice and its wild relataives

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 3, 2008
Publication Date: December 1, 2008
Citation: Wang, X., Jia, Y., Shu, Q., Wu, D. 2008. Haplotype diversity at the Pi-ta locus in cultivated rice and its wild relataives. Phytopathology. 98:1305-1311.

Interpretive Summary: It has been known that a major resistance (R) gene confers specific resistance to a pathogen race that contains a specific avirulence (AVR) gene. Both R and AVR genes coexist in the nature and it is important to identify amino acid residue and conserved structural domains to determine their role in the resistance specificity. A major Nucleotide Binding Site type R gene, Pi-ta in rice, has been effectively deployed for the control of blast disease worldwide. In this study, we examined structural and functional properties of Pi-ta in 51 entries of cultivated weedy rice and 5 additional Oryza species. Sixteen Pi-ta variants were translated to 10 putative proteins with minor changes of amino acid composition. Nucleotide variations were observed mainly in the intron. This is consistent with the fact that the selection pressure on the intron is less intensive in comparison with that on the coding region. Previously it was known that a single amino acid alanine (A) at the position 918 of Pi-ta determines the resistance specificity. We observed that A was only found in Pi-ta and not in other 15 Pi-ta variants. Pi-ta has the lowest polymorphism over all other plant R genes suggesting that Pi-ta has evolved neutrally. This work demonstrates that serine at position 918 of the Pi-ta protein is ancient and the substitution of serine with alanine is one critical step for the evolution of the recognition specificity of the Pi-ta protein. Our data suggest that the plant has evolved a remarkable mechanism to detect the pathogen effector proteins in activating sophisticated multifaceted defense mechanisms.

Technical Abstract: The Pi-ta gene in rice confers resistance to the fungus Magnaporthe oryzae containing AVR-Pita. Pi-ta is predicted to encode a cytoplasmic receptor protein with nucleotide binding sites and leucine rich domain. A panel of 51 oryza accessions consisting of the AA genome species, O. sativa, O. glaberrima, O. rufipogon, O. nivara, O. barthii, and CC genome species, O. officinalis was sequenced to investigate the diversity present in the coding and intron regions of the Pi-ta locus. Two major clades of the Pi-ta variants consisting of 16 different genomic sequences were identified. The presence of the Pi-ta locus in these Oryza species suggests that Pi-ta was present in the ancestor of sativa, glaberrima, rufipogon, nivara and barthii. The Pi-ta variants were expressed constitutively as examined by RT-PCR. Only one Pi-ta allele confers resistance to M. oryzae although the additional 15 variants were translated into 9 proteins highly similar to Pi-ta. Analysis of all DNA sequences using the statistics of Tajima’s D suggest that Pi-ta is evolved neutrally. We suggest that natural variation in the reaction to the races of M. oryzae expressing AVR-Pita can be attributed to certain aspects of sequence variation in the Pi-ta gene.