Originally published as Genetics Published Articles Ahead of Print on July 13, 2008.

Genetics, Vol. 179, 1527-1538, July 2008, Copyright © 2008
doi:10.1534/genetics.108.089805

Molecular Evolution of the Pi-ta Gene Resistant to Rice Blast in Wild Rice (Oryza rufipogon)

Chun-Lin Huang*,{dagger}, Shih-Ying Hwang{ddagger}, Yu-Chung Chiang§ and Tsan-Piao Lin*,1

* Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan, {dagger} Department of Botany, National Museum of Natural Science, Taichung 404, Taiwan, {ddagger} Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan and § Department of Life Science, Pingtung University of Science and Technology, Pingtung 912, Taiwan

1 Corresponding author: Institute of Plant Biology, National Taiwan University, 1 Roosevelt Rd., Section 4, Taipei 106, Taiwan.
E-mail: tpl{at}ntu.edu.tw

Rice blast disease resistance to the fungal pathogen Magnaporthe grisea is triggered by a physical interaction between the protein products of the host R (resistance) gene, Pi-ta, and the pathogen Avr (avirulence) gene, AVR-pita. The genotype variation and resistant/susceptible phenotype at the Pi-ta locus of wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), was surveyed in 36 locations worldwide to study the molecular evolution and functional adaptation of the Pi-ta gene. The low nucleotide polymorphism of the Pi-ta gene of O. rufipogon was similar to that of O. sativa, but greatly differed from what has been reported for other O. rufipogon genes. The haplotypes can be subdivided into two divergent haplogroups named H1 and H2. H1 is derived from H2, with nearly no variation and at a low frequency. H2 is common and is the ancestral form. The leucine-rich repeat (LRR) domain has a high {pi}non/{pi}syn ratio, and the low polymorphism of the Pi-ta gene might have primarily been caused by recurrent selective sweep and constraint by other putative physiological functions. Meanwhile, we provide data to show that the amino acid Ala-918 of H1 in the LRR domain has a close relationship with the resistant phenotype. H1 might have recently arisen during rice domestication and may be associated with the scenario of a blast pathogen–host shift from Italian millet to rice.